Daily Papers

Standard behavior cloning supervises actions without explicitly constraining the future representation paired with each demonstrated action chunk. We introduce JEPA Policy, a diffusion-free framework that uses the action chunk and its observed future representation as paired training targets. Action and future-representation tokens interact in a shared Transformer and are refined through two forward passes. Future prediction can therefore shape the representation used to generate actions. Dual-branch and gradient-routing controls attribute the gain to this shared topology rather than to an auxiliary prediction head alone. Across nine simulated tasks, JEPA Policy improves mean success over the action-only MIP baseline and outperforms Diffusion Policy under the evaluated configurations, while adding 0.29 ms to MIP's model latency. A five-task, 630-episode physical-robot study produces the same pooled ranking. Further audits find no complete representation collapse under action supervision and identify a task-conditioned failure-ranking signal in future-prediction error. These results support paired future-representation supervision as a practical approach to low-latency visuomotor imitation without iterative generative sampling.

We present Multi-Baseline Radiance Fields (MuRF), a general feed-forward approach to solving sparse view synthesis under multiple different baseline settings (small and large baselines, and different number of input views). To render a target novel view, we discretize the 3D space into planes parallel to the target image plane, and accordingly construct a target view frustum volume. Such a target volume representation is spatially aligned with the target view, which effectively aggregates relevant information from the input views for high-quality rendering. It also facilitates subsequent radiance field regression with a convolutional network thanks to its axis-aligned nature. The 3D context modeled by the convolutional network enables our method to synthesis sharper scene structures than prior works. Our MuRF achieves state-of-the-art performance across multiple different baseline settings and diverse scenarios ranging from simple objects (DTU) to complex indoor and outdoor scenes (RealEstate10K and LLFF). We also show promising zero-shot generalization abilities on the Mip-NeRF 360 dataset, demonstrating the general applicability of MuRF.

We introduce GaussianZoom, a generative zoom-in 3D reconstruction system with an iterative progressive framework that combines geometry-consistent scene modeling and multi-scale semantic reasoning to enable high-fidelity extreme zoom-in rendering from low-resolution inputs. To achieve this, we develop a novel multi-view consistent super-resolution module with depth-based feature warping and VLM-driven detail synthesis, ensuring accurate multi-view correspondence while enriching fine-scale appearance beyond the observed resolution. To support zooming across large magnification ranges, we further introduce a new expandable continuous Level-of-Detail hierarchy that dynamically modulates Gaussian visibility for smooth, alias-free cross-scale rendering. Experiments on Mip-NeRF360 and Tanks\&Temples demonstrate that GaussianZoom achieves superior perceptual quality, multi-view consistency, and robustness under extreme magnification, establishing a strong baseline for generative zoom-in 3D scene reconstruction.

Feed-forward 3D Gaussian Splatting methods reconstruct a scene from posed or pose-free images in a single forward pass, yet current approaches predict one Gaussian per input pixel, tying the representation budget to camera resolution rather than scene complexity. A flat wall and a richly textured object thus produce equally many Gaussians despite very different geometric needs. We propose ZipSplat, a token-based feed-forward model that decouples Gaussian placement from the pixel grid. A multi-view backbone extracts dense visual tokens, and k-means clustering compresses them into a compact set of scene tokens. Cross- and self-attention refine these tokens, and a lightweight MLP decodes each into a group of Gaussians with unconstrained 3D positions. Because clustering is applied at inference, a single trained model spans the quality-efficiency curve without retraining. ZipSplat operates without ground-truth poses or intrinsics, yet sets a new state of the art on DL3DV and RealEstate10K with {sim}6{times} fewer Gaussians than pixel-aligned methods, surpassing the best pose-free baseline by 2.1dB and 1.2dB PSNR, respectively. It further generalizes zero-shot to Mip-NeRF360 and ScanNet++, outperforming all comparable baselines. Our project page is at {https://veichta.com/zipsplat{https://veichta.com/zipsplat}}.

3D Gaussian Splatting (3DGS) enables high-quality novel view synthesis, motivating interest in generating higher-resolution renders than those available during training. A natural strategy is to apply super-resolution (SR) to low-resolution (LR) input views, but independently enhancing each image introduces multi-view inconsistencies, leading to blurry renders. Prior methods attempt to mitigate these inconsistencies through learned neural components, temporally consistent video priors, or joint optimization on LR and SR views, but all uniformly apply SR across every image. In contrast, our key insight is that close-up LR views may contain high-frequency information for regions also captured in more distant views and that we can use the camera pose relative to scene geometry to inform where to add SR content. Building on this insight, we propose SplatSuRe, a method that selectively applies SR content only in undersampled regions lacking high-frequency supervision, yielding sharper and more consistent results. Across Tanks & Temples, Deep Blending, and Mip-NeRF 360, our approach surpasses baselines in both fidelity and perceptual quality. Notably, our gains are most significant in localized foreground regions where higher detail is desired.

Reproducing a published 3DGS paper takes weeks of expert engineering before any extension can be proposed. Prior autonomous-research systems read papers, draft hypotheses, and write code, but are limited by short fixed templates, low executability, and weak traceability, and none has been demonstrated end-to-end in a live computer-vision subfield with intense activity. SplatLab is an autonomous research system for 3D Gaussian Splatting that addresses these limitations. Given a research prompt, a target-paper URL, or no input at all, it reproduces a published baseline, proposes an extension, trains and ablates across Mip-NeRF 360 and LLFF, writes the manuscript, and binds every reported number to a logged training run. Five design choices distinguish it: (i) candidates mutate plugins from a verified-reproduction backbone matched to published baselines; (ii) a cascade-weighted Elo tournament across eight islands scores candidates on measured GPU PSNR with verbal-gradient feedback; (iii) a standing falsifier subtracts Elo on failure, integrating stress-test survival into selection; (iv) every reported number is bound to a logged training run, and the run cannot terminate while any claim is unbacked; (v) a seven-category 3DGS taxonomy wraps EVOLVE-BLOCK markers in domain-aligned scaffolds transferable across 3DGS repositories. On PSNR-targeted runs, SplatLab's manuscripts beat their reproduced targets by +0.18 to +3.78 dB, including +3.78 dB on astrophotographic nebula rendering, for which no prior 3DGS method exists. The research cycle compresses from months of graduate-student time to days of mostly autonomous compute. Code, all manuscripts, experiment ledgers, and the cross-run paper store are available on the project page.

Background: The positive predictive value (PPV) of large language model (LLM)-based proofreading for radiology reports is limited due to the low error prevalence. Purpose: To assess whether a three-pass LLM framework enhances PPV and reduces operational costs compared with baseline approaches. Materials and Methods: A retrospective analysis was performed on 1,000 consecutive radiology reports (250 each: radiography, ultrasonography, CT, MRI) from the MIMIC-III database. Two external datasets (CheXpert and Open-i) were validation sets. Three LLM frameworks were tested: (1) single-prompt detector; (2) extractor plus detector; and (3) extractor, detector, and false-positive verifier. Precision was measured by PPV and absolute true positive rate (aTPR). Efficiency was calculated from model inference charges and reviewer remuneration. Statistical significance was tested using cluster bootstrap, exact McNemar tests, and Holm-Bonferroni correction. Results: Framework PPV increased from 0.063 (95% CI, 0.036-0.101, Framework 1) to 0.079 (0.049-0.118, Framework 2), and significantly to 0.159 (0.090-0.252, Framework 3; P<.001 vs. baselines). aTPR remained stable (0.012-0.014; P>=.84). Operational costs per 1,000 reports dropped to USD 5.58 (Framework 3) from USD 9.72 (Framework 1) and USD 6.85 (Framework 2), reflecting reductions of 42.6% and 18.5%, respectively. Human-reviewed reports decreased from 192 to 88. External validation supported Framework 3's superior PPV (CheXpert 0.133, Open-i 0.105) and stable aTPR (0.007). Conclusion: A three-pass LLM framework significantly enhanced PPV and reduced operational costs, maintaining detection performance, providing an effective strategy for AI-assisted radiology report quality assurance.

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.

Detailed profession-specific system prompts raise token use and estimated cost per response without a consistent accuracy gain. We evaluate Scientific Agents, an open-source corpus of 503 profession-specific AGENTS.md profiles, with Gemini 3.8 Flash via OpenRouter in the Pi agent harness. We compare matched profiles with four controls: a minimal baseline ("You are a helpful assistant"), the profile's opening role sentence, a generic scientific rigor guide, and a profile from an unrelated domain. Across nine text-based science benchmarks (4,531 sampled questions, 100 matched profiles), 4,488 items completed all five conditions after API-error retries, scored with automated, rule-based grading. The average profile-baseline accuracy difference is -0.6 percentage points (95% bootstrap interval [-1.5, +0.2] across fixed tasks), and no benchmark shows a statistically clear improvement. Matched profiles produced 1.5-2.3 times as many output tokens and cost 2.2-4.5 times more per successful call. On 60 tool-using BioMysteryBench bioinformatics problems (three runs each for baseline and profile), mean solve rates were 46.7% with the profile and 56.7% at baseline, a difference of -10.0 percentage points (95% interval [-16.7, -3.3]) driven by more frequent token- and time-limit stops under the profile. Longer prompts had one unexpected operational advantage: on SuperGPQA, frequent provider API drops left the short baseline with a correct first-pass answer on only 54.0% of items, against 71.6% with the profile. Generic and mismatched prompts were about as reliable, so this gain comes from prompt length or formatting rather than domain expertise. For the tested model and tasks, loading full profession profiles by default does not improve accuracy and costs considerably more; whether selective retrieval of profile sections or open-ended scientific tasks would change this remains to be tested.

Continuous Glucose Monitoring (CGM) can detect early metabolic subphenotypes (insulin resistance, IR; β-cell dysfunction), but population-scale deployment faces two coupled problems. First, the same physiological state appears through multiple views (CGM time series, venous OGTT, Glucodensity summaries), so single-view representations fail to transfer when deployment shifts the modality or setting. Second, baselines perform inconsistently across these shifts. Both problems point to one remedy: representations that abstract away from any single view to capture higher-level temporal and distributional structure. We propose CGM-JEPA, a self-supervised pretraining framework which predicts masked latent representations rather than raw values, yielding abstraction that transfers across modalities. X-CGM-JEPA adds a masked Glucodensity cross-view objective for complementary distributional information. We pretrain on sim389k unlabeled CGM readings from 228 subjects and evaluate on two clinical cohorts (N=27 and N=17 public-release subsets) across three regimes (cohort generalization, venous-to-CGM transfer, home CGM) under 20-iteration times 2-fold cross-validation. X-CGM-JEPA ranks first or second on AUROC for both endpoints across all three regimes while no baseline does, exceeding the strongest baseline by up to +6.5 pp in cohort generalization and +3.6 pp in venous-to-CGM transfer (paired Wilcoxon, p<0.001). Under modality shift, it matches mean AUROC while redistributing toward weaker subgroups (ethnicity AUROC gap shrinks 25-54%); on sparse in-domain venous data, the distributional view lifts label-aware clustering (ARI +39%, NMI +40%). Code and weights: https://github.com/cruiseresearchgroup/CGM-JEPA

In this position paper, we argue that human baselines in foundation model evaluations must be more rigorous and more transparent to enable meaningful comparisons of human vs. AI performance, and we provide recommendations and a reporting checklist towards this end. Human performance baselines are vital for the machine learning community, downstream users, and policymakers to interpret AI evaluations. Models are often claimed to achieve "super-human" performance, but existing baselining methods are neither sufficiently rigorous nor sufficiently well-documented to robustly measure and assess performance differences. Based on a meta-review of the measurement theory and AI evaluation literatures, we derive a framework with recommendations for designing, executing, and reporting human baselines. We synthesize our recommendations into a checklist that we use to systematically review 115 human baselines (studies) in foundation model evaluations and thus identify shortcomings in existing baselining methods; our checklist can also assist researchers in conducting human baselines and reporting results. We hope our work can advance more rigorous AI evaluation practices that can better serve both the research community and policymakers. Data is available at: https://github.com/kevinlwei/human-baselines

We introduce the Burmese Handwritten Digit Dataset (BHDD), a collection of 87,561 grayscale images of handwritten Burmese digits in ten classes. Each image is 28x28 pixels, following the MNIST format. The training set has 60,000 samples split evenly across classes; the test set has 27,561 samples with class frequencies as they arose during collection. Over 150 people of different ages and backgrounds contributed samples. We analyze the dataset's class distribution, pixel statistics, and morphological variation, and identify digit pairs that are easily confused due to the round shapes of the Myanmar script. Simple baselines (an MLP, a two-layer CNN, and an improved CNN with batch normalization and augmentation) reach 99.40%, 99.75%, and 99.83% test accuracy respectively. BHDD is available under CC BY-SA 4.0 at https://github.com/baseresearch/BHDD

Background manipulation is a practical but under-specified image-forensics setting: the manipulated evidence can sit outside the salient foreground object, while many evaluations emphasize object-centric copy-move, splicing, or generic synthetic edits. We introduce BG-REAL, a public real-data anchored benchmark package for background manipulation detection and localization. The current release is built from Open Images V7 instance-segmentation sources and contains 7,000 processed samples over 1,200 source groups, including 6,000 public-data anchored samples and 1,000 synthetic control samples. BG-REAL covers six edit families, matched authentic controls, source-group splits, mask and leakage QA, 599 human-assisted quality-control rows, three completed external baselines (TruFor, MVSS-Net, and HiFi-Net), and five-seed model evaluation. Beyond aggregate accuracy, we use matched-authentic-control diagnostics to measure how often baselines misclassify re-encoded authentic images as manipulated at a threshold fixed on held-out validation data; false-positive rates range from 0.57 (TruFor, the lowest) to 1.00 (several weak or mask-informed baselines), indicating that re-encoding artifacts are a shared shortcut risk across baselines rather than a problem specific to any one model. The release provides the construction pipeline, evaluation protocol, paper-ready figures, and reproduction documentation. We frame BG-REAL as a background-manipulation-focused complement to general image-manipulation-localization benchmarks, not as a fully real-only or general-purpose benchmark.

We present MIPS, a novel method for program synthesis based on automated mechanistic interpretability of neural networks trained to perform the desired task, auto-distilling the learned algorithm into Python code. We test MIPS on a benchmark of 62 algorithmic tasks that can be learned by an RNN and find it highly complementary to GPT-4: MIPS solves 32 of them, including 13 that are not solved by GPT-4 (which also solves 30). MIPS uses an integer autoencoder to convert the RNN into a finite state machine, then applies Boolean or integer symbolic regression to capture the learned algorithm. As opposed to large language models, this program synthesis technique makes no use of (and is therefore not limited by) human training data such as algorithms and code from GitHub. We discuss opportunities and challenges for scaling up this approach to make machine-learned models more interpretable and trustworthy.

Interest in neural machine translation has grown rapidly as its effectiveness has been demonstrated across language and data scenarios. New research regularly introduces architectural and algorithmic improvements that lead to significant gains over "vanilla" NMT implementations. However, these new techniques are rarely evaluated in the context of previously published techniques, specifically those that are widely used in state-of-theart production and shared-task systems. As a result, it is often difficult to determine whether improvements from research will carry over to systems deployed for real-world use. In this work, we recommend three specific methods that are relatively easy to implement and result in much stronger experimental systems. Beyond reporting significantly higher BLEU scores, we conduct an in-depth analysis of where improvements originate and what inherent weaknesses of basic NMT models are being addressed. We then compare the relative gains afforded by several other techniques proposed in the literature when starting with vanilla systems versus our stronger baselines, showing that experimental conclusions may change depending on the baseline chosen. This indicates that choosing a strong baseline is crucial for reporting reliable experimental results.

India's Right to Information Act, 2005 gives every citizen the right to demand information from public authorities, yet in practice most people cannot make sense of the dense administrative language used in Central Information Commission (CIC) decisions, let alone predict whether an appeal is worth filing. This paper introduces RTI-Bench, a structured dataset of CIC decisions with outcome labels, exemption citations, IRAC-style reasoning components, and procedural timelines. To the best of our knowledge it is the first publicly released structured dataset for Indian RTI administrative decisions. The dataset draws from two sources: 1,218 cases from a publicly available instruction-response corpus (with structured fields added through rule-based extraction), and 298 CIC decision PDFs collected directly from the Commission portal, spanning five commissioners and three document format generations from 2023 to 2026. Label coverage reaches 89% on the instruction-response corpus. For the PDF subset of 239 primary decisions, coverage is 51% in this first release. A random sample of 50 labelled cases was manually reviewed, yielding a label precision of 95.3%. A zero-shot Mistral 7B baseline on 100 cases gives 57.3% accuracy and 37.0% macro-F1 on outcome prediction, well above the majority-class baseline of 14.3% macro-F1. RTI-Bench is available at https://huggingface.co/datasets/joyboseroy/rti-bench

We introduce Version 3 (V3) of the gridded near real-time Multi-Source Weighted-Ensemble Precipitation (MSWEP) product -- the first fully global, historical machine learning powered precipitation (P) dataset, developed to meet the growing demand for timely and accurate P estimates amid escalating climate challenges. MSWEP V3 provides hourly data at 0.1^circ resolution from 1979 to the present, continuously updated with a latency of approximately two hours. Development follows a two-stage process. First, baseline P fields are generated using machine learning model stacks that integrate satellite- and (re)analysis-based P and air-temperature products, along with static variables. The models are trained using hourly and daily observations from 15,959 P gauges worldwide. Second, these baseline P fields are corrected using daily and monthly gauge observations from 57,666 and 86,000 stations globally. To assess MSWEP V3's baseline performance, we evaluated 19 (quasi-) global gridded P products -- including both uncorrected and gauge-based products -- using observations from an independent set of 15,958 gauges excluded from the first training stage. The MSWEP V3 baseline achieved a median daily Kling-Gupta Efficiency (KGE) of 0.69, outperforming all evaluated products. Other uncorrected products achieved median daily KGE values of 0.61 (ERA5), 0.46 (IMERG-L V7), 0.38 (GSMaP V8), and 0.31 (CHIRP). Using leave-one-out cross-validation, the daily gauge correction was found to improve the median daily correlation by 0.09, constrained by the already strong baseline performance. We anticipate that MSWEP V3 -- accessible at www.gloh2o.org/mswep -- will enable more reliable monitoring, forecasting, and management of water-related risks in a variable and changing climate.

We consider the two related problems of detecting if an example is misclassified or out-of-distribution. We present a simple baseline that utilizes probabilities from softmax distributions. Correctly classified examples tend to have greater maximum softmax probabilities than erroneously classified and out-of-distribution examples, allowing for their detection. We assess performance by defining several tasks in computer vision, natural language processing, and automatic speech recognition, showing the effectiveness of this baseline across all. We then show the baseline can sometimes be surpassed, demonstrating the room for future research on these underexplored detection tasks.

Training algorithms, broadly construed, are an essential part of every deep learning pipeline. Training algorithm improvements that speed up training across a wide variety of workloads (e.g., better update rules, tuning protocols, learning rate schedules, or data selection schemes) could save time, save computational resources, and lead to better, more accurate, models. Unfortunately, as a community, we are currently unable to reliably identify training algorithm improvements, or even determine the state-of-the-art training algorithm. In this work, using concrete experiments, we argue that real progress in speeding up training requires new benchmarks that resolve three basic challenges faced by empirical comparisons of training algorithms: (1) how to decide when training is complete and precisely measure training time, (2) how to handle the sensitivity of measurements to exact workload details, and (3) how to fairly compare algorithms that require hyperparameter tuning. In order to address these challenges, we introduce a new, competitive, time-to-result benchmark using multiple workloads running on fixed hardware, the AlgoPerf: Training Algorithms benchmark. Our benchmark includes a set of workload variants that make it possible to detect benchmark submissions that are more robust to workload changes than current widely-used methods. Finally, we evaluate baseline submissions constructed using various optimizers that represent current practice, as well as other optimizers that have recently received attention in the literature. These baseline results collectively demonstrate the feasibility of our benchmark, show that non-trivial gaps between methods exist, and set a provisional state-of-the-art for future benchmark submissions to try and surpass.

Knowledge graphs (KGs) are increasingly used to support large lan guage model (LLM) reasoning, but standard triplet-based KGs treat each relation as globally valid. In many settings, whether a relation should count as evidence depends on the context. We therefore formulate triplet validity as a triplet-specific function of context and refer to this formulation as a Quantum Knowledge Graph (QKG). We instantiate QKG in medicine using a diabetes-centered PrimeKG subgraph, whose 68,651 context-sensitive relations are further annotated with patient-group-specific constraints. We evaluate it in a reasoner--validator pipeline for medical question answering on a KG-grounded subset of MedReason containing 2,788 questions. With Haiku-4.5 as both the Reasoner and the Validator, KG-backed validation significantly improves over a no-validator baseline (+0.61 pp), and QKG with context matching yields the largest gain, outperforming both KG validation without context matching (+0.79 pp) and the no-validator baseline (+1.40 pp; paired McNemar, all p<0.05). Under a stronger validator (Qwen-3.6-Plus), the raw QKG gain over the no-validator baseline grows from +1.40 pp to +5.96 pp; the context-matching gap is non-significant (p=0.73) on the raw set but becomes borderline significant (p=0.05) after adjustment for knowledge leakage and suspicious questions, consistent with a benchmark-gold ceiling rather than a QKG limitation. Taken together, the results support the view that the value of a KG in LLM-based clinical reasoning lies not merely in storing medically related facts, but in representing whether those facts are applicable to the specific patient context. For reproducibility and further research, we release the curated QKG datasets and source code.https://github.com/HKAI-Sci/QKG

Behaviour-Driven Development (BDD) suites accumulate step-text duplication whose maintenance cost is established in prior work. Existing detection techniques require running the tests (Binamungu et al., 2018-2023) or are confined to a single organisation (Irshad et al., 2020-2022), leaving a gap: a purely static, paraphrase-robust, step-level detector usable on any repository. We fill the gap with cukereuse, an open-source Python CLI combining exact hashing, Levenshtein ratio, and sentence-transformer embeddings in a layered pipeline, released alongside an empirical corpus of 347 public GitHub repositories, 23,667 parsed .feature files, and 1,113,616 Gherkin steps. The step-weighted exact-duplicate rate is 80.2 %; the median-repository rate is 58.6 % (Spearman rho = 0.51 with size). The top hybrid cluster groups 20.7k occurrences across 2.2k files. Against 1,020 pairs manually labelled by the three authors under a released rubric (inter-annotator Fleiss' kappa = 0.84 on a 60-pair overlap), we report precision, recall, and F1 with bootstrap 95 % CIs under two protocols: the primary rubric and a score-free second-pass relabelling. The strongest honest pair-level number is near-exact at F1 = 0.822 on score-free labels; the primary-rubric semantic F1 = 0.906 is inflated by a stratification artefact that pins recall at 1.000. Lexical baselines (SourcererCC-style, NiCad-style) reach primary F1 = 0.761 and 0.799. The paper also presents a CDN-structured critique of Gherkin (Cognitive Dimensions of Notations); eight of fourteen dimensions are rated problematic or unsupported. The tool, corpus, labelled pairs, rubric, and pipeline are released under permissive licences.

Emerging personal AI agents are moving toward persistent, multi-source memory. This creates an evaluation problem: systems must decide how to use conflicting or incomplete evidence; they cannot just retrieve facts from one clean history. Existing benchmarks rarely show whether an error came from the evidence given to a method or from the method's conflict-resolution step. We study this as selective QA over conflicting multi-source personal memory: systems answer based on conflicting, sometimes incomplete sources, or abstain when evidence is insufficient. We develop a benchmark containing 18 question templates across 8 reasoning types, 480 personas, 4 random seeds, and 34,560 instances, with controlled source distortions and deterministic ground truth. We evaluate the performance of baselines without access to any source, access to a single source, structured fusion methods, and frontier LLMs. The best trained fusion resolver reaches 80.3% accuracy, while the strongest prompt-only LLM baseline reaches 70.0%. With abstention, the same resolver reaches 85.3% selective accuracy at 78.3% coverage and the best LLM reaches 71.0% selective accuracy at 95.4% coverage. Different models have different strengths across reasoning types. We release the data, code, cached model outputs, and data-generating process for reuse.

This paper provides a baseline system for First-shot-compliant unsupervised anomaly detection (ASD) for machine condition monitoring. First-shot ASD does not allow systems to do machine-type dependent hyperparameter tuning or tool ensembling based on the performance metric calculated with the grand truth. To show benchmark performance for First-shot ASD, this paper proposes an anomaly sound detection system that works on the domain generalization task in the Detection and Classification of Acoustic Scenes and Events (DCASE) 2022 Challenge Task 2: "Unsupervised Anomalous Sound Detection for Machine Condition Monitoring Applying Domain Generalization Technique" while complying with the First-shot requirements introduced in the DCASE 2023 Challenge Task 2 (DCASE2023T2). A simple autoencoder based implementation combined with selective Mahalanobis metric is implemented as a baseline system. The performance evaluation is conducted to set the target benchmark for the forthcoming DCASE2023T2. Source code of the baseline system will be available on GitHub: https://github.com/nttcslab/dcase2023_task2_baseline_ae .

We present miniF2F, a dataset of formal Olympiad-level mathematics problems statements intended to provide a unified cross-system benchmark for neural theorem proving. The miniF2F benchmark currently targets Metamath, Lean, Isabelle (partially) and HOL Light (partially) and consists of 488 problem statements drawn from the AIME, AMC, and the International Mathematical Olympiad (IMO), as well as material from high-school and undergraduate mathematics courses. We report baseline results using GPT-f, a neural theorem prover based on GPT-3 and provide an analysis of its performance. We intend for miniF2F to be a community-driven effort and hope that our benchmark will help spur advances in neural theorem proving.

Benchmark contamination is diagnosed with n-gram overlap, likelihood-based membership inference, or canary strings, and each needs something usually unavailable: the training corpus, a well-chosen test statistic, or foresight at release. A recent alternative reads it off a linear probe on internal activations. We show the natural way to do this does not work, specify one that survives measurement, then find that the correction making it work carries more variance than the null it is tested against. The protocol reports a zero-sum contrast on the depth profile of probe accuracy, recentred on a level-matched placebo baseline, tested against a label-permutation null, with the reference set twice the size of the suspect set. Each choice replaces a simpler alternative we rejected on measurement. Reporting the level of excess separability rather than its shape makes the false positive rate track the size of the analyst's own control set, 0.03 to 0.99 under a true null. Contrasting against a flat depth profile rejects a true null 0.72 of the time when surface decodability rises with depth, and loses all power when it falls. On real transformers the protocol fails a test the simulations did not pose. The recentring subtracts an estimate, and the permutation null holds it fixed. Re-estimated across split seeds on four audits of contaminated checkpoints, its standard deviation is 1.30 to 1.56 times the null's own in every arm: what is subtracted to remove a bias is more variable than what it corrects. The one nominally significant result, p = 0.0075, becomes 0.0745 once that variance is propagated, and no verdict is issued. The simulations missed this because their surface key is the covariate driving item variation; on real text it is a proxy, and degrading key quality in simulation reproduces it. We add a companion measurement and a widened null. No arm shows contamination.

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E), a U-Net-inspired architecture that integrates state-of-the-art ViT foundation models as encoders to predict mIF signals from H&E images. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available ORION dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on two independent datasets. MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.88 for Pan-CK, 0.57 for CD3e, 0.56 for SMA, 0.36 for CD68, and 0.30 for CD20, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that our model effectively captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.

High-quality tool-use data is critical for training language models to interact effectively with external tools. However, existing synthetic approaches typically follow a generate-then-filter paradigm with static post-hoc verification, often yielding inefficient data with imbalanced feature distributions. We propose ToolLoop, a closed-loop framework that decomposes synthesis into three progressive stages: (1) sampling function name combinations as ground truth; (2) backward derivation of user queries; and (3) forward derivation of tool calls. At each stage, dynamic self-feedback iteratively guides the model toward high-quality generation, realizing a transition from generate-then-filter to generate-verify-refine. On the Berkeley Function Calling Leaderboard (BFCL), a 4B parameter model trained with our 11K synthetic examples achieves 86.40% accuracy in non-reasoning mode, while an Isolate variant that removes BFCL-overlapping candidate functions still reaches 86.07\%. Cross-benchmark evaluation on ACEBench further demonstrates strong generalization, with 72.1% overall accuracy using only 18.3% of baseline training data.

Longitudinal chest X-ray (CXR) interpretation requires reasoning over disease evolution across multiple patient visits, yet most existing medical VQA benchmarks focus on single images or short-horizon image pairs. We introduce MI-CXR, a benchmark for standardized evaluation of Multi-Interval longitudinal reasoning over multi-visit CXR sequences, without requiring free-form report generation or additional clinical context. MI-CXR comprises five-way multiple-choice questions over five-visit patient timelines and instantiates three complementary task families: Temporal Event Localization, Interval-wise Change Reasoning, and Global Trajectory Summarization, which assess clinically grounded visual reasoning over time. Evaluating 14 state-of-the-art vision-language models (VLMs) shows low overall performance, with an average accuracy of 29.3%, only modestly above random guessing. Using stage-wise diagnostic probing, we find that models often produce locally plausible interval descriptions but fail to enforce temporal constraints or compose evidence into globally consistent decisions over the full timeline. These findings reveal key limitations of current VLMs and establish MI-CXR as a principled benchmark for longitudinal medical reasoning. The benchmark is available at https://github.com/AIDASLab/MI-CXR

Autonomous coding agents solve repository issues by reading code, running commands, editing files, and submitting patches. Extra inference-time compute yields gains only when it produces a useful repair and supplies reliable evidence for choosing one. Three behaviors decide both, and we argue they are teachable rather than byproducts of scale, so a policy can carry them instead of a scaffold. Location diversity remains narrow, since attempts return to the same site and extra samples add no coverage. Edit diversity is left unexploited, since methodologies that differ resolve complementary issues no single run reaches. Verification misleads, since a test the agent writes for its own patch accepts many incorrect ones. Directing search by execution feedback and scoring each patch against its own reverted tree resolves 52.8% of SWE-bench Verified using 48.1% of the agent-steps an eight-sample baseline spends. Training moves these behaviors into the policy. On the 270 issues held out from SFT and RL training, weighted supervised fine-tuning raises pass@1 from 31.9% to 35.2% and pass@8 from 46.7% to 51.1%. A reinforcement objective then trains the verifier against gold-labeled repairs and incorrect variants, crediting the assertions that detect them. It raises pass@1 to 43.0% and pass@8 to 60.7%, lifts verifier precision from 26.8% to 41.7%, and more than halves false acceptance. Resolution improves on two of three out-of-distribution suites and verifier precision on all three, and the gains hold at 7B, 14B, and 30B against published coder baselines.

We revisit the performance of the classic gradual magnitude pruning (GMP) baseline for large language models, focusing on the classic BERT benchmark on various popular tasks. Despite existing evidence in the literature that GMP performs poorly, we show that a simple and general variant, which we call GMP*, can match and sometimes outperform more complex state-of-the-art methods. Our results provide a simple yet strong baseline for future work, highlight the importance of parameter tuning for baselines, and even improve the performance of the state-of-the-art second-order pruning method in this setting.

Pir\'a is a reading comprehension dataset focused on the ocean, the Brazilian coast, and climate change, built from a collection of scientific abstracts and reports on these topics. This dataset represents a versatile language resource, particularly useful for testing the ability of current machine learning models to acquire expert scientific knowledge. Despite its potential, a detailed set of baselines has not yet been developed for Pir\'a. By creating these baselines, researchers can more easily utilize Pir\'a as a resource for testing machine learning models across a wide range of question answering tasks. In this paper, we define six benchmarks over the Pir\'a dataset, covering closed generative question answering, machine reading comprehension, information retrieval, open question answering, answer triggering, and multiple choice question answering. As part of this effort, we have also produced a curated version of the original dataset, where we fixed a number of grammar issues, repetitions, and other shortcomings. Furthermore, the dataset has been extended in several new directions, so as to face the aforementioned benchmarks: translation of supporting texts from English into Portuguese, classification labels for answerability, automatic paraphrases of questions and answers, and multiple choice candidates. The results described in this paper provide several points of reference for researchers interested in exploring the challenges provided by the Pir\'a dataset.

We present MiMo-7B, a large language model born for reasoning tasks, with optimization across both pre-training and post-training stages. During pre-training, we enhance the data preprocessing pipeline and employ a three-stage data mixing strategy to strengthen the base model's reasoning potential. MiMo-7B-Base is pre-trained on 25 trillion tokens, with additional Multi-Token Prediction objective for enhanced performance and accelerated inference speed. During post-training, we curate a dataset of 130K verifiable mathematics and programming problems for reinforcement learning, integrating a test-difficulty-driven code-reward scheme to alleviate sparse-reward issues and employing strategic data resampling to stabilize training. Extensive evaluations show that MiMo-7B-Base possesses exceptional reasoning potential, outperforming even much larger 32B models. The final RL-tuned model, MiMo-7B-RL, achieves superior performance on mathematics, code and general reasoning tasks, surpassing the performance of OpenAI o1-mini. The model checkpoints are available at https://github.com/xiaomimimo/MiMo.

As spaceborne computing systems increasingly rely on neural network (NN) accelerators, the opacity of commercial, black-box architectures severely restricts the development of verifiable radiation mitigation strategies. Open-source, register-transfer level (RTL)-accessible accelerators resolve this limitation by enabling user-defined instrumentation, yet few have empirical radiation-response baselines. This work establishes a foundational system-level proton-irradiation baseline for an unmitigated open-source Tensil NN accelerator deployed on a Zynq UltraScale+ SoC executing ResNet-20 inference. Under 20 to 58 MeV proton irradiation, we delivered 4.29 times 10^{10} p/cm^{2} within monitored operational windows. Seven workload interruptions required two restarts of the notebook process, four reboots or board resets, and one power-cycle sequence. Two output-corruption events returned incorrect CIFAR-10 classes without loss of service. In the longer event, the accelerator returned a class absent from the ten-image CIFAR-10 pool for 39 consecutive inputs at normal cadence. The process remained alive, while the kernel log, limited memory test, and sampled power showed no anomaly. Observation of the stuck-class sequence ended with scheduled bitstream reconfiguration. All nine onsets occurred under the nominal 4 cm beam, which exposed the SoC, LPDDR4, and additional board circuitry; none occurred under the 2 cm SoC-centered field. This pattern shows a field association but does not establish LPDDR4 as the cause because field size was confounded with run order and dose. Linux-managed accelerators require end-to-end content checks and recovery that reaches the state in which corruption can persist. This baseline documents availability loss and silent output corruption, supporting future software hardening of COTS FPGA-SoCs for neural-network inference in space systems.

Data products are reusable, self-contained assets designed for specific business use cases. Automating their discovery and generation is of great industry interest, as it enables discovery in large data lakes and supports analytical Data Product Requests (DPRs). Currently, there is no benchmark established specifically for data product discovery. Existing datasets focus on answering single factoid questions over individual tables rather than collecting multiple data assets for broader, coherent products. To address this gap, we introduce DPBench, the first user-request-driven data product benchmark over hybrid table-text corpora. Our framework systematically repurposes existing table-text QA datasets by clustering related tables and passages into coherent data products, generating professional-level analytical requests that span both data sources, and validating benchmark quality through multi-LLM evaluation. DPBench preserves full provenance while producing actionable, analyst-like data product requests. Baseline experiments with hybrid retrieval methods establish the feasibility of DPR evaluation, reveal current limitations, and point to new opportunities for automatic data product discovery research. Code and datasets are available at: https://anonymous.4open.science/r/data-product-benchmark-BBA7/

Current evaluation protocols for Vision-Language Models (VLMs) in Radiology Report Generation (RRG) rely on report-level metrics that measure lexical overlap or aggregate clinical correctness. However, such metrics do not test whether individual diagnostic statements stem from the actual pathological evidence visible in the image. This allows models to achieve competitive scores by exploiting learned priors or spurious correlations, a failure mode we refer to as vision shortcut. We introduce SHOVIR, a benchmark for evaluating vision shortcut behavior in RRG. SHOVIR extends two spatially annotated chest X-ray datasets, MIMIC-CXR and PadChest-GR, with per-box CheXpert labels, and defines image-level and disease-level occlusion experiments that contrast baseline performance on clean images against localized, region-specific perturbations. Comparing predictions across these conditions isolates two failure modes at the disease-class level: direct shortcuts, where a finding persists after its visual evidence is removed, and contextual shortcuts, where detection degrades once co-occurring pathologies are occluded despite the target region remaining intact. Benchmarking eight state-of-the-art VLMs, we find that shortcut behavior varies substantially across architectures and datasets. Models achieving the highest baseline report quality do not necessarily rank highest in spatial grounding, revealing that clinically fluent generation can coexist with shallow reliance on visual evidence. These findings expose a blind spot in current RRG evaluation and motivate region-aware assessment protocols.

Fashion attribute extraction is evaluated inconsistently: results are reported as single aggregate numbers across image types that pose different problems, fields that are not visible in an image are scored as ordinary negatives, and the effect of vocabulary mismatch between datasets is acknowledged but not measured. We release the MODA General Attribute Suite, a four-track benchmark that keeps these problems separate by construction. Each track (localized garment crops, catalogue product images, applicability-aware full-body photographs, and product text) carries its own frozen test set, input contract, metric, and leakage unit, and the tracks are never averaged. The protocol requires label-blind prediction, SHA-256 commitment of prediction files before any label is opened, a fail-closed scorer, and a 10,000-sample paired cluster bootstrap at each track's natural leakage unit; promotion requires a positive interval on every track rather than a favourable mean. We release the scorers, the split builders, our own prediction files with their hashes including the runs we lose, and the MODA_NER(V) model checkpoints for three of the four tracks. The text model is not distributed; its benchmark is. We report baseline results, six interventions that did not improve them, and the limitations of the evidence.

This report presents the dataset and the evaluation setup of the Sound Event Localization & Detection (SELD) task for the DCASE 2020 Challenge. The SELD task refers to the problem of trying to simultaneously classify a known set of sound event classes, detect their temporal activations, and estimate their spatial directions or locations while they are active. To train and test SELD systems, datasets of diverse sound events occurring under realistic acoustic conditions are needed. Compared to the previous challenge, a significantly more complex dataset was created for DCASE 2020. The two key differences are a more diverse range of acoustical conditions, and dynamic conditions, i.e. moving sources. The spatial sound scenes are created using real room impulse responses captured in a continuous manner with a slowly moving excitation source. Both static and moving sound events are synthesized from them. Ambient noise recorded on location is added to complete the generation of scene recordings. A baseline SELD method accompanies the dataset, based on a convolutional recurrent neural network, to provide benchmark scores for the task. The baseline is an updated version of the one used in the previous challenge, with input features and training modifications to improve its performance.

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

Question Answering (QA) returns concise answers or answer lists from natural language text given a context document. Many resources go into curating QA datasets to advance robust models' development. There is a surge of QA datasets for languages like English, however, this is not true for Amharic. Amharic, the official language of Ethiopia, is the second most spoken Semitic language in the world. There is no published or publicly available Amharic QA dataset. Hence, to foster the research in Amharic QA, we present the first Amharic QA (AmQA) dataset. We crowdsourced 2628 question-answer pairs over 378 Wikipedia articles. Additionally, we run an XLMR Large-based baseline model to spark open-domain QA research interest. The best-performing baseline achieves an F-score of 69.58 and 71.74 in reader-retriever QA and reading comprehension settings respectively.

Some security-development settings require local models that map an objective to an ordered, checkable plan. We present a low-rank decomposition adapter and release a case-disjoint corpus with 24 authored decompositions and 83 derived next-step examples across 24 satellite-security cases. To prevent reference-plan leakage, prompts contain one objective and eight shuffled SPARTA candidates. The evaluation candidate sets are constructed with oracle inclusion of every reference technique, so this study measures selection from a controlled set, not retrieval. On six fixed cases and five decoding seeds, mean scores vary across adapters and prompted Qwen2.5 baselines; a separate greedy check over three adapter training seeds shows non-negligible training variance. A 24-fold greedy leave-one-case-out control at the two compact sizes likewise shows tradeoffs: at 1.5B, adapter precision is 0.583 against 0.480 for two-shot prompting, while recall is 0.586 against 0.660. Case-resampling intervals for adapter precision relative to the strongest prompted baseline cross zero at 1.5B and 7B. The adapter is also substantially more format-compliant, which prevents attributing all score differences to selection. Autoregressive next-step accuracy is 0.08, 0.06, and 0.29 at 0.5B, 1.5B, and 7B. We therefore offer the formulation, leakage-controlled dataset, reproducibility package, and descriptive analysis as a proof of concept, not evidence of a reliable stand-alone decomposition system or a general adapter advantage. A separate diagnostic tests contract reuse.

We present scPilot, the first systematic framework to practice omics-native reasoning: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and on-demand bioinformatics tools. scPilot converts core single-cell analyses, i.e., cell-type annotation, developmental-trajectory reconstruction, and transcription-factor targeting, into step-by-step reasoning problems that the model must solve, justify, and, when needed, revise with new evidence. To measure progress, we release scBench, a suite of 9 expertly curated datasets and graders that faithfully evaluate the omics-native reasoning capability of scPilot w.r.t various LLMs. Experiments with o1 show that iterative omics-native reasoning lifts average accuracy by 11% for cell-type annotation and Gemini-2.5-Pro cuts trajectory graph-edit distance by 30% versus one-shot prompting, while generating transparent reasoning traces explain marker gene ambiguity and regulatory logic. By grounding LLMs in raw omics data, scPilot enables auditable, interpretable, and diagnostically informative single-cell analyses. Code, data, and package are available at https://github.com/maitrix-org/scPilot

A method is presented for accelerating inference in transformer language models by exploiting the low effective rank of the token activation manifold at each layer. The method decomposes each activation vector into a subspace component and a residual, computes the linear-layer output on the subspace component via a cached low-rank weight image at reduced memory bandwidth, and applies a per-token gate that determines whether the residual correction is computed or skipped. The gate ensures that the output distribution is preserved to within a controllable tolerance. Validation on three model families (GPT-2 124M, GPT-J 6B, OPT 6.7B) on AMD MI300X demonstrates effective speedups of 3.0x to 10.5x on linear-layer weight reads with perplexity ratios below 1.00 and top-1 token agreement above 98%. The method requires no retraining, no architectural modification, and no approximation of the attention mechanism. At the operating point (k = 256, ε = 0.05) on GPT-J 14 6B, the accelerated model produces character-for-character identical output to the baseline.

Computer architecture has long used benchmarks to make progress measurable. LLM agents create a different measurement problem: success is not merely writing code or tuning parameters. The agent must interpret workloads, choose mechanisms, use simulators, predict performance, satisfy hard constraints, and decide which feasible design is worth evaluating. This paper introduces ArchEval, a benchmark and platform for evaluating LLM agents on computer architecture design and optimization. It contains 20 challenges across CPU core mechanisms, system architecture, memory systems, accelerators, and compute-in-memory, backed by eight simulators. Each challenge is posed under three settings: L1 full harness, with repeated simulator feedback; L2 simulator-code container, where simulator source is available but the agent must assemble its own workflow; and L3 agent-only, with no runnable feedback before submission. Each run reports baseline-normalized verifier performance and records the full trajectory, connecting results to workload analysis, simulator-tool use, prediction, constraint handling, and artifact integrity. Initial results show a sharp boundary in current agents. With L1 support, all four evaluated agents reach or exceed baseline and improve real designs across diverse simulators. Removing support exposes weaknesses: many agents fail to turn simulator source into useful experiments, and L3 predictions often disagree with verifier results. In L3, only GPT-5.5 + Codex remains above baseline, reaching 1.21x geomean performance and a 65% win rate; the other three fall below baseline. Even GPT-5.5 + Codex has only a 15% performance-modeling pass rate. ArchEval frames today's agents as useful optimization assistants rather than autonomous architects, and identifies capabilities needed next: simulator-tool use, calibrated prediction, pre-feedback judgment, and useful mechanism discovery.

The use of machine learning (ML) based techniques has become increasingly popular in the field of bioacoustics over the last years. Fundamental requirements for the successful application of ML based techniques are curated, agreed upon, high-quality datasets and benchmark tasks to be learned on a given dataset. However, the field of bioacoustics so far lacks such public benchmarks which cover multiple tasks and species to measure the performance of ML techniques in a controlled and standardized way and that allows for benchmarking newly proposed techniques to existing ones. Here, we propose BEANS (the BEnchmark of ANimal Sounds), a collection of bioacoustics tasks and public datasets, specifically designed to measure the performance of machine learning algorithms in the field of bioacoustics. The benchmark proposed here consists of two common tasks in bioacoustics: classification and detection. It includes 12 datasets covering various species, including birds, land and marine mammals, anurans, and insects. In addition to the datasets, we also present the performance of a set of standard ML methods as the baseline for task performance. The benchmark and baseline code is made publicly available at https://github.com/earthspecies/beans in the hope of establishing a new standard dataset for ML-based bioacoustic research.

This paper presents a comprehensive methodology and comparative performance analysis for the automated classification and object detection of peripheral blood cells (PBCs) in microscopic images. Addressing the critical challenge of data scarcity and heterogeneity, robust data pipeline was first developed to standardize and merge four public datasets (PBC, BCCD, Chula, Sickle Cell) into a unified resource. Then employed a state-of-the-art Faster R-CNN object detection framework, leveraging a ResNet-50-FPN backbone. Comparative training rigorously evaluated a randomly initialized baseline model (Regimen 1) against a Transfer Learning Regimen (Regimen 2), initialized with weights pre-trained on the Microsoft COCO dataset. The results demonstrate that the Transfer Learning approach achieved significantly faster convergence and superior stability, culminating in a final validation loss of 0.08666, a substantial improvement over the baseline. This validated methodology establishes a robust foundation for building high-accuracy, deployable systems for automated hematological diagnosis.

Peptide therapeutics are widely regarded as the "third generation" of drugs, yet progress in peptide Machine Learning (ML) are hindered by the absence of standardized benchmarks. Here we present PepBenchmark, which unifies datasets, preprocessing, and evaluation protocols for peptide drug discovery. PepBenchmark comprises three components: (1) PepBenchData, a well-curated collection comprising 29 canonical-peptide and 6 non-canonical-peptide datasets across 7 groups, systematically covering key aspects of peptide drug development, representing, to the best of our knowledge, the most comprehensive AI-ready dataset resource to date; (2) PepBenchPipeline, a standardized preprocessing pipeline that ensures consistent dataset cleaning, construction, splitting, and feature transformation, mitigating quality issues common in ad hoc pipelines; and (3) PepBenchLeaderboard, a unified evaluation protocol and leaderboard with strong baselines across 4 major methodological families: Fingerprint-based, GNN-based, PLM-based, and SMILES-based models. Together, PepBenchmark provides the first standardized and comparable foundation for peptide drug discovery, facilitating methodological advances and translation into real-world applications. The data and code are publicly available at https://github.com/ZGCI-AI4S-Pep/PepBenchmark/.

Reinforcement Learning (RL) for Large Language Models (LLMs) often suffers from training collapse in long-horizon tasks due to exploding gradient variance. To mitigate this, a baseline is commonly introduced for advantage computation; however, traditional value models remain difficult to optimize, and standard group-based baselines overlook sequence heterogeneity. Although classic optimal baseline theory can achieve global variance reduction, it neglects token heterogeneity and requires prohibitive gradient-based computation. In this work, we derive the Optimal Token Baseline (OTB) from first principles, proving that gradient updates should be weighted inversely to their cumulative gradient norm. To ensure efficiency, we propose the Logit-Gradient Proxy that approximates the gradient norm using only forward-pass probabilities. Our method achieves training stability and matches the performance of large group sizes (N=32) with only N=4, reducing token consumption by over 65% across single-turn and tool-integrated reasoning tasks.

The deployment of machine learning models in operational contexts represents a significant investment for any organisation. Consequently, the risk of these models being misappropriated by competitors needs to be addressed. In recent years, numerous proposals have been put forth to detect instances of model stealing. However, these proposals operate under implicit and disparate data and model access assumptions; as a consequence, it remains unclear how they can be effectively compared to one another. Our evaluation shows that a simple baseline that we introduce performs on par with existing state-of-the-art fingerprints, which, on the other hand, are much more complex. To uncover the reasons behind this intriguing result, this paper introduces a systematic approach to both the creation of model fingerprinting schemes and their evaluation benchmarks. By dividing model fingerprinting into three core components -- Query, Representation and Detection (QuRD) -- we are able to identify sim100 previously unexplored QuRD combinations and gain insights into their performance. Finally, we introduce a set of metrics to compare and guide the creation of more representative model stealing detection benchmarks. Our approach reveals the need for more challenging benchmarks and a sound comparison with baselines. To foster the creation of new fingerprinting schemes and benchmarks, we open-source our fingerprinting toolbox.

Evaluating whether text-to-image models follow explicit spatial instructions is difficult to automate. Object detectors may miss targets or return multiple plausible detections, and simple geometric tests can become ambiguous in borderline cases. Spatial evaluation is naturally a selective prediction problem, the checker may abstain when evidence is weak and report confidence so that results can be interpreted as a risk coverage tradeoff rather than a single score. We introduce SpatialBench-UC, a small, reproducible benchmark for pairwise spatial relations. The benchmark contains 200 prompts (50 object pairs times 4 relations) grouped into 100 counterfactual pairs obtained by swapping object roles. We release a benchmark package, versioned prompts, pinned configs, per-sample checker outputs, and report tables, enabling reproducible and auditable comparisons across models. We also include a lightweight human audit used to calibrate the checker's abstention margin and confidence threshold. We evaluate three baselines, Stable Diffusion 1.5, SD 1.5 BoxDiff, and SD 1.4 GLIGEN. The checker reports pass rate and coverage as well as conditional pass rates on decided samples. The results show that grounding methods substantially improve both pass rate and coverage, while abstention remains a dominant factor due mainly to missing detections.

Machine learning-based Type 2 diabetes risk prediction models obtain good internal validation results but lose effectiveness in real-world applications due to deficient external testing and fairness assessment. We developed a multi-dimensional framework evaluating discrimination, calibration, interpretability, and algorithmic fairness on nationally representative populations. An XGBoost model was trained on NHANES 2015-2020 (n=15,685) using eight non-laboratory predictors: age, sex, race/ethnicity, BMI, smoking status, physical activity, history of heart attack, and history of stroke. External validation was performed on BRFSS 2020-2022 (n=1,285,783) under realistic distribution shift. Internal validation showed good discrimination (AUC=0.794, 95% CI 0.788-0.800), with performance loss on external validation (AUC=0.717, relative decrease: -9.7%, p<0.001). Fairness analysis revealed severe bias: elderly adults (>=60) showed AUC=0.607 vs 0.742 for young adults (difference=0.135, p<0.001); obese individuals showed AUC=0.698 vs 0.735 for normal weight (difference=0.037, p<0.001). Gender showed comparable performance (male=0.723 vs female=0.712, p=0.142). Calibration revealed risk overestimation (Brier score=0.123). SHAP analysis identified age, BMI, and physical activity as primary risk drivers. Populations with highest diabetes risk receive the worst algorithmic performance, underscoring the need for fairness-aware, age-stratified deployment strategies before clinical use.

Ultrasound is the most widely deployed imaging modality worldwide, yet clinical AI remains fragmented into narrow single-task models that fail when device, operator, or anatomy changes. Here we present SonoCorpus, an open resource unifying 456,963 images and 1,626,085 expert masks from 53 public datasets spanning 24 clinical applications and 17 countries, and SonoBase, an interactive segmentation foundation model pretrained on it. Across fifteen evaluation datasets introducing new organs, devices, operators, and geographies, SonoBase outperforms SAM2, MedSAM2, and the concept-promptable MedSAM3 on every dataset and matches per-dataset specialist models trained on the same data; on fully external data it exceeds the accuracy these baselines achieve on their own in-distribution benchmarks. Ejection fraction derived from its segmentations falls within inter-observer variability (6.63\% error), with fewer misclassifications at the defibrillator-candidacy threshold than either promptable baseline (13\% versus 18--42\%); fetal head-circumference (1.81~mm) and gestational-age (1.2 days) errors fall below inter-observer variability. Where a baseline fails outright, one in four test cases, SonoBase recovers a usable segmentation in 81\% of them, including on handheld probes operated by minimally trained users in two low- and middle-income countries (Sierra Leone and Tanzania). Five labeled examples can help the model adapt to a new setting, and the identical training protocol transfers well to newer models such as SAM3, locating the advantage in ultrasound-specific pretraining rather than any single architecture. To ensure reproducibility and enable the community to build on SonoBase as a platform, we release all checkpoints, optimizer states, data-split indices, deduplication hashes, and starter code.

Scientific question answering (SQA) is an important task aimed at answering questions based on papers. However, current SQA datasets have limited reasoning types and neglect the relevance between tables and text, creating a significant gap with real scenarios. To address these challenges, we propose a QA benchmark for scientific tables and text with diverse reasoning types (SciTaT). To cover more reasoning types, we summarize various reasoning types from real-world questions. To involve both tables and text, we require the questions to incorporate tables and text as much as possible. Based on SciTaT, we propose a strong baseline (CaR), which combines various reasoning methods to address different reasoning types and process tables and text at the same time. CaR brings average improvements of 12.9% over other baselines on SciTaT, validating its effectiveness. Error analysis reveals the challenges of SciTaT, such as complex numerical calculations and domain knowledge.

Many benchmarks for automated causal inference evaluate a system's performance based on a single numerical output, such as an Average Treatment Effect (ATE). This approach conflates two distinct steps in causal analysis: identification-formulating a valid research design under stated assumptions-and estimation-implementing that design numerically on finite data. We introduce CausalReasoningBenchmark, a benchmark of 173 queries across 138 real-world datasets, curated from 85 peer-reviewed research papers and four widely-used causal-inference textbooks. For each query a system must produce (i) a structured identification specification that names the strategy, the treatment, outcome, and control variables, and all design-specific elements, and (ii) a point estimate with a standard error. By scoring these two components separately, our benchmark enables granular diagnosis: it distinguishes failures in causal reasoning from errors in numerical execution. Baseline results with a state-of-the-art LLM show that, while the model correctly identifies the high-level strategy in 84 % of cases, full identification-specification correctness drops to only 30 %, revealing that the bottleneck lies in the nuanced details of research design rather than in computation. CausalReasoningBenchmark is publicly available on Hugging Face and is designed to foster the development of more robust automated causal-inference systems.

Background and Objective: Colorectal cancer prevention relies on early detection of polyps during colonoscopy. Existing public datasets, such as CVC-ClinicDB and Kvasir-SEG, provide valuable benchmarks but are limited by small sample sizes, curated image selection, or lack of real-world artifacts. There remains a need for datasets that capture the complexity of clinical practice, particularly in resource-constrained settings. Methods: We introduce a dataset, BUET Polyp Dataset (BPD), of colonoscopy images collected using Olympus 170 and Pentax i-Scan series endoscopes under routine clinical conditions. The dataset contains images with corresponding expert-annotated binary masks, reflecting diverse challenges such as motion blur, specular highlights, stool artifacts, blood, and low-light frames. Annotations were manually reviewed by clinical experts to ensure quality. To demonstrate baseline performance, we provide benchmark results for classification using VGG16, ResNet50, and InceptionV3, and for segmentation using UNet variants with VGG16, ResNet34, and InceptionV4 backbones. Results: The dataset comprises 1,288 images with polyps from 164 patients with corresponding ground-truth masks and 1,657 polyp-free images from 31 patients. Benchmarking experiments achieved up to 90.8% accuracy for binary classification (VGG16) and a maximum Dice score of 0.64 with InceptionV4-UNet for segmentation. Performance was lower compared to curated datasets, reflecting the real-world difficulty of images with artifacts and variable quality.

Evaluating large language models (LLMs) on AMLworld's smallest test splits is costly because each of over a million targets requires a separate graph prompt. Sampling reduces this cost, but small balanced subsets change unweighted precision and F1. We introduce AMLworld-Compact, an evaluation set that retains every illicit test transaction and samples benign transactions from supervised-score strata. Its HT-Coreset protocol reduces evaluation targets by 271x and 611x on HI-Small and LI-Small. Horvitz-Thompson weights give unbiased full-test confusion-count estimates for fixed predictions; recall is exact, while precision and F1 are ratio estimates. In a held-out study using Graph Feature Preprocessor (GFP) features, one boosted-tree family defines strata for evaluating the other over 500 draws per configuration. At the released sizes, F1 RMSE is 0.00-2.58 percentage points versus 4.44-7.41 for uniform sampling with HT weights; conservative intervals remain broad. Under the evaluated graph prompts, seven open-weight LLMs have weighted precision near the predict-all-illicit baseline. In an outcome-stratified audit of 1,000 HI-Small few-shot outputs from one run per model, lexical checks pass for 84.5% of correct and 56.2% of incorrect binary verdicts, so these markers do not establish correctness. We release the evaluation sets, construction code, and audit tools at https://huggingface.co/datasets/typhoon-ai/AMLworldCompactEval and https://github.com/nat-nischw/AMLworld-Compact.

Knowledge tracing (KT) is the problem of predicting students' future performance based on their historical interactions with intelligent tutoring systems. Recently, many works present lots of special methods for applying deep neural networks to KT from different perspectives like model architecture, adversarial augmentation and etc., which make the overall algorithm and system become more and more complex. Furthermore, due to the lack of standardized evaluation protocol liu2022pykt, there is no widely agreed KT baselines and published experimental comparisons become inconsistent and self-contradictory, i.e., the reported AUC scores of DKT on ASSISTments2009 range from 0.721 to 0.821 minn2018deep,yeung2018addressing. Therefore, in this paper, we provide a strong but simple baseline method to deal with the KT task named simpleKT. Inspired by the Rasch model in psychometrics, we explicitly model question-specific variations to capture the individual differences among questions covering the same set of knowledge components that are a generalization of terms of concepts or skills needed for learners to accomplish steps in a task or a problem. Furthermore, instead of using sophisticated representations to capture student forgetting behaviors, we use the ordinary dot-product attention function to extract the time-aware information embedded in the student learning interactions. Extensive experiments show that such a simple baseline is able to always rank top 3 in terms of AUC scores and achieve 57 wins, 3 ties and 16 loss against 12 DLKT baseline methods on 7 public datasets of different domains. We believe this work serves as a strong baseline for future KT research. Code is available at https://github.com/pykt-team/pykt-toolkitWe merged our model to the \textsc{pyKT benchmark at https://pykt.org/.}.

Background and Objective: Clinicians expect recurrence risk to climb with cancer severity. In a UK multicentre trial, an unconstrained XGBoost model learnt that higher tumour stage and carcinoma in situ predicted lower recurrence risk, and discrimination, calibration, and SHAP were all blind to it. We developed a counterfactual testing framework to detect this inversion and a monotonic-constraint framework to remove it without hurting performance. Methods: BOXIT enrolled 472 patients with protocol-mandated cystoscopy across 51 UK sites (2007-2012); 435 had at least two years' follow-up (153 recurrences, 35.2%). We developed a counterfactual direction test and a monotonic-constraint correction, with constraint directions drawn from the EORTC and EAU risk systems, and evaluated both against unconstrained XGBoost and logistic regression on 18 predictors (seven directed) over 50 cross-validation folds. The test worsened each patient on one directed feature at a time to check whether risk fell; SHAP direction and calibration were also assessed. Key Findings and Limitations: Tumour stage and carcinoma in situ were associated with lower recurrence, opposite to medical intuition; the unconstrained model reversed carcinoma in situ counterfactuals in 90.2% of cases and stage in 74.3%. Discrimination (ΔAUC 0.005, p=0.47), calibration, and SHAP magnitude were all blind to the inversion. Monotonic constraints eliminated every violation at no cost to discrimination (0.723 vs 0.718) and outperformed EORTC (p=8.9e-16). Limitations: single trial, internal-external validation only. Conclusions and Clinical Implications: A model that had learned this inversion passed every conventional check. A counterfactual direction test, run as a single refit with pre-specified monotonic constraints, catches this failure at no cost to performance and should be routine before clinical deployment.

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

Retrieval-augmented QA pipelines often route retrieved passages through an LLM rewriter before a smaller reader, lifting F1 by tens of points on multi-hop benchmarks; this gain is typically credited to improved evidence quality. We ask whether that lift is causally driven by the gold answer string appearing in the rewritten context rather than by curation per se, using a controlled intervention audit. For each rewritten context we re-run the reader after one of four controlled edits to the compile output: removing the gold answer span, replacing a length-matched random non-answer span (placebo), or injecting the gold into rewrites where it was absent (at the prefix or at a midpoint sentence boundary). Across twelve completed (cell, baseline) intervention runs spanning three reader families (Qwen2.5-7B, Qwen3.5-35B, GLM-4.7), two datasets (HotpotQA, 2WikiMultihopQA), and three compiler arrangements (MA-only, MB-only, MA+verify), removing the gold answer drops reader F1 by 28 to 64 points beyond the length-matched placebo on paired answer-in-compile strata, and prepending the gold into rewrites that lacked it raises F1 by +0.7 to +9.7 points in 10 of 12 (cell, baseline) combinations. A companion five-sentinel audit shows the conventional single-[MASK] probe is itself sentinel-fragile: on 2Wiki it reports a +4.12~F1 ``non-leakage residual'' that flips to -3.33 to -7.81~F1 under four alternative sentinels and fails an equivalence test for three of those four (1/4~pass). We do not propose a new rewriter or mitigation; we release the intervention runner and the sentinel panel so that other rewriter-gain claims can be tested against the same standard.

Automated cheque processing requires localising key fields (date, legal amount, IFSC code, account number, signature, and payee name) before any recognition step. The IDRBT Cheque Image Dataset is, to our knowledge, the only public collection of Indian bank cheques, but it ships without field annotations and with no stated licence, so its redistribution terms are unclear. We address both limitations. First, we release six-field bounding-box annotations for all 112 cheques in the dataset, distributed annotations-only and keyed to the original filenames so that the IDRBT redistribution terms are respected. Second, we release 295 fully redistributable synthetic cheque images produced by a cut-paste pipeline that composites annotated field regions from real cheques onto content-erased, bank-specific canvas templates; because patches are pasted at their source coordinates, annotations carry forward unchanged. Third, we provide a ResNet-50 direct-regression baseline that predicts all six fields in a single forward pass, and use it for a controlled test of the synthetic data. The test is sobering: because cheque layouts are rigid, a no-learning baseline that simply predicts each field's mean training box already reaches 0.691 mean IoU and 80% accuracy at IoU >= 0.5, and once seed variance and training compute are accounted for, the cut-paste synthetic data yields no measurable improvement over real data alone (an equal-compute real-only model matches or beats the synthetic-augmented model on every aggregate metric). We report this negative result in full, since it cautions against assuming appearance-only augmentation helps fixed-layout documents and points instead to layout-varying synthesis. The annotations and synthetic images are released as reusable resources on the Hugging Face Hub under permissive licences.

Breast cancer is one of the most threatening diseases in women's life; thus, the early and accurate diagnosis plays a key role in reducing the risk of death in a patient's life. Mammography stands as the reference technique for breast cancer screening; nevertheless, many countries still lack access to mammograms due to economic, social, and cultural issues. Latest advances in computational tools, infrared cameras and devices for bio-impedance quantification, have given a chance to emerge other reference techniques like thermography, infrared thermography, electrical impedance tomography and biomarkers found in blood tests, therefore being faster, reliable and cheaper than other methods. In the last two decades, the techniques mentioned above have been considered as parallel and extended approaches for breast cancer diagnosis, as well many authors concluded that false positives and false negatives rates are significantly reduced. Moreover, when a screening method works together with a computational technique, it generates a "computer-aided diagnosis" system. The present work aims to review the last breakthroughs about the three techniques mentioned earlier, suggested machine learning techniques to breast cancer diagnosis, thus, describing the benefits of some methods in relation with other ones, such as, logistic regression, decision trees, random forest, deep and convolutional neural networks. With this, we studied several hyperparameters optimization approaches with parzen tree optimizers to improve the performance of baseline models. An exploratory data analysis for each database and a benchmark of convolutional neural networks for the database of thermal images are presented. The benchmark process, reviews image classification techniques with convolutional neural networks, like, Resnet50, NasNetmobile, InceptionResnet and Xception.

While recent multimodal large language models (MLLMs) have advanced automated ECG interpretation, they still face two key limitations: (1) insufficient multimodal synergy between time series signals and visual ECG representations, and (2) limited explainability in linking diagnoses to granular waveform evidence. We introduce GEM, the first MLLM unifying ECG time series, 12-lead ECG images and text for grounded and clinician-aligned ECG interpretation. GEM enables feature-grounded analysis, evidence-driven reasoning, and a clinician-like diagnostic process through three core innovations: a dual-encoder framework extracting complementary time series and image features, cross-modal alignment for effective multimodal understanding, and knowledge-guided instruction generation for generating high-granularity grounding data (ECG-Grounding) linking diagnoses to measurable parameters (e.g., QRS/PR Intervals). Additionally, we propose the Grounded ECG Understanding task, a clinically motivated benchmark designed to comprehensively assess the MLLM's capability in grounded ECG understanding. Experimental results on both existing and our proposed benchmarks show GEM significantly improves predictive performance (CSN 7.4% uparrow), explainability (22.7% uparrow), and grounding (24.8% uparrow), making it more suitable for real-world clinical applications. GitHub repository: https://github.com/lanxiang1017/GEM.git

This paper identifies the misinterpretation of the context can be a significant issue during the reasoning process of large language models, spanning from smaller models like Llama3.2-3B-Instruct to cutting-edge ones like DeepSeek-R1. For example, in the phrase "10 dollars per kilo," LLMs might not recognize that "per" means "for each," leading to calculation errors. We introduce a novel, post-training approach called **Stick to the Facts (SIFT)** to tackle this. SIFT leverages increasing inference-time compute to ground LLM reasoning in contexts. At the core of SIFT lies the *Sticker*, which is generated by the model itself to explicitly emphasize the key information within the context. Given the curated Sticker, SIFT generates two predictions -- one from the original query and one from the query augmented with the Sticker. If they differ, the Sticker is sequentially refined via *forward* optimization (to better align the extracted facts with the query) and *inverse* generation (to conform with the model's inherent tendencies) for more faithful reasoning outcomes. Studies across diverse models (from 3B to 100B+) and benchmarks (e.g., GSM8K, MATH-500) reveal consistent performance improvements. Notably, SIFT improves the pass@1 accuracy of DeepSeek-R1 on AIME2024 from 78.33% to **85.67**%, establishing a new state-of-the-art in the open-source community. The code is available at https://github.com/zhijie-group/SIFT.

In Brazil, all legal professionals must demonstrate their knowledge of the law and its application by passing the OAB exams, the national bar exams. The OAB exams therefore provide an excellent benchmark for the performance of legal information systems since passing the exam would arguably signal that the system has acquired capacity of legal reasoning comparable to that of a human lawyer. This article describes the construction of a new data set and some preliminary experiments on it, treating the problem of finding the justification for the answers to questions. The results provide a baseline performance measure against which to evaluate future improvements. We discuss the reasons to the poor performance and propose next steps.

Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS^2) is the major analytical technique in proteomics that identifies peptides by ionizing them, fragmenting them, and using the resulting mass spectra to identify and quantify proteins in biological samples. In MS^2 analysis, peptide fragment ion probability prediction plays a critical role, enhancing the accuracy of peptide identification from mass spectra as a complement to the intensity information. Current approaches rely on global statistics of fragmentation, which assumes that a fragment's probability is uniform across all peptides. Nevertheless, this assumption is oversimplified from a biochemical principle point of view and limits accurate prediction. To address this gap, we present Pep2Prob, the first comprehensive dataset and benchmark designed for peptide-specific fragment ion probability prediction. The proposed dataset contains fragment ion probability statistics for 608,780 unique precursors (each precursor is a pair of peptide sequence and charge state), summarized from more than 183 million high-quality, high-resolution, HCD MS^2 spectra with validated peptide assignments and fragmentation annotations. We establish baseline performance using simple statistical rules and learning-based methods, and find that models leveraging peptide-specific information significantly outperform previous methods using only global fragmentation statistics. Furthermore, performance across benchmark models with increasing capacities suggests that the peptide-fragmentation relationship exhibits complex nonlinearities requiring sophisticated machine learning approaches.

Preference optimization methods typically begin training with a well-trained SFT model as a reference model. In RLHF and DPO, a regularization term is used during the preference optimization process to prevent the policy model from deviating too far from the reference model's distribution, thereby avoiding the generation of anomalous responses. When the reference model is already well-aligned with the given data or only requires slight adjustments, this approach can produce a well-aligned model. However, if the reference model is not aligned with the given data and requires significant deviation from its current state, a regularization term may actually hinder the model alignment. In this study, we propose Modulated Intervention Preference Optimization (MIPO) to address this issue. MIPO modulates the degree of intervention from the reference model based on how well the given data is aligned with it. If the data is well-aligned, the intervention is increased to prevent the policy model from diverging significantly from reference model. Conversely, if the alignment is poor, the interference is reduced to facilitate more extensive training. We compare the performance of MIPO and DPO using Mistral-7B and Llama3-8B in Alpaca Eval 2.0 and MT-Bench. The experimental results demonstrate that MIPO consistently outperforms DPO across various evaluation scenarios.

Extracting textual information from scanned medical documents, such as external laboratory reports and manually filled forms, has been a major challenge in modern electronic health records (EHRs). Recent advancements in vision language models (VLMs) have shown great promise over traditional OCR tools. However, at this point, most clinical OCR studies were conducted on private, institutional data. To our knowledge, there are few publicly available datasets for evaluating OCR models in the clinical domain. Furthermore, common scanning artifacts that undermine OCR performance are not reflected in those datasets, leaving a systematic evaluation unfeasible. Therefore, we release a publicly available, realistic-looking OCR benchmark dataset, ClinOCR-Bench, with 384 scanned images across 6 subsets: Normal, Handwriting, Poor Quality, Rotation, Tables, and Mix-artifacts. ClinOCR-Bench features: 1) diverse document types and layouts, 2) full coverage of common EHR scan artifacts, 3) protected health information-free, 4) template-aware train/test split, and 5) adequate sample size for OCR benchmarking. Baseline OCR performance was evaluated using state-of-the-art open-weight and proprietary VLMs. The dataset and documentation are available on GitHub (https://github.com/ClinOCR-Bench/ClinOCR-Bench).

Detecting LLM reasoning failures at inference time without ground-truth labels has motivated a wide range of confidence baselines, including self-consistency, semantic entropy, and P(True), built on within-question sampling and self-evaluation. Operad theory, the formalism for systems built by iterated substitution, suggests a complementary diagnostic: a model's direct answer to a compositional query should agree with the answer it produces by composing a stated decomposition of the same query. We instantiate this idea as operadic consistency (OC), a per-question signal. Across twelve instruction-tuned LLMs (4B to 671B parameters, open-weights and closed-source) on four multi-hop QA datasets, OC is strongly correlated with accuracy on every dataset (Pearson r in [0.86, 0.94], all p leq 0.0004), and is the only signal we evaluate with r geq 0.85 uniformly across all four datasets. Chain-of-thought self-consistency (CoT-SC; Wang et al., 2023) matches OC on HotpotQA and DROP (r = 0.93, 0.87) but drops to r approx 0.45 on MuSiQue and StrategyQA. At the per-question level, OC contributes information beyond CoT-SC and semantic entropy on every dataset (cluster-robust p leq 10^{-16} for the OC coefficient), and the conclusion is robust to additionally controlling for constructed decomposition-aware baselines (p leq 10^{-13}). The same signal yields selective-prediction improvements (accuracy at fixed coverage) over a tuned CoT-SC baseline at the equal-cost K = 3 budget (AUARC lifts of +0.086 to +0.096 and AUROC lifts of +0.092 to +0.164; 95% CIs exclude zero on every cell). On five frontier thinking models, where the decomposition is extracted from the model's own chain of thought, the same equal-cost comparison gives positive selective-prediction point-estimate lift on all 16 (dataset, budget, metric) cells tested, with 95% CIs excluding zero on 12 of the 16.

In Reinforcement Learning with Verifiable Rewards (RLVR), constructing a robust advantage baseline is critical for policy gradients, effectively guiding the policy model to reinforce desired behaviors. Recent research has introduced Generalist Value Models (such as V_0), which achieve pre-trained value estimation by explicitly encoding model capabilities in-context, eliminating the need to synchronously update the value model alongside the policy model. In this paper, we propose V_{0.5}, which adaptively fuses the baseline predicted by such value model (acting as a prior) with the empirical mean derived from sparse rollouts. This constructs a robust baseline that balances computational efficiency with extremely low variance. Specifically, we introduce a real-time statistical testing and dynamic budget allocation. This balances the high variance caused by sparse sampling against the systematic bias (or hallucinations) inherent in the value model's prior. By constructing a hypothesis test to evaluate the prior's reliability in real-time, the system dynamically allocates additional rollout budget on demand. This mechanism minimizes the baseline estimator's Mean Squared Error (MSE), guaranteeing stable policy gradients, even under extreme sparsity with a group size of 4. Extensive evaluations across six mathematical reasoning benchmarks demonstrate that V_{0.5} significantly outperforms GRPO and DAPO, achieving faster convergence and over some 10% performance improvement.

A/B tests are typically analyzed via frequentist p-values and confidence intervals; but these inferences are wholly unreliable if users endogenously choose samples sizes by *continuously monitoring* their tests. We define *always valid* p-values and confidence intervals that let users try to take advantage of data as fast as it becomes available, providing valid statistical inference whenever they make their decision. Always valid inference can be interpreted as a natural interface for a sequential hypothesis test, which empowers users to implement a modified test tailored to them. In particular, we show in an appropriate sense that the measures we develop tradeoff sample size and power efficiently, despite a lack of prior knowledge of the user's relative preference between these two goals. We also use always valid p-values to obtain multiple hypothesis testing control in the sequential context. Our methodology has been implemented in a large scale commercial A/B testing platform to analyze hundreds of thousands of experiments to date.

To enable building and testing models on long-document comprehension, we introduce QuALITY, a multiple-choice QA dataset with context passages in English that have an average length of about 5,000 tokens, much longer than typical current models can process. Unlike in prior work with passages, our questions are written and validated by contributors who have read the entire passage, rather than relying on summaries or excerpts. In addition, only half of the questions are answerable by annotators working under tight time constraints, indicating that skimming and simple search are not enough to consistently perform well. Our baseline models perform poorly on this task (55.4%) and significantly lag behind human performance (93.5%).

Same-model self-verification, prompting a model to audit its own predicted answer, is a plausible confidence signal for selective prediction, but its practical value remains unclear once strong likelihood-based baselines are taken seriously. We evaluate self-verification against two such baselines, LL-AVG and LL-SUM, on ARC-Challenge and TruthfulQA-MC across multiple model families, scales, and prompt variants. We measure not only correctness ranking, but also abstention quality through AURC and operating-point analyses. The results are sharply task- and model-dependent. On ARC-Challenge, self-verification substantially improves over LL-AVG for Phi-2 and the Qwen models, with the largest gains appearing in Qwen-7B. On TruthfulQA-MC, however, the signal is less reliable: smaller models can become prompt-sensitive, DeepSeek-R1-Distill-8B degrades relative to LL-AVG, and LL-SUM often remains the stronger practical baseline. We therefore do not treat self-verification as a general-purpose uncertainty estimator. In this setting, it is better understood as a conditional confidence signal whose value depends on task type, model family, prompt formulation, and, crucially, the baseline it must beat.

Despite their widespread applications, Large Language Models (LLMs) often struggle to express uncertainty, posing a challenge for reliable deployment in high stakes and safety critical domains like clinical diagnostics. Existing standard baseline methods such as model logits and elicited probabilities produce overconfident and poorly calibrated estimates. In this work, we propose Approximate Bayesian Computation (ABC), a likelihood-free Bayesian inference, based approach that treats LLMs as a stochastic simulator to infer posterior distributions over predictive probabilities. We evaluate our ABC approach on two clinically relevant benchmarks: a synthetic oral lesion diagnosis dataset and the publicly available GretelAI symptom-to-diagnosis dataset. Compared to standard baselines, our approach improves accuracy by up to 46.9\%, reduces Brier scores by 74.4\%, and enhances calibration as measured by Expected Calibration Error (ECE) and predictive entropy.

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically rely on published synthetic procedures and Top-K accuracy based on single ground-truth, which does not capture the open-ended nature of real-world synthesis planning. We propose a new benchmarking framework for single-step retrosynthesis that evaluates both general-purpose and chemistry-specialized LLMs using ChemCensor, a novel metric for chemical plausibility. By emphasizing plausibility over exact match, this approach better aligns with human synthesis planning practices. We also introduce CREED, a novel dataset comprising millions of ChemCensor-validated reaction records for LLM training, and use it to train a model that improves over the LLM baselines under this benchmark.

Changes produced by coding agents can pass functional tests while leaving repository contribution requirements unmet. Following repository-specific norms requires identifying guidance dispersed across repository sources and interpreting its conditions and exceptions. Retrieval and documentation approaches supply general context, but agents must still determine which norms apply. We introduce RepoNorm to acquire explicit and implicit repository norms independently of coding tasks. It checks norm content and applicability using repository evidence, consults Git history when needed, and delivers norm packages to existing coding agents. Our evaluation uses three coding models and 121 tasks from RepoNormBench. Against the baseline with no additional generated guidance (Raw), relative improvements are 7.42-10.77% for Overall Norm Compliance Rate (NCR), 31.64-45.44% for Contribution NCR, and 11.34-17.69% for Prompt-omitted NCR. All three coding models also obtain higher values on these NCR measures with RepoNorm than with CodeWiki documentation. Functional success rates show observed gains of 5.79-9.09 percentage points over Raw; the paired comparisons do not reach the significance threshold. Sampled precision is 86% with RepoNorm's default configuration.

Machine learning in high-stakes domains such as healthcare requires not only strong predictive performance but also reliable uncertainty quantification (UQ) to support human oversight. Multi-label text classification (MLTC) is a central task in this domain, yet remains challenging due to label imbalances, dependencies, and combinatorial complexity. Existing MLTC benchmarks are increasingly saturated and may be affected by training data contamination, making it difficult to distinguish genuine reasoning capabilities from memorization. We introduce MADE, a living MLTC benchmark derived from {m}edical device {ad}verse {e}vent reports and continuously updated with newly published reports to prevent contamination. MADE features a long-tailed distribution of hierarchical labels and enables reproducible evaluation with strict temporal splits. We establish baselines across more than 20 encoder- and decoder-only models under fine-tuning and few-shot settings (instruction-tuned/reasoning variants, local/API-accessible). We systematically assess entropy-/consistency-based and self-verbalized UQ methods. Results show clear trade-offs: smaller discriminatively fine-tuned decoders achieve the strongest head-to-tail accuracy while maintaining competitive UQ; generative fine-tuning delivers the most reliable UQ; large reasoning models improve performance on rare labels yet exhibit surprisingly weak UQ; and self-verbalized confidence is not a reliable proxy for uncertainty. Our work is publicly available at https://hhi.fraunhofer.de/aml-demonstrator/made-benchmark.

Static benchmarks measure a model frozen at training time. Real systems face distribution shift: new categories, paraphrased queries, drift: and must recover online via user corrections. No existing benchmark measures recovery speed under correction streams. We introduce OCRR (Online Correction Recovery Rate): a benchmark that streams a corpus through a classification system, applies oracle or stochastic corrections to wrong predictions, and reports two curves: novel-class accuracy and original-distribution accuracy versus correction count. We evaluate the substrate alongside nine baseline algorithms from five families plus seven bounded-storage variants of the substrate for the Pareto sweep, including standard online-learning baselines (river), continual-learning methods (EWC, A-GEM, LwF), retrieval/parametric hybrids (kNN-LM), parameter-efficient fine-tuning of a 1.5 B-parameter encoder (LoRA on DeBERTa-v3-large), and a hash-chained append-only substrate (Substrate). On Banking77 and CLINC150, under oracle and sparse correction policies, the substrate is the only system that simultaneously recovers novel-class accuracy (88.7 +/- 2.9 %) and retains original-distribution accuracy (95.4 +/- 0.8 %) beating the next-best published continual-learning baseline by 32.6 percentage points at equal memory budget, and beating LoRA-on-DeBERTa-v3-large by 84.6 percentage points on retention. We further find that classification accuracy remains stable at 99 % even as approximate-nearest-neighbour recall@5 degrades from 0.69 to 0.23 across 10 k to 10 M corpus scales, suggesting the substrate's margin-band majority vote is robust to retrieval imperfection in a way that pure top-k recall metrics do not predict. Code and data are available at https://github.com/adriangrassi/ocrr-benchmark.

The demand for inference on extremely large scale LLMs has seen enormous growth in the recent months. It made evident the colossal shortage of dedicated hardware capable of efficient and fast processing of the involved compute and memory movement. The problem is aggravated by the exploding raise in the lengths of the sequences being processed, since those require efficient on-chip storage of the KV-cache of size proportional to the sequence length. To make the required compute feasible and fit the involved data into available memory, numerous quantization techniques have been proposed that allow accurate quantization for both weights and activations. One of the main recent breakthroughs in this direction was introduction of the family of Block Floating Point (BFP) formats characterized by a block of mantissas with a shared scale factor. These enable memory- power-, and compute- efficient hardware support of the tensor operations and provide extremely good quantization accuracy. The main issues preventing widespread application of block formats is caused by the presence of outliers in weights and activations since those affect the accuracy of the other values in the same block. In this paper, we focus on the most critical problem of limited KV-cache storage. We propose a novel approach enabling usage of low precision BFP formats without compromising the resulting model accuracy. We exploit the common channel-wise patterns exhibited by the outliers to rearrange them in such a way, that their quantization quality is significantly improved. The methodology yields 2x savings in the memory footprint without significant degradation of the model's accuracy. Importantly, the rearrangement of channels happens at the compile time and thus has no impact on the inference latency.

Multi-omics sequences contain complex biological patterns, yet deciphering their mechanisms for automated scientific discovery remains challenging. As large language models (LLMs) interpret these sequences, evaluating both predictions and scientific reasoning is critical. However, existing benchmarks for multi-omics sequence tasks rely on classification and regression metrics, neglecting whether models grasp the underlying biological evidence. We introduce OmicsBench, the first reasoning benchmark for multi-omics sequences, comprising 1,160 expert-validated questions across six tasks spanning DNA regulation, RNA processing, and protein function. OmicsBench requires traceable evidence chains, evaluated using instance-specific rubrics developed with domain experts. Evaluating 17 LLMs reveals an inverse relationship: while scientific LLMs outperform general-purpose LLMs in sequence classification accuracy, they fail to provide valid evidence to support their predictions. One plausible interpretation is shortcut learning: specialized models may rely on statistical patterns rather than the biological mechanisms needed for scientific discovery. Motivated by this finding, we introduce tool-augmented on-policy distillation (TA-OPD), a post-training method to align sequence prediction with evidence-grounded biological reasoning. Across five Qwen3.5 models spanning 0.8B to 27B parameters, TA-OPD consistently strengthens biological evidence grounding while improving predictive performance on most tasks. These gains persist across model scales, indicating that stronger sequence reasoning does not arise solely from increased model capacity, but can be improved through evidence-aware training. Together, OmicsBench and TA-OPD provide a framework for diagnosing reasoning failures in multi-omics LLMs and a path toward models whose predictions are better grounded in biologically meaningful evidence.

Recent advances in test-time scaling have led to the emergence of thinking LLMs that exhibit self-reflective behaviors and multi-step reasoning. While RL drives this self-improvement paradigm, a recent study (Gandhi et al., 2025) shows that RL alone does not truly instill these new reasoning abilities - it merely draws out behaviors already present in the base models. This raises a question: How can we train the models that don't exhibit such thinking behavior to develop it in the first place? To this end, we propose ThinkTuning, a GRPO-based interactive training approach where we augment the rollouts of a student model with the guidance from a teacher model. A simple idea from classroom practice inspires our method: a teacher poses a problem, lets the student try an answer, then gives corrective feedback -- enough to point the mind in the right direction and then show the solution. Each piece of feedback reshapes the student's thoughts, leading them to arrive at the correct solution. Similarly, we find that this type of implicit supervision through feedback from a teacher model of the same size improves the reasoning capabilities of the student model. In particular, on average, our method shows a 3.85% improvement over zero-shot baselines across benchmarks, and on MATH-500, AIME and GPQA-Diamond it shows 2.08%, 2.23% and 3.99% improvements over the vanilla-GRPO baseline. Source code is available at https://github.com/3rdAT/ThinkTuning.

Membership inference attacks (MIA) attempt to verify the membership of a given data sample in the training set for a model. MIA has become relevant in recent years, following the rapid development of large language models (LLM). Many are concerned about the usage of copyrighted materials for training them and call for methods for detecting such usage. However, recent research has largely concluded that current MIA methods do not work on LLMs. Even when they seem to work, it is usually because of the ill-designed experimental setup where other shortcut features enable "cheating." In this work, we argue that MIA still works on LLMs, but only when multiple documents are presented for testing. We construct new benchmarks that measure the MIA performances at a continuous scale of data samples, from sentences (n-grams) to a collection of documents (multiple chunks of tokens). To validate the efficacy of current MIA approaches at greater scales, we adapt a recent work on Dataset Inference (DI) for the task of binary membership detection that aggregates paragraph-level MIA features to enable MIA at document and collection of documents level. This baseline achieves the first successful MIA on pre-trained and fine-tuned LLMs.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Users increasingly rely on large language models (LLMs) to analyse collections of independent inputs, such as product reviews or social media posts, and return a single aggregated answer. This setting requires multi-instance processing (MIP), where a model combines information from multiple instances into one prediction. We study a task in which the model must infer a binary label for each instance, and identify the most frequent label among the full instance set. The correct answer should be invariant to instance order. By evaluating fifteen LLMs across five datasets and seven instance order patterns, with each instance set held fixed across patterns, we find substantial order sensitivity. Accuracy can differ by about 90 percentage points between the best and worst order patterns, with models generally more accurate when majority-label instances appear at the start than when they appear in the middle or at the end. For subsets of models, available reasoning traces and gradient-based attribution reveal uneven emphasis across positions. Traces disproportionately mention early instances, while attribution scores are generally higher near the beginning and end than in the middle. These results show that instance order can systematically bias aggregated predictions, highlighting the need to evaluate MIP across different input arrangements.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and pi-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's certified miss-rate constraint, a low-discrimination signal forces the threshold below the entire test-benign mass. We compose three signals derived from a synthesis order's public annotation: k-mer Jaccard similarity to known toxins, the trimmed-mean score of a five-LLM judge panel, and cosine similarity to clustered embedding centroids. Fused under a monotone logistic aggregator and calibrated by Conformal Risk Control, the resulting screener certifies E[FNR] le α. Across ten leave-one-taxonomic-family-out folds at α=0.05 on UniProt KW-0800 reviewed toxins, the calibrated screener achieves 0% test miss rate on every fold and 0% test false-flag rate on nine of ten folds. The bound's finite-sample slack 1/(n_{cal}+1) caps the certifiable miss rate at 1.77% on our 200-hazard subsample; reaching procurement-grade α=10^{-3} requires an 18times larger calibration set, which the full reviewed UniProt KW-0800 corpus is large enough to deliver. The binding constraint on certifiable DNA-synthesis screening is calibration data, not algorithms. Code: https://github.com/najmulhasan-code/crc-screen

Multi-agent large language model (LLM) systems can improve reasoning by spending more computation, but deployment requires deciding when extra collaboration is worth its cost. We isolate this decision by running every problem under four protocols while holding the solver fixed within each setting: direct solving (Baseline), iterative self-correction (Single), planner-executor-reviewer collaboration (PER), and multi-agent deliberation (Broadcast). The primary benchmark comprises 4,181 competition-level math problems; paired robustness checks cover four benchmarks spanning competition math, biology, and broader science with two solver families. Across fixed policies, trained routers, and frozen LLM routers, conservative policies under-escalate, whereas higher-solve frozen routers often over-escalate. A post-answer, pre-collaboration gpt-oss-120b probe ranks Baseline failures with 0.8847 AUROC (4,151 parseable cases; 95% CI [0.8732, 0.8955]). The same score remains informative for predicting whether any collaboration helps (0.7683 AUPRC), but is much weaker for identifying PER- or Broadcast-specific value (0.1674 and 0.1041 AUPRC). Separately, the pre-answer self-confidence gate reaches 78.0% solve at 45K tokens, compared with 73.8% at 71.3K for a frozen gpt-oss-120b router and 92.4% for a retrospective fixed-order oracle. Across 10 paired model-condition settings, the oracle adds 23.2-58.3 points of retrospective coverage over Baseline, but protocol profiles vary by task. In the six settings with held-out router evaluations, oracle gaps remain 18.5-28.9 points. Confidence can therefore support initial escalation, while protocol-specific cost-aware routing remains unresolved.

This paper investigates the use of prior computation to estimate the value function to improve sample efficiency in on-policy policy gradient methods in reinforcement learning. Our approach is to estimate the value function from prior computations, such as from the Q-network learned in DQN or the value function trained for different but related environments. In particular, we learn a new value function for the target task while combining it with a value estimate from the prior computation. Finally, the resulting value function is used as a baseline in the policy gradient method. This use of a baseline has the theoretical property of reducing variance in gradient computation and thus improving sample efficiency. The experiments show the successful use of prior value estimates in various settings and improved sample efficiency in several tasks.

Software engineering tools increasingly rely on LLM based agents to localize files to change to resolve a software issue. Most AI agents explore repositories linearly, that is, visiting one directory or file per step. We postulate that this is a structural mismatch for changes that span several subsystems. We compare linear sequential exploration against non-linear, domain-scoped parallel agentic exploration. Using SWE Bench Pro as initial benchmark, we focus on ansible as an exemplar. We construct an approach for persistent-session evaluation of GitHub issues anchored at a single base commit. We compare our non-linear domain-agent file traversal system against a base LLM without direct repository access, a single agent Recursive Language Model (RLM) baseline with a persistent Python REPL and an external CLI baseline using Codex 5.5 High. Domain scoped parallel agent spawning with a small Haiku-class model achieves the highest micro F1 among Haiku class models by a large margin. Domain-agents is the second highest behind only the much larger Codex 5.5 High on our own expanded benchmark including over more recent PRs from 2025 and 2026. On the original, curated, 2020 SWE-bench Pro benchmark, a larger Sonnet plain LLM baseline attains higher micro F1 by predicting few files, leading to higher precision, but at significantly lower all gold recall. We also present three additional findings. First, documentation evolution is a latent dependency unresolved by any approach. Second, naive file system access can degrade localization driven by test-file over prediction. Lastly, forced multi-agent consultation does not measurably help and raises token cost substantially.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Counterfactual explanations are most useful when they can be generated with low latency, remain close to the factual input, and satisfy input-domain, categorical, and actionability constraints. Achieving these objectives simultaneously is challenging for deep neural networks. Heuristic methods are often fast but may return invalid counterfactuals, whereas exact methods can certify global proximity but may not finish within practical time limits. We introduce DASH, a batched heuristic search method for finding close, valid, and actionable counterfactuals for deep neural networks under ell_1, ell_2, and ell_infty objectives. DASH uses directional Lipschitz bounds and local affine models to generate anchors, then ranks and expands promising regions with batched network evaluations. We compare DASH against nine prior heuristic methods and time-limited exact mixed-integer baselines on four tabular datasets, with network depths from 2 to 32, and evaluate scalability on PBMC3k. Across 9,000 tabular query-norm cases, DASH returns a valid counterfactual within 5% of the best heuristic-observed valid distance in 94.6% of cases, with a median CPU search runtime of 0.061 s. PGD-bisect, the baseline with the highest pooled within-5% coverage, meets this criterion in 41.1% of cases, with a median runtime of 0.298 s. These results show that the proposed search maintains high valid proximity across norms while keeping its search runtime practical.

Medical image segmenters often get worse when sites, scanner vendors, or protocols change. Continual test-time adaptation (CTTA) addresses this problem without target labels, but it can be impossible to update a model on a non-stationary stream and can lead to a lot of errors. We examine a more reasonable and meaningful alternative: parameter-frozen inference enhancement(PIE). We use a source-trained segmenter that learns about anatomy-preserving scale and flip views, maps their predictions back to the native location, and averages the probabilities. We do not modify the weights of the model or the normalization statistics. On a cardiac MRI stream from M\&Ms, which is trained on vendor A and evaluated sequentially on vendors B, C, and D, PIE has 0.7786 mean Dice, compared to 0.7680 for source-only inference and 0.7388--0.7416 for five other online-adaptation baselines. The controlled ablations show that performance saturates at 28 views, and confidence weighting, class-prior correction, connected-component filtering, morphological refinement, and inter-slice smoothing have no effect or cause negative transfer. Qualitative results on cardiac MRI and fundus images are also consistent with the frozen ensemble keeping thinner and nested anatomical structures. These results provide a strong, stable baseline for medical CTTA and expose an important failure mode: adaptation and handcrafted refinement can be less reliable than carefully designed inference.

We present DM-Bench, the first benchmark designed to evaluate large language model (LLM) performance across real-world decision-making tasks faced by individuals managing diabetes in their daily lives. Unlike prior health benchmarks that are either generic, clinician-facing or focused on clinical tasks (e.g., diagnosis, triage), DM-Bench introduces a comprehensive evaluation framework tailored to the unique challenges of prototyping patient-facing AI solutions in diabetes, glucose management, metabolic health and related domains. Our benchmark encompasses 7 distinct task categories, reflecting the breadth of real-world questions individuals with diabetes ask, including basic glucose interpretation, educational queries, behavioral associations, advanced decision making and long term planning. Towards this end, we compile a rich dataset comprising one month of time-series data encompassing glucose traces and metrics from continuous glucose monitors (CGMs) and behavioral logs (e.g., eating and activity patterns) from 15,000 individuals across three different diabetes populations (type 1, type 2, pre-diabetes/general health and wellness). Using this data, we generate a total of 360,600 personalized, contextual questions across the 7 tasks. We evaluate model performance on these tasks across 5 metrics: accuracy, groundedness, safety, clarity and actionability. Our analysis of 8 recent LLMs reveals substantial variability across tasks and metrics; no single model consistently outperforms others across all dimensions. By establishing this benchmark, we aim to advance the reliability, safety, effectiveness and practical utility of AI solutions in diabetes care.

Recent machine learning papers often report 1-2 percentage point improvements from a single run on a benchmark. These gains are highly sensitive to random seeds, data ordering, and implementation details, yet are rarely accompanied by uncertainty estimates or significance tests. It is therefore unclear when a reported +1-2% reflects a real algorithmic advance versus noise. We revisit this problem under realistic compute budgets, where only a few runs are affordable. We propose a simple, PC-friendly evaluation protocol based on paired multi-seed runs, bias-corrected and accelerated (BCa) bootstrap confidence intervals, and a sign-flip permutation test on per-seed deltas. The protocol is intentionally conservative and is meant as a guardrail against over-claiming. We instantiate it on CIFAR-10, CIFAR-10N, and AG News using synthetic no-improvement, small-gain, and medium-gain scenarios. Single runs and unpaired t-tests often suggest significant gains for 0.6-2.0 point improvements, especially on text. With only three seeds, our paired protocol never declares significance in these settings. We argue that such conservative evaluation is a safer default for small gains under tight budgets.

Large pre-trained language models have shown promise for few-shot learning, completing text-based tasks given only a few task-specific examples. Will models soon solve classification tasks that have so far been reserved for human research assistants? Existing benchmarks are not designed to measure progress in applied settings, and so don't directly answer this question. The RAFT benchmark (Real-world Annotated Few-shot Tasks) focuses on naturally occurring tasks and uses an evaluation setup that mirrors deployment. Baseline evaluations on RAFT reveal areas current techniques struggle with: reasoning over long texts and tasks with many classes. Human baselines show that some classification tasks are difficult for non-expert humans, reflecting that real-world value sometimes depends on domain expertise. Yet even non-expert human baseline F1 scores exceed GPT-3 by an average of 0.11. The RAFT datasets and leaderboard will track which model improvements translate into real-world benefits at https://raft.elicit.org .

Hyperparameter optimization (HPO) is crucial for fine-tuning machine learning models but can be computationally expensive. To reduce costs, Multi-fidelity HPO (MF-HPO) leverages intermediate accuracy levels in the learning process and discards low-performing models early on. We compared various representative MF-HPO methods against a simple baseline on classical benchmark data. The baseline involved discarding all models except the Top-K after training for only one epoch, followed by further training to select the best model. Surprisingly, this baseline achieved similar results to its counterparts, while requiring an order of magnitude less computation. Upon analyzing the learning curves of the benchmark data, we observed a few dominant learning curves, which explained the success of our baseline. This suggests that researchers should (1) always use the suggested baseline in benchmarks and (2) broaden the diversity of MF-HPO benchmarks to include more complex cases.

While Large Language Models (LLMs) excel on standardized medical exams, high scores often fail to translate to high-quality responses for real-world medical queries. Current evaluations rely heavily on multiple-choice questions, failing to capture the unstructured, ambiguous, and long-tail complexities inherent in genuine user inquiries. To bridge this gap, we introduce QuarkMedBench, an ecologically valid benchmark tailored for real-world medical LLM assessment. We compiled a massive dataset spanning Clinical Care, Wellness Health, and Professional Inquiry, comprising 20,821 single-turn queries and 3,853 multi-turn sessions. To objectively evaluate open-ended answers, we propose an automated scoring framework that integrates multi-model consensus with evidence-based retrieval to dynamically generate 220,617 fine-grained scoring rubrics (~9.8 per query). During evaluation, hierarchical weighting and safety constraints structurally quantify medical accuracy, key-point coverage, and risk interception, effectively mitigating the high costs and subjectivity of human grading. Experimental results demonstrate that the generated rubrics achieve a 91.8% concordance rate with clinical expert blind audits, establishing highly dependable medical reliability. Crucially, baseline evaluations on this benchmark reveal significant performance disparities among state-of-the-art models when navigating real-world clinical nuances, highlighting the limitations of conventional exam-based metrics. Ultimately, QuarkMedBench establishes a rigorous, reproducible yardstick for measuring LLM performance on complex health issues, while its framework inherently supports dynamic knowledge updates to prevent benchmark obsolescence.

We set out to reproduce a recent hallucination-mitigation result on the POPE benchmark. The LLaVA-1.5-7B baseline we measured, 82.21 F1 on the adversarial split, sat 1.21 to 8.67 points above the adversarial baselines we planned to compare against (81.00, 79.30, and 73.54). We looked at the evaluation code and found a readout choice that moves F1 on its own. A two-token logit readout decides yes versus no by comparing two vocabulary IDs, 3582 ("yes") and 1217 ("no"). Across 9,000 greedy-decode questions spanning all three splits, neither ID is generated even once. The model emits " Yes" (token 3869) and " No" (token 1939), because SentencePiece prepends a space byte after the prompt suffix "ASSISTANT:". Read with an eight-token lookup that covers the space-prefixed surface forms, LLaVA-1.5-7B scores F1 0.8221, 0.8498, and 0.8713 on the adversarial, popular, and random splits. That 6.13-point adversarial shift exceeds the adversarial gain reported by five of the six papers we surveyed. None of them states its readout, and our reference ran under 4-bit NF4 quantization, so we cannot say how much of any reported gain a matched evaluation would keep. That comparison stays unresolved until readout and precision are matched. On the fixed baseline we run nine inference-time corrections of our own (none beat it) and dissect why the adversarial split resists logit-level intervention. In a 3,000-question probe, wrong predictions draw more image attention than correct ones (Cohen's d=-0.46, p=1.4times10^{-24}), the opposite of what grounding-based corrections assume. A four-readout audit across four further VLMs from three tokenizer families confirms the confound is protocol-level, not model-specific: porting the LLaVA-1.5 IDs verbatim drops F1 to 0.00 on the two disjoint-vocabulary models, whereas a tokenizer-derived readout holds between 0.80 and 0.92.

Electrocardiography (ECG) is one of the most widely used tests for diagnosing cardiovascular disease. Yet several remote clinics still utilize paper ECG printouts for their analysis due to limited connectivity and computational capacity. As a result, vast numbers of physical ECGs obtained in remote areas still remain incapable of being accessed by contemporary artificial-intelligence (AI)-based decision support as they require high computational resources or strong high-speed internet connectivity. This causes several cases where conditions like acute coronary occlusion (ACS) is overlooked and reperfusion therapy delayed. Although prior work has tackled digitization and diagnosis separately, and utilized advanced AI models for them, there still remains a lack of a compute-light, on-device framework that reconstructs paper ECGs at high fidelity, while accurately supporting multiple clinically relevant endpoints. We address this need with an end-to-end lightweight on-device digitization-to-diagnosis pipeline that converts a smartphone photo or scan of a paper ECG into a calibrated 12-lead signal and screens for Myocardial Infarction (MI) pathologies, with SHapley Additive exPlanations (SHAP) to support interpretability. Trained and evaluated on 21,799 ECGs from the PTB-XL dataset and further validated on hospital-acquired ECG-Matrix dataset, the complete system runs in <30 s per ECG on CPU-only resources, achieving 95.51% accuracy (F1 = 0.9519) for MI detection on PTB-XL and 88.89% accuracy (F1 = 0.8862) for OMI detection on ECG-Matrix. This work showcases that legacy paper records can be reliably democratized in any part of the world, providing a scalable decision support when digital ECG export, connectivity, or high-end compute are unavailable

Existing code reasoning methods primarily supervise final code outputs, ignoring intermediate states, often leading to reward hacking where correct answers are obtained through inconsistent reasoning. We propose StepCodeReasoner, a framework that introduces explicit intermediate execution-state supervision. By automatically inserting structured print-based execution-trace anchors into code, the model is trained to predict runtime states at each step, transforming code reasoning into a verifiable, stepwise execution modeling problem. Building on this execution-aware method, we introduce Bi-Level GRPO, a reinforcement learning algorithm for structured credit assignment at two levels: inter-trajectory, comparing alternative execution paths, and intra-trajectory, rewarding intermediate accuracy based on its impact on downstream correctness. Extensive experiments demonstrate that StepCodeReasoner achieves SOTA performance in code reasoning. In particular, our 7B model achieves 91.1\% on CRUXEval and 86.5\% on LiveCodeBench, outperforming the CodeReasoner-7B baseline (86.0\% and 77.7\%) and GPT-4o (85.6\% and 75.1\%). Furthermore, on the execution-trace benchmark REval, our model scores 82.9\%, outperforming baseline CodeReasoner-7B (72.3\%), its 14B counterpart (81.1\%), and GPT-4o (77.3\%). Additionally, our approach also improves code generation performance, demonstrating that explicit execution modeling enhances both code reasoning and code generation.

Across medical specialties, clinical practice is anchored in evidence-based guidelines that codify best studied diagnostic and treatment pathways. These pathways routinely fall short for the long tail of real-world care not covered by guidelines. Most medical large language models (LLMs), however, are trained to encode common, guideline-focused medical knowledge in their parameters. Current evaluations test models primarily on recalling and reasoning with this memorized content, often in multiple-choice settings. Given the fundamental importance of evidence-based reasoning in medicine, it is neither feasible nor reliable to depend on memorization in practice. To address this gap, we introduce OGCaReBench, a free-form retrieval-focused benchmark aimed at evaluating LLMs at answering clinical questions that require going beyond typical guidelines. Extracted from published medical case reports and validated by medical experts, OGCaReBench contains long-form clinical questions requiring free-text answers, providing a systematic framework for assessing open-ended medical reasoning in rare, case-based scenarios. Our experiments reveal that even the best-performing baseline (GPT-5.2) correctly answers only 56% of our benchmark with specialized models only reaching 42%. Augmenting models with retrieved medical articles improves this performance to up to 82% (using GPT-5.2) highlighting the importance of evidence-grounding for real-world medical reasoning tasks. This work thus establishes a foundation for benchmarking and advancing both general-purpose and medical LLMs to produce reliable answers in challenging clinical contexts.

Keyword-matching benchmarks can credit small models for tool use they never perform. We document such a false positive in a matched-architecture pair of Spanish security language models and propose a ladder of strict, cheap diagnostics. A 661.6M parameter model (approx. 65% code/technical text; no dedicated SFT) and a 1,109M model (web-heavy multi-phase curriculum; 6B-token tool-SFT) share decoder, tokenizer, and special tokens, scoring almost identically on lenient tool-use metrics (B4: 0.660 vs. 0.650). Verbatim-reproduction checks on training examples separate them completely: the 600M emits valid tool calls with generalized arguments on 6/6 examples; the 1B does so on 0/6 across checkpoints. A first-token probe localizes the 1B's failure to a missing prior (prob. 10^{-4}--10^{-5} on <|tool_call|>), which was erased by its web-heavy training phase. A targeted SFT recipe (diverse corpus, 5x higher learning rate, 2,202 steps, ~3.3 GPU-hours) repairs the 1B using three orders of magnitude fewer tokens than the failed phase. On all 269 corpus rows, valid emission rises from 0.100 to 0.959 (600M: 0.926). On 238 unseen prompts, the repaired 1B passes 0.536 vs. the 600M's 0.428 (p = 0.004). Embedding-drift checks show the repair did not move the trigger token's tied embedding (97.7% of the bf16 table remains bit-identical), meaning changes live in the surrounding network. Both models over-trigger, rarely answering negative prompts without a call (0.09 for 600M, 0.17 for repaired 1B). Factorial analyses confirm all repair configurations install the format, though suppression benefits from a diverse corpus remain a hypothesis due to seed sensitivity. This cheap diagnostic ladder costs minutes of CPU time and should gate tool-use claims on small models.

We present a single-GPU (H100, bf16) evaluation of GPT-OSS-20B (Mixture-of-Experts; 20.9B total, approx. 3.61B active) against dense baselines Qwen3-32B and Yi-34B across multiple dimensions. We measure true time-to-first-token (TTFT), full-decode throughput (TPOT), end-to-end latency percentiles, peak VRAM with past key values (PKV) held, and energy via a consistent nvidia-smi-based sampler. At a 2048-token context with 64-token decode, GPT-OSS-20B delivers higher decode throughput and tokens per Joule than dense baselines Qwen3-32B and Yi-34B, while substantially reducing peak VRAM and energy per 1000 generated tokens; its TTFT is higher due to MoE routing overhead. With only 17.3% of parameters active (3.61B of 20.9B), GPT-OSS-20B provides about 31.8% higher decode throughput and 25.8% lower energy per 1000 generated tokens than Qwen3-32B at 2048/64, while using 31.7% less peak VRAM. Normalized by active parameters, GPT-OSS-20B shows markedly stronger per-active-parameter efficiency (APE), underscoring MoE's deployment advantages. We do not evaluate accuracy; this is a deployment-focused study. We release code and consolidated results to enable replication and extension.

Multiple-choice QA benchmarks usually evaluate small language models (SLMs) as direct answerers, but deployed language-model systems increasingly rely on external scaffolds such as tools, code, and repeated model calls. We introduce Code-Guided Reasoning (CGR), an evaluation protocol and generated-program resource for measuring when executable reasoning scaffolds improve SLM performance on MCQA tasks. CGR standardizes six components: a normalized item interface, a direct solver prompt, a generator prompt, a Python scaffold, solver-call and extraction helpers, and a three-channel result record. On 20,498 retained result rows from a locally prepared MCQA bundle and six metadata-registered solver models, the observed non-zero-baseline partition shows 66.21% macro assisted accuracy versus 38.11% direct accuracy, a +28.10 percentage-point difference with a pair-bootstrap interval of [20.32, 36.43]. Under a stricter Ab > 30% direct-signal gate, the macro difference is +14.11 points. These estimates are descriptive. Assisted inference uses a larger solver-call budget, answer extraction is brittle, Time-MQA contains the observed regressions, and some generated programs violate the no-hard-coding instruction. CGR provides the trace package needed to interpret these results, including direct, assisted, and generator-side answers, partition definitions, generated programs, response metadata, and audits.

Given the importance of remote sensing, surprisingly little attention has been paid to it by the representation learning community. To address it and to establish baselines and a common evaluation protocol in this domain, we provide simplified access to 5 diverse remote sensing datasets in a standardized form. Specifically, we investigate in-domain representation learning to develop generic remote sensing representations and explore which characteristics are important for a dataset to be a good source for remote sensing representation learning. The established baselines achieve state-of-the-art performance on these datasets.

Mixed Integer Linear Programming (MILP) is a fundamental tool for modeling combinatorial optimization problems. Recently, a growing body of research has used machine learning to accelerate MILP solving. Despite the increasing popularity of this approach, there is a lack of a common repository that provides distributions of similar MILP instances across different domains, at different hardness levels, with standardized test sets. In this paper, we introduce Distributional MIPLIB, a multi-domain library of problem distributions for advancing ML-guided MILP methods. We curate MILP distributions from existing work in this area as well as real-world problems that have not been used, and classify them into different hardness levels. It will facilitate research in this area by enabling comprehensive evaluation on diverse and realistic domains. We empirically illustrate the benefits of using Distributional MIPLIB as a research vehicle in two ways. We evaluate the performance of ML-guided variable branching on previously unused distributions to identify potential areas for improvement. Moreover, we propose to learn branching policies from a mix of distributions, demonstrating that mixed distributions achieve better performance compared to homogeneous distributions when there is limited data and generalize well to larger instances. The dataset is publicly available at https://sites.google.com/usc.edu/distributional-miplib/home.

Conformal prediction is a powerful tool to generate uncertainty sets with guaranteed coverage using any predictive model, under the assumption that the training and test data are i.i.d.. Recently, it has been shown that adversarial examples are able to manipulate conformal methods to construct prediction sets with invalid coverage rates, as the i.i.d. assumption is violated. To address this issue, a recent work, Randomized Smoothed Conformal Prediction (RSCP), was first proposed to certify the robustness of conformal prediction methods to adversarial noise. However, RSCP has two major limitations: (i) its robustness guarantee is flawed when used in practice and (ii) it tends to produce large uncertainty sets. To address these limitations, we first propose a novel framework called RSCP+ to provide provable robustness guarantee in evaluation, which fixes the issues in the original RSCP method. Next, we propose two novel methods, Post-Training Transformation (PTT) and Robust Conformal Training (RCT), to effectively reduce prediction set size with little computation overhead. Experimental results in CIFAR10, CIFAR100, and ImageNet suggest the baseline method only yields trivial predictions including full label set, while our methods could boost the efficiency by up to 4.36times, 5.46times, and 16.9times respectively and provide practical robustness guarantee. Our codes are available at https://github.com/Trustworthy-ML-Lab/Provably-Robust-Conformal-Prediction.

Repeatedly sampling short sequence windows from a human pangenome requires an access representation as well as compression. panvram stores each assembly as a reference-relative block archive and pools these archives on a GPU. For 558 haplotype assemblies, the default q4k representation occupies 16.642 GB of persistent pools including the decoded reference; a packed-reference, compact-directory representation occupies 11.634 GB. These quantities are not peak application memory. In the C1 experiment, default and fully compact forms delivered 743,271 and 736,762 windows/s; a separate public Colab run delivered 741,931 and 680,760 windows/s. All are batch API measurements and must not be pooled as repeated trials of an identical environment. Full-decoding checks compared reconstructed FASTA checksums with the manifest. On the CPU, the M6 shuffled-window workload at the same cohort cardinality reported 26 requests/s for AGC and 145,222 requests/s for refrel3 q4k. This comparison concerns one-thread requests of 4 KiB on the recorded warm-cache workload, not all genome-access patterns. AGC provides the smaller incremental archive: 5.40 MB/assembly versus 13.04 MB/assembly for refrel3 q16k, with different exclusions; the size pair is not the same refrel3 configuration as the q4k timing pair. We derive an expected-work expression for fixed independent granules and distinguish it from an empirical median-latency predictor. Cohort-scale counter and DRAM measurements motivate a locality hypothesis, but do not establish a causal per-miss latency or independently reproduce a model-failure verdict. The window-cost verdict at N=558 is published with its harness and raw timings.

Accurate whole-cell and nuclear segmentation is essential for precision pathology and spatial omics, yet routine hematoxylin and eosin (H&E) staining provides limited cytoplasmic contrast, restricting analyses to nuclei. Multiplex immunofluorescence (mIF) facilitates precise whole-cell delineation but remains constrained by cost and accessibility. We introduce VitaminP, a cross-modal learning framework enabling whole cell segmentation from H&E images. By learning from paired H&E-mIF data, VitaminP transfers molecular boundary information from mIF to overcome cytoplasmic contrast in H&E, establishing cross-modal supervision as a general strategy for recovering missing biological structure. We train VitaminP on 14 public datasets covering 34 cancer types and over 7 million instances, integrating publicly available labels with extensive annotations generated in this study, forming one of the largest resources for segmentation. VitaminP outperforms four state-of-the-art methods and generalizes to unseen datasets, including an in-house dataset spanning 24 rare cancer types. We further developed VitaminPScope, an open-source platform providing an interface for scalable inference and enabling broad adoption.

We introduce a new -- currently 42 gigabyte -- ``living'' dataset of phone images of dog feces, annotated with manually drawn or AI-assisted polygon labels. There are 6k full resolution images and 4k detailed polygon annotations. The collection and annotation of images started in late 2020 and the dataset grows by roughly 1GB a month. We train VIT and MaskRCNN baseline models to explore the difficulty of the dataset. The best model achieves a pixelwise average precision of 0.858 on a 691-image validation set and 0.847 on a small independently captured 30-image contributor test set. The most recent snapshot of dataset is made publicly available through three different distribution methods: one centralized (Girder) and two decentralized (IPFS and BitTorrent). We study of the trade-offs between distribution methods and discuss the feasibility of each with respect to reliably sharing open scientific data. The code to reproduce the experiments is hosted on GitHub, and the data is published under the Creative Commons Attribution 4.0 International license. Model weights are made publicly available with the dataset. Experimental hardware, time, energy, and emissions are quantified.

Background. The rapid and growing popularity of machine learning (ML) applications has led to an increasing interest in MLOps, that is, the practice of continuous integration and deployment (CI/CD) of ML-enabled systems. Aims. Since changes may affect not only the code but also the ML model parameters and the data themselves, the automation of traditional CI/CD needs to be extended to manage model retraining in production. Method. In this paper, we present an initial investigation of the MLOps practices implemented in a set of ML-enabled systems retrieved from GitHub, focusing on GitHub Actions and CML, two solutions to automate the development workflow. Results. Our preliminary results suggest that the adoption of MLOps workflows in open-source GitHub projects is currently rather limited. Conclusions. Issues are also identified, which can guide future research work.

Recent autonomous penetration testing papers report high benchmark scores while adding multi-component security harnesses around frontier LLMs. Because these systems often change both architecture and backbone model, it is difficult to tell how much performance comes from the harness rather than from the underlying model. This paper presents a controlled study on the 104-task XBOW benchmark using default coding CLI agents as plain-agent baselines. We first run Codex, OpenCode, and Pi with the same GPT-5 model, budget, target interface, and scoring rule. This phase identifies the strongest same-model baseline and tests whether security-specific prompt variants improve its observed score. We then compare the default Codex scaffold with published MAPTA and PentestGPT V2 results under the closest available model matches. Finally, we repeat the plain-agent experiment with GPT-5.2 and GPT-5.5 to measure model scaling inside the same scaffold. The results show a mixed but practical picture. Specialised harnesses can add measurable benchmark lift and may improve cost efficiency, but plain coding agents already solve a large share of the benchmark; repeated plain-agent runs can match or exceed some published architecture scores in union coverage, and newer models substantially improve the same scaffold. Future evaluations should report model-matched plain-agent baselines before attributing benchmark gains to architecture design alone.

Stereo image and video generation, stereo geometry estimation, and condition-controlled view synthesis require paired data in which the variables that determine binocular geometry -- camera baseline, intrinsics, scene depth, and camera motion -- are known and controllable. Existing stereo resources provide subsets of these variables, but resources commonly used for stereo generation evaluation do not, to our knowledge, provide scene-paired, calibrated multi-baseline right-view ground truth with jointly recorded intrinsics, dense metric depth, and per-frame poses in a single controlled source. We introduce StereoGenBench, a synthetic Unreal Engine benchmark designed to make baseline-regime sensitivity and target-camera consistency measurable under matched scene content. Each scene is rendered with a rigid six-camera lateral array, yielding up to 15 calibrated view pairs; adjacent baselines are sampled from inter-pupillary to wide-baseline regimes; focal length is sampled independently; and every view is released with RGB, metric depth, intrinsics, per-pair baselines, and per-frame poses. The splits include two evaluation families for narrow and wide baseline regimes and a train-only family for broader all-pairs coverage. We release the dataset, evaluation code, reference results, Croissant metadata, and generation code/configuration for extension with compatible assets. The dataset is available at https://huggingface.co/datasets/stereo-dataset/stereo-dataset

AI virtual cells aim to predict cellular responses to specified interventions, yet held-out predictive performance alone does not establish use of the supplied perturbation information. This prediction-claim gap matters in agentic model discovery, where language-model agents generate and revise predictors using score-based feedback. We introduce CELLAUDIT, which audits input-use claims by asking whether an input can enter the cited computation, whether fitted predictions depend on it, and whether that dependence improves prediction of observed response. On a paired morphology-transcriptomics perturbation benchmark (BBBC047), an agent-selected predictor attains a mean held-out Global Pearson correlation coefficient (PCC) of 0.3153 but remains invariant to compound replacement; a control-profile-only predictor reaches 0.3142. Source inspection identifies a compound-query pathway blocked by singleton key-value attention, and the invariance persists after refitting with disjoint control wells. In a stratified audit of 48 candidates across two linked tasks, 47 change predictions under compound replacement on both held-out folds, but only 20 show target-loss gains with intervals above zero on both folds. On BBBC047, falsification-guided revisions recover positive mean compound contributions while retaining gains over the control-profile-only baseline. In matched sci-Plex searches, audit-enriched feedback yields higher held-out performance and larger mean compound and dose contributions across five trajectories, although paired intervals span zero. Refitting fixed designs on an independently acquired cohort shows predictive generalization need not imply generalization of input-use claims: dose contribution persists, whereas support for compound identity does not. CELLAUDIT adds a falsification layer to agentic model discovery, moving from generate-score-revise toward discover-falsify-revise.

Computer-use agents pay full frontier inference to re-derive routines their user has already performed, because an agent's memory today records what the user said, not what the user did. We compile passively captured screen activity into agent memory with a deterministic, zero-model pipeline: it segments a local capture stream into typed activity frames, bounded episodes carrying application, site, timing, input volume, and evidence pointers back to the raw rows, with no model in the loop, so the output is byte-identical, cacheable, and mechanically auditable. On one professional's single-user corpus of 128,756 frames over 51 active days, the compiler reduces a day of raw capture to a prompt-ready context block 86x smaller in 68 ms, and an agent reading that block answers questions about the day at 98.4% accuracy (Wilson 95% CI 91.7-99.7%) against an independent oracle, versus 66-80% for an LLM summary of the same capture, a mid-tier model reading the block matching a frontier one. The same compiler doubles as a demand-side cost instrument. Read off passive, pre-delegation human activity rather than agent rollouts, it supplies two parameters that agent-cost models assume but, to our knowledge, have not measured: the Routine Overhead Ratio R and the routine recurrence h. We report first values of R, a modeled upper bound, at 60-343x, and a delegable recurrence of 9.0% in-sample and 7.7% out-of-sample, for a realistic all-fleet token ceiling near 8%; a compiled routine replays deterministically with the model out of the loop, demonstrated live at zero model tokens on a guard-matched hit. Schema, compiler, and evaluation harness are open.

Research agents explain planned experiments. We measure predictive credit with paired forecasts sharing an intervention, forecaster, and outcome while varying description, matched explanation, and donor context. Five checks track commitment, delivery, predictive gain, alignment, and known-signal uptake. Across 336 prospective states in controlled learning, 12 Tox21 endpoints, and 24 OpenML tasks, v5's frozen credit decision was inconclusive. Tox21's preregistered ROC AUC interval-score harm test was unmet (D-M=-.0026, 95 percent interval [-.0174, .0104]); OpenML's joint formation, point-equivalence, and repeatability rule was unmet. Matched point-accuracy gains over description remained unconfirmed, and Tox21/OpenML seed-donor intervals spanned zero. Under requested DeepSeek V4 Pro, matched and donor cards reduced secondary Tox21 drift by 64.5 and 59.1 percent. A DeepSeek V4 Flash replay raised matched point MAE from .01823 to .02020 and missed matched-donor interval-score equivalence. OpenML full-card assignment widened nominal 80 percent intervals by 21 percent, with 49.3 percent coverage versus 51.4 percent for description and content in 66/144 cards. Direct-text Flash delivered all 144 notes without detectable matched point-accuracy gain. A researcher-authored mechanism positive control lowered point MAE by 2.60 percentage points versus description. The protocol measures predictive credit for research-agent benchmarks and scientific forecasting; natural-explanation credit remained unconfirmed at the tested donor resolutions.

We introduce a new, highly challenging benchmark and a dataset -- FungiTastic -- based on data continuously collected over a twenty-year span. The dataset originates in fungal records labeled and curated by experts. It consists of about 350k multi-modal observations that include more than 650k photographs from 5k fine-grained categories and diverse accompanying information, e.g., acquisition metadata, satellite images, and body part segmentation. FungiTastic is the only benchmark that includes a test set with partially DNA-sequenced ground truth of unprecedented label reliability. The benchmark is designed to support (i) standard close-set classification, (ii) open-set classification, (iii) multi-modal classification, (iv) few-shot learning, (v) domain shift, and many more. We provide baseline methods tailored for almost all the use-cases. We provide a multitude of ready-to-use pre-trained models on HuggingFace and a framework for model training. A comprehensive documentation describing the dataset features and the baselines are available at https://bohemianvra.github.io/FungiTastic/ and https://www.kaggle.com/datasets/picekl/fungitastic.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics profiling, we compared drug-response panel (DRP) descriptors against omics features for predictive capacity using gradient boosting tree models across the GDSC and CCLE drug response datasets. DRP descriptors consistently outperformed omics data across key performance metrics, with variable performance across different drugs. Using complementary explainability approaches, we confirmed known MAPK-inhibitor sensitivity signatures, and identified novel potential biomarker candidates for MEK1/2 and BTK/MNK inhibitors. Lastly, to demonstrate the utility of this approach in distinguishing phenotypes, we applied our models to the breast cancer line MCF7 versus the non-tumorigenic MCF10A, and successfully identified compounds that selectively inhibit MCF7 while sparing the non-tumorigenic MCF10A. This methodology, developed using focused drug and cell line panels, supports early-stage drug development by facilitating rational cell line selection and compound prioritisation, enabling more efficient biomarker identification and candidate assessment.

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

AI research agents combine prior knowledge, public sources, and experimental feedback to produce useful results. The Discovery Certification Protocol (DCP) turns claims about these results into executable recovery and feedback tests. Gate 1 validates useful improvement on sealed evaluation. Gate 2 gives matched agents the registered starting information and observed Web content while withholding the target research history. Every valid method reaching the numerical target supplies a recovery witness and triggers the Core veto. DCP Core requires adequate controls, zero observed recoveries, and a finite-sample bound on recovery in one fresh registered episode. Optional Gate 3 measures the average effect of truthful feedback relative to a specified neutral policy from a shared checkpoint. DCP Evidence adds this effect after independent null calibration and a registered effect margin. Two controlled audits exercise the complete protocol in SQLite optimization and virtual catalyst control under different models. Each produced zero recoveries in 96 episodes, with an upper bound of 0.0468. Each paired study yielded 30 truthful recoveries and zero neutral recoveries, with passing 60-pair null studies. Additional cases exercise Core, recovered, and audit-incomplete decisions. A deterministic, LLM-free verifier reproduces the decisions from frozen evidence. DCP provides a common evidence language for useful outcomes, alternative routes, and feedback effects across AI research.