Daily Papers

Foundation models (FMs) for the Earth system learn statistical relationships between physical variables across massive datasets to enable versatile downstream applications through finetuning, separating them from task-specific weather models. Here, we introduce Earth System Foundation Model (ESFM), a fully open model building on the 3D Swin UNet backbone of the pioneering Aurora model. ESFM introduces extensions that increase functionality and foster adoption in climate sciences. First, the encoding scheme and training protocols have been extended to handle diverse datasets, including those containing missing values across all spatio-temporal dimensions such as satellite data, as well as station data, all under one backbone. Axial attention is introduced to capture inter-variable dependencies. As a result ESFM skillfully predicts variables in regions or on pressure levels where no data is present at the initial time, while preserving inter-variable relationships, for example between temperature, pressure, and humidity. Individual variable tokenization enables different sets of variables to be shuffled during training and simplifies the process of building extensions for new downstream tasks. Adaptive layer norm-based ensembles allow for a simple yet effective way to transform deterministic ESFM to a probabilistic FM. We present findings using dense gridded data (ERA5, CMIP6), regionally masked dense data, sparse gridded MODIS satellite data, and station data. Results demonstrate competitive or superior performance relative to state-of-the-art benchmarks. Case studies of Super Typhoon Doksuri (2023) and 2024 sudden stratospheric warming events show accurate positional and magnitude estimations of extreme weather. ESFM retains the strengths of previous foundation models, such as long-term stability, but facilitates application to a variety of downstream tasks.

Accurate Multivariate Time Series (MTS) forecasting is crucial for collaborative design of complex systems, Digital Twin building, and maintenance ahead of time. However, the collaborative industrial environment presents new challenges for MTS forecasting models: models should decouple complex inter-variable dependencies while addressing non-stationary distribution shift brought by environmental changes. To address these challenges and improve collaborative sensing reliability, we propose a Patch-Based Dual-Branch Channel-Temporal Forecasting Network (D-CTNet). Particularly, with a parallel dual-branch design incorporating linear temporal modeling layer and channel attention mechanism, our method explicitly decouples and jointly learns intra-channel temporal evolution patterns and dynamic multivariate correlations. Furthermore, a global patch attention fusion module goes beyond the local window scope to model long range dependencies. Most importantly, aiming at non-stationarity, a Frequency-Domain Stationarity Correction mechanism adaptively suppresses distribution shift impacts from environment change by spectrum alignment. Evaluations on seven benchmark datasets show that our model achieves better forecasting accuracy and robustness compared with state-of-the-art methods. Our work shows great promise as a new forecasting engine for industrial collaborative systems.

Code translation is a crucial activity in the software development and maintenance process, and researchers have recently begun to focus on using pre-trained large language models (LLMs) for code translation. However, existing LLMs only learn the contextual semantics of code during pre-training, neglecting executability information closely related to the execution state of the code, which results in unguaranteed code executability and unreliable automated code translation. To address this issue, we propose ExeCoder, an LLM specifically designed for code translation, aimed at utilizing executability representations such as functional semantics, syntax structures, and variable dependencies to enhance the capabilities of LLMs in code translation. To evaluate the effectiveness of ExeCoder, we manually enhanced the widely used benchmark TransCoder-test, resulting in a benchmark called TransCoder-test-X that serves LLMs. Evaluation of TransCoder-test-X indicates that ExeCoder achieves state-of-the-art performance in code translation, surpassing existing open-source code LLMs by over 10.88% to 38.78% and over 27.44% to 42.97% on two metrics, and even outperforms the renowned closed-source LLM GPT-4o. Website: https://execoder4trans.github.io/

Mobile usage traces are critical for tasks such as user behavior prediction and app recommendation, yet their use is constrained by privacy restrictions and costly large-scale data collection. Although generative models perform well on general time series, their application to mobile usage data remains challenging because (i) limited user activity causes severe sparsity, (ii) heterogeneous variable types complicate joint modeling, and (iii) functional differences across apps create pronounced usage imbalance. To address these challenges, we propose Multivariate-Imaging Diffusion (MIDiff), a diffusion-based framework operating in an imaging space defined by Cross-Gramian Angular Sum Field (C-GASF). C-GASF transforms sparse multivariate sequences into correlation images, while MIDiff employs Triple Attention in a U-Net to preserve temporal consistency and variable dependencies. Experiments show that MIDiff achieves state-of-the-art performance across fidelity metrics. In particular, it obtains a Discriminative Accuracy (DA) of 0.1526, compared with 0.3476 for the strongest baseline, ZITS-VAE, demonstrating its effectiveness in generating realistic and diverse mobile usage traces. Our code is available at https://github.com/YilaiLiu-HKU/MIDiff.

Spiking Neural Networks (SNNs) have emerged as an energy-efficient alternative to conventional neural networks, demonstrating strong performance in computer vision and robotics. More recently, SNNs have been applied to time series forecasting (TSF), with methods exploring spiking temporal backbones, spike-compatible positional encodings, Fourier-domain processing, and redesigned neuron dynamics. However, existing SNN forecasting approaches process variables independently, lacking explicit mechanisms for modeling inter-variable dependencies. This is a critical limitation in multivariate settings, where cross-variable correlations carry substantial predictive information. We propose Spiking Fourier Graph Operators (SpikF-GO), which addresses this gap by combining a hypervariate graph formulation in which every scalar observation becomes a graph node with spike-driven spectral processing. SpikF-GO introduces a Hard Concrete frequency gate for learnable sparse frequency selection and a Complex LIF gate that applies independent spiking neurons to real and imaginary Fourier components, preserving binary, event-driven computation throughout the spectral domain. We further present a variant incorporating Central Pattern Generator-based positional encodings for stronger long-range temporal modeling. Evaluated on eight benchmarks under a unified experimental protocol, SpikF-GO achieves the best average rank among all SNN methods and outperforms its ANN counterpart, FourierGNN, at reduced energy cost. SpikF-GO maintains competitive accuracy even at substantially smaller embedding dimensions, thereby achieving significant energy reductions. To our knowledge, this is among the first works to bring graph-based multivariate modeling into the spiking domain for TSF and the first to provide a unified comparison across SNN forecasting architectures under a common experimental protocol.

Multivariable time series forecasting methods can integrate information from exogenous variables, leading to significant prediction accuracy gains. Transformer architecture has been widely applied in various time series forecasting models due to its ability to capture long-range sequential dependencies. However, a na\"ive application of transformers often struggles to effectively model complex relationships among variables over time. To mitigate against this, we propose a novel architecture, namely the Spectral Operator Neural Network (Sonnet). Sonnet applies learnable wavelet transformations to the input and incorporates spectral analysis using the Koopman operator. Its predictive skill relies on the Multivariable Coherence Attention (MVCA), an operation that leverages spectral coherence to model variable dependencies. Our empirical analysis shows that Sonnet yields the best performance on 34 out of 47 forecasting tasks with an average mean absolute error (MAE) reduction of 1.1% against the most competitive baseline (different per task). We further show that MVCA -- when put in place of the na\"ive attention used in various deep learning models -- can remedy its deficiencies, reducing MAE by 10.7% on average in the most challenging forecasting tasks.

This work addresses the challenge of forecasting urban water dynamics by developing a multi-input, multi-output deep learning model that incorporates both endogenous variables (e.g., water height or discharge) and exogenous factors (e.g., precipitation history and forecast reports). Unlike conventional forecasting, the proposed model, AquaCast, captures both inter-variable and temporal dependencies across all inputs, while focusing forecast solely on endogenous variables. Exogenous inputs are fused via an embedding layer, eliminating the need to forecast them and enabling the model to attend to their short-term influences more effectively. We evaluate our approach on the LausanneCity dataset, which includes measurements from four urban drainage sensors, and demonstrate state-of-the-art performance when using only endogenous variables. Performance also improves with the inclusion of exogenous variables and forecast reports. To assess generalization and scalability, we additionally test the model on three large-scale synthesized datasets, generated from MeteoSwiss records, the Lorenz Attractors model, and the Random Fields model, each representing a different level of temporal complexity across 100 nodes. The results confirm that our model consistently outperforms existing baselines and maintains a robust and accurate forecast across both real and synthetic datasets.

Virtual sensing techniques allow for inferring signals at new unmonitored locations by exploiting spatio-temporal measurements coming from physical sensors at different locations. However, as the sensor coverage becomes sparse due to costs or other constraints, physical proximity cannot be used to support interpolation. In this paper, we overcome this challenge by leveraging dependencies between the target variable and a set of correlated variables (covariates) that can frequently be associated with each location of interest. From this viewpoint, covariates provide partial observability, and the problem consists of inferring values for unobserved channels by exploiting observations at other locations to learn how such variables can correlate. We introduce a novel graph-based methodology to exploit such relationships and design a graph deep learning architecture, named GgNet, implementing the framework. The proposed approach relies on propagating information over a nested graph structure that is used to learn dependencies between variables as well as locations. GgNet is extensively evaluated under different virtual sensing scenarios, demonstrating higher reconstruction accuracy compared to the state-of-the-art.

Multivariate Time Series Classification (MTSC) is crucial in extensive practical applications, such as environmental monitoring, medical EEG analysis, and action recognition. Real-world time series datasets typically exhibit complex dynamics. To capture this complexity, RNN-based, CNN-based, Transformer-based, and hybrid models have been proposed. Unfortunately, current deep learning-based methods often neglect the simultaneous construction of local features and global dependencies at different time scales, lacking sufficient feature extraction capabilities to achieve satisfactory classification accuracy. To address these challenges, we propose a novel Multiscale Periodic Time Series Network (MPTSNet), which integrates multiscale local patterns and global correlations to fully exploit the inherent information in time series. Recognizing the multi-periodicity and complex variable correlations in time series, we use the Fourier transform to extract primary periods, enabling us to decompose data into multiscale periodic segments. Leveraging the inherent strengths of CNN and attention mechanism, we introduce the PeriodicBlock, which adaptively captures local patterns and global dependencies while offering enhanced interpretability through attention integration across different periodic scales. The experiments on UEA benchmark datasets demonstrate that the proposed MPTSNet outperforms 21 existing advanced baselines in the MTSC tasks.

Photovoltaic (PV) power forecasting plays a crucial role in optimizing the operation and planning of PV systems, thereby enabling efficient energy management and grid integration. However, un certainties caused by fluctuating weather conditions and complex interactions between different variables pose significant challenges to accurate PV power forecasting. In this study, we propose PV-Client (Cross-variable Linear Integrated ENhanced Transformer for Photovoltaic power forecasting) to address these challenges and enhance PV power forecasting accuracy. PV-Client employs an ENhanced Transformer module to capture complex interactions of various features in PV systems, and utilizes a linear module to learn trend information in PV power. Diverging from conventional time series-based Transformer models that use cross-time Attention to learn dependencies between different time steps, the Enhanced Transformer module integrates cross-variable Attention to capture dependencies between PV power and weather factors. Furthermore, PV-Client streamlines the embedding and position encoding layers by replacing the Decoder module with a projection layer. Experimental results on three real-world PV power datasets affirm PV-Client's state-of-the-art (SOTA) performance in PV power forecasting. Specifically, PV-Client surpasses the second-best model GRU by 5.3% in MSE metrics and 0.9% in accuracy metrics at the Jingang Station. Similarly, PV-Client outperforms the second-best model SVR by 10.1% in MSE metrics and 0.2% in accuracy metrics at the Xinqingnian Station, and PV-Client exhibits superior performance compared to the second-best model SVR with enhancements of 3.4% in MSE metrics and 0.9% in accuracy metrics at the Hongxing Station.

Multivariate time series forecasting (MTSF) is crucial for decision-making to precisely forecast the future values/trends, based on the complex relationships identified from historical observations of multiple sequences. Recently, Spatial-Temporal Graph Neural Networks (STGNNs) have gradually become the theme of MTSF model as their powerful capability in mining spatial-temporal dependencies, but almost of them heavily rely on the assumption of historical data integrity. In reality, due to factors such as data collector failures and time-consuming repairment, it is extremely challenging to collect the whole historical observations without missing any variable. In this case, STGNNs can only utilize a subset of normal variables and easily suffer from the incorrect spatial-temporal dependency modeling issue, resulting in the degradation of their forecasting performance. To address the problem, in this paper, we propose a novel Graph Interpolation Attention Recursive Network (named GinAR) to precisely model the spatial-temporal dependencies over the limited collected data for forecasting. In GinAR, it consists of two key components, that is, interpolation attention and adaptive graph convolution to take place of the fully connected layer of simple recursive units, and thus are capable of recovering all missing variables and reconstructing the correct spatial-temporal dependencies for recursively modeling of multivariate time series data, respectively. Extensive experiments conducted on five real-world datasets demonstrate that GinAR outperforms 11 SOTA baselines, and even when 90% of variables are missing, it can still accurately predict the future values of all variables.

Recent studies have extended the application of large language models (LLMs) to geographic problems, revealing surprising geospatial competence even without explicit spatial supervision. However, LLMs still face challenges in spatial consistency, multi-hop reasoning, and geographic bias. To address these issues, we propose GeoSR, a self-refining agentic reasoning framework that embeds core geographic principles -- most notably Tobler's First Law of Geography -- into an iterative prediction loop. In GeoSR, the reasoning process is decomposed into three collaborating agents: (1) a variable-selection agent that selects relevant covariates from the same location; (2) a point-selection agent that chooses reference predictions at nearby locations generated by the LLM in previous rounds; and (3) a refine agent that coordinates the iterative refinement process by evaluating prediction quality and triggering further rounds when necessary. This agentic loop progressively improves prediction quality by leveraging both spatial dependencies and inter-variable relationships. We validate GeoSR on tasks ranging from physical-world property estimation to socioeconomic prediction. Experimental results show consistent improvements over standard prompting strategies, demonstrating that incorporating geostatistical priors and spatially structured reasoning into LLMs leads to more accurate and equitable geospatial predictions. The code of GeoSR is available at https://github.com/JinfanTang/GeoSR.

Denoising diffusion probabilistic models (DDPMs) have recently achieved leading performances in many generative tasks. However, the inherited iterative sampling process costs hindered their applications to speech synthesis. This paper proposes FastDiff, a fast conditional diffusion model for high-quality speech synthesis. FastDiff employs a stack of time-aware location-variable convolutions of diverse receptive field patterns to efficiently model long-term time dependencies with adaptive conditions. A noise schedule predictor is also adopted to reduce the sampling steps without sacrificing the generation quality. Based on FastDiff, we design an end-to-end text-to-speech synthesizer, FastDiff-TTS, which generates high-fidelity speech waveforms without any intermediate feature (e.g., Mel-spectrogram). Our evaluation of FastDiff demonstrates the state-of-the-art results with higher-quality (MOS 4.28) speech samples. Also, FastDiff enables a sampling speed of 58x faster than real-time on a V100 GPU, making diffusion models practically applicable to speech synthesis deployment for the first time. We further show that FastDiff generalized well to the mel-spectrogram inversion of unseen speakers, and FastDiff-TTS outperformed other competing methods in end-to-end text-to-speech synthesis. Audio samples are available at https://FastDiff.github.io/.

We propose the Distance-informed Neural Process (DNP), a novel variant of Neural Processes that improves uncertainty estimation by combining global and distance-aware local latent structures. Standard Neural Processes (NPs) often rely on a global latent variable and struggle with uncertainty calibration and capturing local data dependencies. DNP addresses these limitations by introducing a global latent variable to model task-level variations and a local latent variable to capture input similarity within a distance-preserving latent space. This is achieved through bi-Lipschitz regularization, which bounds distortions in input relationships and encourages the preservation of relative distances in the latent space. This modeling approach allows DNP to produce better-calibrated uncertainty estimates and more effectively distinguish in- from out-of-distribution data. Empirical results demonstrate that DNP achieves strong predictive performance and improved uncertainty calibration across regression and classification tasks.

In this paper, we present NUWA-Infinity, a generative model for infinite visual synthesis, which is defined as the task of generating arbitrarily-sized high-resolution images or long-duration videos. An autoregressive over autoregressive generation mechanism is proposed to deal with this variable-size generation task, where a global patch-level autoregressive model considers the dependencies between patches, and a local token-level autoregressive model considers dependencies between visual tokens within each patch. A Nearby Context Pool (NCP) is introduced to cache-related patches already generated as the context for the current patch being generated, which can significantly save computation costs without sacrificing patch-level dependency modeling. An Arbitrary Direction Controller (ADC) is used to decide suitable generation orders for different visual synthesis tasks and learn order-aware positional embeddings. Compared to DALL-E, Imagen and Parti, NUWA-Infinity can generate high-resolution images with arbitrary sizes and support long-duration video generation additionally. Compared to NUWA, which also covers images and videos, NUWA-Infinity has superior visual synthesis capabilities in terms of resolution and variable-size generation. The GitHub link is https://github.com/microsoft/NUWA. The homepage link is https://nuwa-infinity.microsoft.com.

Diffusion models have revolutionized image generation, and their extension to video generation has shown promise. However, current video diffusion models~(VDMs) rely on a scalar timestep variable applied at the clip level, which limits their ability to model complex temporal dependencies needed for various tasks like image-to-video generation. To address this limitation, we propose a frame-aware video diffusion model~(FVDM), which introduces a novel vectorized timestep variable~(VTV). Unlike conventional VDMs, our approach allows each frame to follow an independent noise schedule, enhancing the model's capacity to capture fine-grained temporal dependencies. FVDM's flexibility is demonstrated across multiple tasks, including standard video generation, image-to-video generation, video interpolation, and long video synthesis. Through a diverse set of VTV configurations, we achieve superior quality in generated videos, overcoming challenges such as catastrophic forgetting during fine-tuning and limited generalizability in zero-shot methods.Our empirical evaluations show that FVDM outperforms state-of-the-art methods in video generation quality, while also excelling in extended tasks. By addressing fundamental shortcomings in existing VDMs, FVDM sets a new paradigm in video synthesis, offering a robust framework with significant implications for generative modeling and multimedia applications.

Attention-based transformers have become the standard architecture in many deep learning fields, primarily due to their ability to model long-range dependencies and handle variable-length input sequences. However, the attention mechanism with its quadratic complexity is a significant bottleneck in the transformer architecture. This algorithm is only uni-directional in the decoder and converges to a static pattern in over-parametrized decoder-only models. I address this issue by developing a generative function as attention or activation replacement. It still has the auto-regressive character by comparing each token with the previous one. In my test setting with nanoGPT this yields a smaller loss while having a smaller model. The loss further drops by incorporating an average context vector. This concept of attention replacement is distributed under the GNU AGPL v3 license at https://gitlab.com/Bachstelze/causal_generation.

We present Timer-XL, a generative Transformer for unified time series forecasting. To uniformly predict 1D and 2D time series, we generalize next token prediction, predominantly adopted for causal generation of 1D sequences, to multivariate next token prediction. The proposed paradigm uniformly formulates various forecasting scenarios as a long-context generation problem. We opt for the generative Transformer, which can capture global-range and causal dependencies while providing contextual flexibility, to implement unified forecasting on univariate series characterized by non-stationarity, multivariate time series with complicated dynamics and correlations, and covariate-informed contexts that include both endogenous and exogenous variables. Technically, we propose a universal TimeAttention to facilitate generative Transformers on time series, which can effectively capture fine-grained intra- and inter-series dependencies of flattened time series tokens (patches) and is further strengthened by position embeddings in both temporal and variable dimensions. Timer-XL achieves state-of-the-art performance across challenging forecasting benchmarks through a unified approach. As a large time series model, it demonstrates notable model transferability by large-scale pre-training, as well as contextual flexibility in token lengths, positioning it as a one-for-all forecaster.

On-device large language models (LLMs) are catalyzing novel mobile applications such as UI task automation and personalized email auto-reply, without giving away users' private data. However, on-device LLMs still suffer from unacceptably long inference latency, especially the time to first token (prefill stage) due to the need of long context for accurate, personalized content generation, as well as the lack of parallel computing capacity of mobile CPU/GPU. To enable practical on-device LLM, we present mllm-NPU, the first-of-its-kind LLM inference system that efficiently leverages on-device Neural Processing Unit (NPU) offloading. Essentially, mllm-NPU is an algorithm-system co-design that tackles a few semantic gaps between the LLM architecture and contemporary NPU design. Specifically, it re-constructs the prompt and model in three levels: (1) At prompt level, it divides variable-length prompts into multiple fixed-sized chunks while maintaining data dependencies; (2) At tensor level, it identifies and extracts significant outliers to run on the CPU/GPU in parallel with minimal overhead; (3) At block level, it schedules Transformer blocks in an out-of-order manner to the CPU/GPU and NPU based on their hardware affinity and sensitivity to accuracy. Compared to competitive baselines, mllm-NPU achieves 22.4x faster prefill speed and 30.7x energy savings on average, and up to 32.8x speedup in an end-to-end real-world application. For the first time, mllm-NPU achieves more than 1,000 tokens/sec prefilling for a billion-sized model (Qwen1.5-1.8B), paving the way towards practical on-device LLM.

Recent code large language models (LLMs) have shown promising performance in generating standalone functions but face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 680 real-world code repositories and introduce two new repository-level metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 15.2% to 45.8% and Static Validity Rate by 10.9% to 42.2% across three distinct code LLMs, while maintaining competitive performance in widely-recognized similarity metrics. Furthermore, our generalizability evaluation confirms ToolGen's consistent performance when applied to diverse code LLMs, including various model architectures and scales.

Block coordinate descent (BCD) methods are widely used for large-scale numerical optimization because of their cheap iteration costs, low memory requirements, amenability to parallelization, and ability to exploit problem structure. Three main algorithmic choices influence the performance of BCD methods: the block partitioning strategy, the block selection rule, and the block update rule. In this paper we explore all three of these building blocks and propose variations for each that can significantly improve the progress made by each BCD iteration. We (i) propose new greedy block-selection strategies that guarantee more progress per iteration than the Gauss-Southwell rule; (ii) explore practical issues like how to implement the new rules when using "variable" blocks; (iii) explore the use of message-passing to compute matrix or Newton updates efficiently on huge blocks for problems with sparse dependencies between variables; and (iv) consider optimal active manifold identification, which leads to bounds on the "active-set complexity" of BCD methods and leads to superlinear convergence for certain problems with sparse solutions (and in some cases finite termination at an optimal solution). We support all of our findings with numerical results for the classic machine learning problems of least squares, logistic regression, multi-class logistic regression, label propagation, and L1-regularization.

Current learning-based Automated Vulnerability Repair (AVR) approaches, while promising, often fail to generalize effectively in real-world scenarios. Our diagnostic analysis reveals three fundamental weaknesses in state-of-the-art AVR approaches: (1) limited cross-repository generalization, with performance drops on unseen codebases; (2) inability to capture long-range dependencies, causing a performance degradation on complex, multi-hunk repairs; and (3) over-reliance on superficial lexical patterns, leading to significant performance drops on vulnerabilities with minor syntactic variations like variable renaming. To address these limitations, we propose SeCuRepair, a semantics-aligned, curriculum-driven, and reasoning-enhanced framework for vulnerability repair. At its core, SeCuRepair adopts a reason-then-edit paradigm, requiring the model to articulate why and how a vulnerability should be fixed before generating the patch. This explicit reasoning enforces a genuine understanding of repair logic rather than superficial memorization of lexical patterns. SeCuRepair also moves beyond traditional supervised fine-tuning and employs semantics-aware reinforcement learning, rewarding patches for their syntactic and semantic alignment with the oracle patch rather than mere token overlap. Complementing this, a difficulty-aware curriculum progressively trains the model, starting with simple fixes and advancing to complex, multi-hunk coordinated edits. We evaluate SeCuRepair on strict, repository-level splits of BigVul and newly crafted PrimeVul_AVR datasets. SeCuRepair significantly outperforms all baselines, surpassing the best-performing baselines by 34.52% on BigVul and 31.52% on PrimeVulAVR in terms of CodeBLEU, respectively. Comprehensive ablation studies further confirm that each component of our framework contributes to its final performance.

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

Universal Dependencies is an open community effort to create cross-linguistically consistent treebank annotation for many languages within a dependency-based lexicalist framework. The annotation consists in a linguistically motivated word segmentation; a morphological layer comprising lemmas, universal part-of-speech tags, and standardized morphological features; and a syntactic layer focusing on syntactic relations between predicates, arguments and modifiers. In this paper, we describe version 2 of the guidelines (UD v2), discuss the major changes from UD v1 to UD v2, and give an overview of the currently available treebanks for 90 languages.

We show that there is a general, informative and reliable procedure for discovering causal relations when, for all the investigator knows, both latent variables and selection bias may be at work. Given information about conditional independence and dependence relations between measured variables, even when latent variables and selection bias may be present, there are sufficient conditions for reliably concluding that there is a causal path from one variable to another, and sufficient conditions for reliably concluding when no such causal path exists.

Are pairs of words that tend to occur together also likely to stand in a linguistic dependency? This empirical question is motivated by a long history of literature in cognitive science, psycholinguistics, and NLP. In this work we contribute an extensive analysis of the relationship between linguistic dependencies and statistical dependence between words. Improving on previous work, we introduce the use of large pretrained language models to compute contextualized estimates of the pointwise mutual information between words (CPMI). For multiple models and languages, we extract dependency trees which maximize CPMI, and compare to gold standard linguistic dependencies. Overall, we find that CPMI dependencies achieve an unlabelled undirected attachment score of at most approx 0.5. While far above chance, and consistently above a non-contextualized PMI baseline, this score is generally comparable to a simple baseline formed by connecting adjacent words. We analyze which kinds of linguistic dependencies are best captured in CPMI dependencies, and also find marked differences between the estimates of the large pretrained language models, illustrating how their different training schemes affect the type of dependencies they capture.

Variable names are critical for conveying intended program behavior. Machine learning-based program analysis methods use variable name representations for a wide range of tasks, such as suggesting new variable names and bug detection. Ideally, such methods could capture semantic relationships between names beyond syntactic similarity, e.g., the fact that the names average and mean are similar. Unfortunately, previous work has found that even the best of previous representation approaches primarily capture relatedness (whether two variables are linked at all), rather than similarity (whether they actually have the same meaning). We propose VarCLR, a new approach for learning semantic representations of variable names that effectively captures variable similarity in this stricter sense. We observe that this problem is an excellent fit for contrastive learning, which aims to minimize the distance between explicitly similar inputs, while maximizing the distance between dissimilar inputs. This requires labeled training data, and thus we construct a novel, weakly-supervised variable renaming dataset mined from GitHub edits. We show that VarCLR enables the effective application of sophisticated, general-purpose language models like BERT, to variable name representation and thus also to related downstream tasks like variable name similarity search or spelling correction. VarCLR produces models that significantly outperform the state-of-the-art on IdBench, an existing benchmark that explicitly captures variable similarity (as distinct from relatedness). Finally, we contribute a release of all data, code, and pre-trained models, aiming to provide a drop-in replacement for variable representations used in either existing or future program analyses that rely on variable names.

Masked diffusion models have recently emerged as a flexible framework for discrete generative modeling. However, a key limitation of standard masked diffusion is its inability to effectively capture dependencies among tokens that are predicted concurrently, leading to degraded generation quality when dependencies among tokens are important. To explicitly model dependencies among tokens, we propose Variational Masked Diffusion (VMD), a framework that introduces latent variables into the masked diffusion process. Through controlled experiments on synthetic datasets, we demonstrate that VMD successfully learns dependencies that conventional masked diffusion fails to capture. We further validate the effectiveness of our approach on Sudoku puzzles and text datasets, where learning of dependencies among tokens improves global consistency. Across these domains, VMD enhances both generation quality and dependency awareness, highlighting the value of integrating variational inference into masked diffusion. Our code is available at: https://riccizz.github.io/VMD.

Pre-trained models (PTMs) are machine learning models that have been trained in advance, often on large-scale data, and can be reused for new tasks, thereby reducing the need for costly training from scratch. Their widespread adoption introduces a new class of software dependency, which we term Software Dependencies 2.0, extending beyond conventional libraries to learned behaviors embodied in trained models and their associated artifacts. The integration of PTMs as software dependencies in real projects remains unclear, potentially threatening maintainability and reliability of modern software systems that increasingly rely on them. Objective: In this study, we investigate Software Dependencies 2.0 in open-source software (OSS) projects by examining the reuse of PTMs, with a focus on how developers manage and integrate these models. Specifically, we seek to understand: (1) how OSS projects structure and document their PTM dependencies; (2) what stages and organizational patterns emerge in the reuse pipelines of PTMs within these projects; and (3) the interactions among PTMs and other learned components across pipeline stages. We conduct a mixed-methods analysis of a statistically significant random sample of 401 GitHub repositories from the PeaTMOSS dataset (28,575 repositories reusing PTMs from Hugging Face and PyTorch Hub). We quantitatively examine PTM reuse by identifying patterns and qualitatively investigate how developers integrate and manage these models in practice.

Package dependencies are a critical control point in modern software supply chains. Dependency changes can substantially alter a project's security posture. As AI coding agents increasingly modify software via pull requests, it is unclear whether their dependency decisions introduce distinct security risks. We study 117,062 dependency changes from agent- and human-authored pull requests across seven ecosystems. Agents select known-vulnerable versions more often than humans (2.46% vs. 1.64%), and their vulnerable selections are more disruptive to remediate, with 36.8% requiring major-version upgrades compared to 12.9% for humans, despite patched alternatives existing in most cases. At the aggregate level, agent-driven dependency work yields a net vulnerability increase of 98, whereas human-authored work yields a net reduction of 1,316. These findings motivate pull-request-time vulnerability screening and registry-aware guardrails to make agent-driven dependency updates safer.

Understanding the interplay between intra-modality dependencies (the contribution of an individual modality to a target task) and inter-modality dependencies (the relationships between modalities and the target task) is fundamental to advancing multi-modal learning. However, the nature of and interaction between these dependencies within current benchmark evaluations remains poorly characterized. In this work, we present a large-scale empirical study to quantify these dependencies across 23 visual question-answering benchmarks using multi-modal large language models (MLLMs) covering domains such as general and expert knowledge reasoning, optical character recognition, and document understanding. Our findings show that the reliance on vision, question (text), and their interaction varies significantly, both across and within benchmarks. We discover that numerous benchmarks intended to mitigate text-only biases have inadvertently amplified image-only dependencies. This characterization persists across model sizes and types, with models often obtaining high performance by using each modality independently and showing limited dependence on their interaction. We provide a quantitative characterization of multi-modal datasets, enabling a principled approach to multi-modal benchmark design and evaluation.

While large language models (LLMs) have shown considerable promise in code generation, real-world software development demands advanced repository-level reasoning. This includes understanding dependencies, project structures, and managing multi-file changes. However, the ability of LLMs to effectively comprehend and handle complex code repositories has yet to be fully explored. To address challenges, we introduce a hierarchical benchmark designed to evaluate repository dependency understanding (DependEval). Benchmark is based on 15,576 repositories collected from real-world websites. It evaluates models on three core tasks: Dependency Recognition, Repository Construction, and Multi-file Editing, across 8 programming languages from actual code repositories. Our evaluation of over 25 LLMs reveals substantial performance gaps and provides valuable insights into repository-level code understanding.

Uncertainty quantification (UQ) is a perspective approach to detecting Large Language Model (LLM) hallucinations and low quality output. In this work, we address one of the challenges of UQ in generation tasks that arises from the conditional dependency between the generation steps of an LLM. We propose to learn this dependency from data. We train a regression model, which target variable is the gap between the conditional and the unconditional generation confidence. During LLM inference, we use this learned conditional dependency model to modulate the uncertainty of the current generation step based on the uncertainty of the previous step. Our experimental evaluation on nine datasets and three LLMs shows that the proposed method is highly effective for uncertainty quantification, achieving substantial improvements over rivaling approaches.

Predicting the dependencies between observations from multiple time series is critical for applications such as anomaly detection, financial risk management, causal analysis, or demand forecasting. However, the computational and numerical difficulties of estimating time-varying and high-dimensional covariance matrices often limits existing methods to handling at most a few hundred dimensions or requires making strong assumptions on the dependence between series. We propose to combine an RNN-based time series model with a Gaussian copula process output model with a low-rank covariance structure to reduce the computational complexity and handle non-Gaussian marginal distributions. This permits to drastically reduce the number of parameters and consequently allows the modeling of time-varying correlations of thousands of time series. We show on several real-world datasets that our method provides significant accuracy improvements over state-of-the-art baselines and perform an ablation study analyzing the contributions of the different components of our model.

Coopetition refers to simultaneous cooperation and competition among actors wherein actors 'cooperate to grow the pie and compete to split it up.' Modern socio-technical systems are characterized by strategic coopetition wherein actors concomitantly cooperate to create value and compete to capture it. While conceptual modeling languages such as i* provide rich qualitative representations of strategic dependencies, they lack mechanisms for quantitative analysis of dynamic trade-offs. Conversely, classical game theory offers mathematical rigor but strips away contextual richness. This report bridges this gap by developing computational foundations that formalize two critical dimensions of coopetition: interdependence and complementarity. We ground interdependence in i* structural dependency analysis, translating depender-dependee-dependum relationships into quantitative interdependence coefficients via a structured translation framework. We formalize complementarity following Brandenburger and Nalebuff's Added Value concept, modeling synergistic value creation with validated parameterization. We integrate structural dependencies with bargaining power in value appropriation and introduce a game-theoretic formulation where Nash Equilibrium incorporates structural interdependence. Validation combines over 22,000 experimental trials across power and logarithmic specifications with the Samsung-Sony S-LCD joint venture (2004-2011). Under strict historical alignment scoring, logarithmic specifications achieve 58/60 compared to power functions (46/60), producing realistic 41% cooperation increases aligning with documented S-LCD patterns while power functions produce 166% increases exceeding realistic bounds. Statistical significance confirmed at p < 0.001, Cohen's d > 9.

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

Large language models have achieved striking results in interactive theorem proving, particularly in Lean. However, most benchmarks for LLM-based proof automation are drawn from mathematics in the Mathlib ecosystem, whereas proofs in software verification are developed inside definition-rich codebases with substantial project-specific libraries. We introduce VeriSoftBench, a benchmark of 500 Lean 4 proof obligations drawn from open-source formal-methods developments and packaged to preserve realistic repository context and cross-file dependencies. Our evaluation of frontier LLMs and specialized provers yields three observations. First, provers tuned for Mathlib-style mathematics transfer poorly to this repository-centric setting. Second, success is strongly correlated with transitive repository dependence: tasks whose proofs draw on large, multi-hop dependency closures are less likely to be solved. Third, providing curated context restricted to a proof's dependency closure improves performance relative to exposing the full repository, but nevertheless leaves substantial room for improvement. Our benchmark and evaluation suite are released at https://github.com/utopia-group/VeriSoftBench.

Application Programming Interfaces (APIs) facilitate the integration of third-party dependencies within the code of client applications. However, changes to an API, such as deprecation, modification of parameter names or types, or complete replacement with a new API, can break existing client code. These changes are called breaking dependency updates; It is often tedious for API users to identify the cause of these breaks and update their code accordingly. In this paper, we explore the use of Large Language Models (LLMs) to automate client code updates in response to breaking dependency updates. We evaluate our approach on the BUMP dataset, a benchmark for breaking dependency updates in Java projects. Our approach leverages LLMs with advanced prompts, including information from the build process and from the breaking dependency analysis. We assess effectiveness at three granularity levels: at the build level, the file level, and the individual compilation error level. We experiment with five LLMs: Google Gemini-2.0 Flash, OpenAI GPT4o-mini, OpenAI o3-mini, Alibaba Qwen2.5-32b-instruct, and DeepSeek V3. Our results show that LLMs can automatically repair breaking updates. Among the considered models, OpenAI's o3-mini is the best, able to completely fix 27% of the builds when using prompts that include contextual information such as the buggy line, API differences, error messages, and step-by-step reasoning instructions. Also, it fixes 78% of the individual compilation errors. Overall, our findings demonstrate the potential for LLMs to fix compilation errors due to breaking dependency updates, supporting developers in their efforts to stay up-to-date with changes in their dependencies.

Self-supervised representation learning has shown remarkable success in a number of domains. A common practice is to perform data augmentation via hand-crafted transformations intended to leave the semantics of the data invariant. We seek to understand the empirical success of this approach from a theoretical perspective. We formulate the augmentation process as a latent variable model by postulating a partition of the latent representation into a content component, which is assumed invariant to augmentation, and a style component, which is allowed to change. Unlike prior work on disentanglement and independent component analysis, we allow for both nontrivial statistical and causal dependencies in the latent space. We study the identifiability of the latent representation based on pairs of views of the observations and prove sufficient conditions that allow us to identify the invariant content partition up to an invertible mapping in both generative and discriminative settings. We find numerical simulations with dependent latent variables are consistent with our theory. Lastly, we introduce Causal3DIdent, a dataset of high-dimensional, visually complex images with rich causal dependencies, which we use to study the effect of data augmentations performed in practice.

We present Probabilistic Structure Integration (PSI), a system for learning richly controllable and flexibly promptable world models from data. PSI consists of a three-step cycle. The first step, Probabilistic prediction, involves building a probabilistic graphical model Psi of the data, in the form of a random-access autoregressive sequence model. Psi supports a complete set of learned conditional distributions describing the dependence of any variables in the data on any other set of variables. In step 2, Structure extraction, we show how to extract underlying low-dimensional properties in the data, corresponding to a diverse set of meaningful "intermediate structures", in a zero-shot fashion via causal inference on Psi. Step 3, Integration, completes the cycle by converting these structures into new token types that are then continually mixed back into the training diet as conditioning signals and prediction targets. Each such cycle augments the capabilities of Psi, both allowing it to model the underlying data better, and creating new control handles -- akin to an LLM-like universal prompting language. We train an instance of Psi on 1.4 trillion tokens of internet video data; we use it to perform a variety of useful video prediction and understanding inferences; we extract state-of-the-art optical flow, self-supervised depth and object segmentation; and we use these structures to support a full cycle of predictive improvements.

Tests that cause spurious failures without any code changes, i.e., flaky tests, hamper regression testing, increase maintenance costs, may shadow real bugs, and decrease trust in tests. While the prevalence and importance of flakiness is well established, prior research focused on Java projects, thus raising the question of how the findings generalize. In order to provide a better understanding of the role of flakiness in software development beyond Java, we empirically study the prevalence, causes, and degree of flakiness within software written in Python, one of the currently most popular programming languages. For this, we sampled 22352 open source projects from the popular PyPI package index, and analyzed their 876186 test cases for flakiness. Our investigation suggests that flakiness is equally prevalent in Python as it is in Java. The reasons, however, are different: Order dependency is a much more dominant problem in Python, causing 59% of the 7571 flaky tests in our dataset. Another 28% were caused by test infrastructure problems, which represent a previously undocumented cause of flakiness. The remaining 13% can mostly be attributed to the use of network and randomness APIs by the projects, which is indicative of the type of software commonly written in Python. Our data also suggests that finding flaky tests requires more runs than are often done in the literature: A 95% confidence that a passing test case is not flaky on average would require 170 reruns.

With the availability of various instruction datasets, a pivotal challenge is how to effectively select and integrate these instructions to fine-tune large language models (LLMs). Previous research mainly focuses on selecting individual high-quality instructions. However, these works overlooked the joint interactions and dependencies between different categories of instructions, leading to suboptimal selection strategies. Moreover, the nature of these interaction patterns remains largely unexplored, let alone optimize the instruction set with regard to them. To fill these gaps, in this paper, we: (1) systemically investigate interaction and dependency patterns between different categories of instructions, (2) manage to optimize the instruction set concerning the interaction patterns using a linear programming-based method, and optimize the learning schema of SFT using an instruction dependency taxonomy guided curriculum learning. Experimental results across different LLMs demonstrate improved performance over strong baselines on widely adopted benchmarks.

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

This article studies the change in the prediction accuracy of a response variable when the number of predictors increases, and all variables follow a multivariate normal distribution. Assuming that the correlations between variables are independently drawn, I show that adding variables leads to globally increasing returns to scale when the mean of the correlation distribution is zero. The speed of learning depends positively on the variance of the correlation distribution. I use simulations to study the more complex case of correlation distributions with a non-zero mean and find a pattern of decreasing returns followed by increasing returns to scale - as long as the variance of correlations is not degenerate, in which case globally decreasing returns emerge. I train a collaborative filtering algorithm using the MovieLens 1M dataset to analyze returns from adding variables in a more realistic setting and find globally increasing returns to scale across 2,000 variables. The results suggest significant scale advantages from additional variables in prediction tasks.

The rise of large language models (LLMs) has enabled LLM-based applications (a.k.a. AI agents or co-pilots), a new software paradigm that combines the strength of LLM and conventional software. Diverse LLM applications from different tenants could design complex workflows using multiple LLM requests to accomplish one task. However, they have to use the over-simplified request-level API provided by today's public LLM services, losing essential application-level information. Public LLM services have to blindly optimize individual LLM requests, leading to sub-optimal end-to-end performance of LLM applications. This paper introduces Parrot, an LLM service system that focuses on the end-to-end experience of LLM-based applications. Parrot proposes Semantic Variable, a unified abstraction to expose application-level knowledge to public LLM services. A Semantic Variable annotates an input/output variable in the prompt of a request, and creates the data pipeline when connecting multiple LLM requests, providing a natural way to program LLM applications. Exposing Semantic Variables to the public LLM service allows it to perform conventional data flow analysis to uncover the correlation across multiple LLM requests. This correlation opens a brand-new optimization space for the end-to-end performance of LLM-based applications. Extensive evaluations demonstrate that Parrot can achieve up to an order-of-magnitude improvement for popular and practical use cases of LLM applications.

The presence of distribution shifts poses a significant challenge for deploying modern machine learning models in real-world applications. This work focuses on the target shift problem in a regression setting (Zhang et al., 2013; Nguyen et al., 2016). More specifically, the target variable y (also known as the response variable), which is continuous, has different marginal distributions in the training source and testing domain, while the conditional distribution of features x given y remains the same. While most literature focuses on classification tasks with finite target space, the regression problem has an infinite dimensional target space, which makes many of the existing methods inapplicable. In this work, we show that the continuous target shift problem can be addressed by estimating the importance weight function from an ill-posed integral equation. We propose a nonparametric regularized approach named ReTaSA to solve the ill-posed integral equation and provide theoretical justification for the estimated importance weight function. The effectiveness of the proposed method has been demonstrated with extensive numerical studies on synthetic and real-world datasets.

Dependency tree structures capture long-distance and syntactic relationships between words in a sentence. The syntactic relations (e.g., nominal subject, object) can potentially infer the existence of certain named entities. In addition, the performance of a named entity recognizer could benefit from the long-distance dependencies between the words in dependency trees. In this work, we propose a simple yet effective dependency-guided LSTM-CRF model to encode the complete dependency trees and capture the above properties for the task of named entity recognition (NER). The data statistics show strong correlations between the entity types and dependency relations. We conduct extensive experiments on several standard datasets and demonstrate the effectiveness of the proposed model in improving NER and achieving state-of-the-art performance. Our analysis reveals that the significant improvements mainly result from the dependency relations and long-distance interactions provided by dependency trees.

Spurious correlations allow flexible models to predict well during training but poorly on related test distributions. Recent work has shown that models that satisfy particular independencies involving correlation-inducing nuisance variables have guarantees on their test performance. Enforcing such independencies requires nuisances to be observed during training. However, nuisances, such as demographics or image background labels, are often missing. Enforcing independence on just the observed data does not imply independence on the entire population. Here we derive mmd estimators used for invariance objectives under missing nuisances. On simulations and clinical data, optimizing through these estimates achieves test performance similar to using estimators that make use of the full data.

In discriminative settings such as regression and classification there are two random variables at play, the inputs X and the targets Y. Here, we demonstrate that the Variational Information Bottleneck can be viewed as a compromise between fully empirical and fully Bayesian objectives, attempting to minimize the risks due to finite sampling of Y only. We argue that this approach provides some of the benefits of Bayes while requiring only some of the work.

A central premise in mechanistic interpretability is that meaningful concepts in language models are represented by linear features in activation space. For such features to support reliable interventions, manipulating one feature should not substantially alter the effects of others. In practice, however, feature entanglement leads to interference such that localized interventions can have unintended downstream effects. Motivated by the Independent Causal Mechanisms principle, we propose to constrain internal features to be almost orthogonal. We argue that this promotes modular representations amenable to causal intervention. We formalize this problem by characterizing the gap between an idealized isolated intervention and its realized effect on model outputs in terms of feature interference. We upper-bound the propagation of feature interference in terms of the self-coherence of the feature dictionary, and relate this discrepancy to an explicit orthogonality regularization on the dictionary itself. Empirically, we show that this regularization enables more isolated interventions on mathematical reasoning concepts while preserving model performance. Our code is available under https://github.com/mrtzmllr/sae-icm.

Large language models (LLMs) can reliably distinguish grammatical from ungrammatical sentences, but how grammatical knowledge is represented within the models remains an open question. We investigate whether different syntactic phenomena recruit shared or distinct components in LLMs. Using a functional localization approach inspired by cognitive neuroscience, we identify the LLM units most responsive to 67 English syntactic phenomena in seven open-weight models. These units are consistently recruited across sentences containing the phenomena and causally support the models' syntactic performance. Critically, different types of syntactic agreement (e.g., subject-verb, anaphor, determiner-noun) recruit overlapping sets of units, suggesting that agreement constitutes a meaningful functional category for LLMs. This pattern holds in English, Russian, and Chinese; and further, in a cross-lingual analysis of 57 diverse languages, structurally more similar languages share more units for subject-verb agreement. Taken together, these findings reveal that syntactic agreement-a critical marker of syntactic dependencies-constitutes a meaningful category within LLMs' representational spaces.

Supervised multi-modal learning involves mapping multiple modalities to a target label. Previous studies in this field have concentrated on capturing in isolation either the inter-modality dependencies (the relationships between different modalities and the label) or the intra-modality dependencies (the relationships within a single modality and the label). We argue that these conventional approaches that rely solely on either inter- or intra-modality dependencies may not be optimal in general. We view the multi-modal learning problem from the lens of generative models where we consider the target as a source of multiple modalities and the interaction between them. Towards that end, we propose inter- & intra-modality modeling (I2M2) framework, which captures and integrates both the inter- and intra-modality dependencies, leading to more accurate predictions. We evaluate our approach using real-world healthcare and vision-and-language datasets with state-of-the-art models, demonstrating superior performance over traditional methods focusing only on one type of modality dependency.

Gradients can be employed for sensitivity analysis. Here, we leverage the advantages of the Loss Landscape to comprehend which independent variables impact the dependent variable. We seek to grasp the loss landscape by utilizing first, second, and third derivatives through automatic differentiation. we know that Spearman's rank correlation coefficient can detect the monotonic relationship between two variables. However, I have found that second-order gradients, with certain configurations and parameters, provide information that can be visualized similarly to Spearman results, In this approach, we incorporate a loss function with an activation function, resulting in a non-linear pattern. Each exploration of the loss landscape through retraining yields new valuable information. Furthermore, the first and third derivatives are also beneficial, as they indicate the extent to which independent variables influence the dependent variable.

The success of long short-term memory (LSTM) neural networks in language processing is typically attributed to their ability to capture long-distance statistical regularities. Linguistic regularities are often sensitive to syntactic structure; can such dependencies be captured by LSTMs, which do not have explicit structural representations? We begin addressing this question using number agreement in English subject-verb dependencies. We probe the architecture's grammatical competence both using training objectives with an explicit grammatical target (number prediction, grammaticality judgments) and using language models. In the strongly supervised settings, the LSTM achieved very high overall accuracy (less than 1% errors), but errors increased when sequential and structural information conflicted. The frequency of such errors rose sharply in the language-modeling setting. We conclude that LSTMs can capture a non-trivial amount of grammatical structure given targeted supervision, but stronger architectures may be required to further reduce errors; furthermore, the language modeling signal is insufficient for capturing syntax-sensitive dependencies, and should be supplemented with more direct supervision if such dependencies need to be captured.

There has been a recent surge of interest in time series modeling using the Transformer architecture. However, forecasting multivariate time series with Transformer presents a unique challenge as it requires modeling both temporal (cross-time) and variate (cross-variate) dependencies. While Transformer-based models have gained popularity for their flexibility in capturing both sequential and cross-variate relationships, it is unclear how to best integrate these two sources of information in the context of the Transformer architecture while optimizing for both performance and efficiency. We re-purpose the Transformer architecture to effectively model both cross-time and cross-variate dependencies. Our approach begins by embedding each variate independently into a variate-wise representation that captures its cross-time dynamics, and then models cross-variate dependencies through attention mechanisms on these learned embeddings. Gating operations in both cross-time and cross-variate modeling phases regulate information flow, allowing the model to focus on the most relevant features for accurate predictions. Our method achieves state-of-the-art performance across 13 real-world datasets and can be seamlessly integrated into other Transformer-based and LLM-based forecasters, delivering performance improvements up to 20.7\% over original models. Code is available at this repository: https://github.com/nyuolab/Gateformer.

Dynamic languages (such as Python and JavaScript) offer flexibility and simplified type handling for programming, but this can also lead to an increase in type-related errors and additional overhead for compile-time type inference. As a result, type inference for dynamic languages has become a popular research area. Existing approaches typically achieve type inference through static analysis, machine learning, or large language models (LLMs). However, current work only focuses on the direct dependencies of variables related to type inference as the context, resulting in incomplete contextual information and thus affecting the accuracy of type inference. To address this issue, this paper proposes a method called TypePro, which leverages LLMs for type inference in dynamic languages. TypePro supplements contextual information by conducting inter-procedural code slicing. Then, TypePro proposes a set of candidate complex types based on the structural information of data types implied in the slices, thereby addressing the lack of domain knowledge of LLMs. We conducted experiments on the ManyTypes4Py and ManyTypes4TypeScript datasets, achieving Top-1 exact match (EM) rates of 88.9% and 86.6%, respectively. Notably, TypePro improves the Top-1 Exact Match by 7.1 and 10.3 percentage points over the second-best approach, showing the effectiveness and robustness of TypePro.

Independence testing is a fundamental and classical statistical problem that has been extensively studied in the batch setting when one fixes the sample size before collecting data. However, practitioners often prefer procedures that adapt to the complexity of a problem at hand instead of setting sample size in advance. Ideally, such procedures should (a) allow stopping earlier on easy tasks (and later on harder tasks), hence making better use of available resources, and (b) continuously monitor the data and efficiently incorporate statistical evidence after collecting new data, while controlling the false alarm rate. It is well known that classical batch tests are not tailored for streaming data settings: valid inference after data peeking requires correcting for multiple testing but such corrections generally result in low power. Following the principle of testing by betting, we design sequential kernelized independence tests (SKITs) that overcome such shortcomings. We exemplify our broad framework using bets inspired by kernelized dependence measures, e.g, the Hilbert-Schmidt independence criterion. Our test is valid under non-i.i.d. time-varying settings, for which there exist no batch tests. We demonstrate the power of our approaches on both simulated and real data.

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix. For compositional data, the covariance structure is specified from log ratios of variables, so unless we try to "open" the data via a normalization, this implies changes in the definition and interpretation of partial correlations. In the present work, we elucidate how results derived by Aitchison (1986) lead to a natural definition of partial correlation that has a number of advantages over current measures of association. For this, we show that the residuals of log-ratios between a variable with a reference, when adjusting for all remaining variables including the reference, are reference-independent. Since the reference itself can be controlled for, correlations between residuals are defined for the variables directly without the necessity to recur to ratios except when specifying which variables are partialled out. Thus, perhaps surprisingly, partial correlations do not have the problems commonly found with measures of pairwise association on compositional data. They are well-defined between two variables, are properly scaled, and allow for negative association. By design, they are subcompositionally incoherent, but they share this property with conventional partial correlations (where results change when adjusting for the influence of fewer variables). We discuss the equivalence with normalization-based approaches whenever the normalizing variables are controlled for. We also discuss the partial variances and correlations we obtain from a previously studied data set of Roman glass cups.

Stochastic gradient Markov Chain Monte Carlo (SGMCMC) is considered the gold standard for Bayesian inference in large-scale models, such as Bayesian neural networks. Since practitioners face speed versus accuracy tradeoffs in these models, variational inference (VI) is often the preferable option. Unfortunately, VI makes strong assumptions on both the factorization and functional form of the posterior. In this work, we propose a new non-parametric variational approximation that makes no assumptions about the approximate posterior's functional form and allows practitioners to specify the exact dependencies the algorithm should respect or break. The approach relies on a new Langevin-type algorithm that operates on a modified energy function, where parts of the latent variables are averaged over samples from earlier iterations of the Markov chain. This way, statistical dependencies can be broken in a controlled way, allowing the chain to mix faster. This scheme can be further modified in a "dropout" manner, leading to even more scalability. We test our scheme for ResNet-20 on CIFAR-10, SVHN, and FMNIST. In all cases, we find improvements in convergence speed and/or final accuracy compared to SG-MCMC and VI.

Given only observational data X = g(Z), where both the latent variables Z and the generating process g are unknown, recovering Z is ill-posed without additional assumptions. Existing methods often assume linearity or rely on auxiliary supervision and functional constraints. However, such assumptions are rarely verifiable in practice, and most theoretical guarantees break down under even mild violations, leaving uncertainty about how to reliably understand the hidden world. To make identifiability actionable in the real-world scenarios, we take a complementary view: in the general settings where full identifiability is unattainable, what can still be recovered with guarantees, and what biases could be universally adopted? We introduce the problem of diverse dictionary learning to formalize this view. Specifically, we show that intersections, complements, and symmetric differences of latent variables linked to arbitrary observations, along with the latent-to-observed dependency structure, are still identifiable up to appropriate indeterminacies even without strong assumptions. These set-theoretic results can be composed using set algebra to construct structured and essential views of the hidden world, such as genus-differentia definitions. When sufficient structural diversity is present, they further imply full identifiability of all latent variables. Notably, all identifiability benefits follow from a simple inductive bias during estimation that can be readily integrated into most models. We validate the theory and demonstrate the benefits of the bias on both synthetic and real-world data.

In this work we show how large language models (LLMs) can learn statistical dependencies between otherwise unconditionally independent variables due to dataset selection bias. To demonstrate the effect, we developed a masked gender task that can be applied to BERT-family models to reveal spurious correlations between predicted gender pronouns and a variety of seemingly gender-neutral variables like date and location, on pre-trained (unmodified) BERT and RoBERTa large models. Finally, we provide an online demo, inviting readers to experiment further.

Visual Auto-Regressive (VAR) models significantly reduce inference steps through the "next-scale" prediction paradigm. However, progressive multi-scale generation incurs substantial memory overhead due to cumulative KV caching, limiting practical deployment. We observe a scale-depth asymmetric dependency in VAR: early scales exhibit extreme sensitivity to network depth, while later scales remain robust to depth reduction. Inspired by this, we propose VARiant: by equidistant sampling, we select multiple subnets ranging from 16 to 2 layers from the original 30-layer VAR-d30 network. Early scales are processed by the full network, while later scales utilize subnet. Subnet and the full network share weights, enabling flexible depth adjustment within a single model. However, weight sharing between subnet and the entire network can lead to optimization conflicts. To address this, we propose a progressive training strategy that breaks through the Pareto frontier of generation quality for both subnets and the full network under fixed-ratio training, achieving joint optimality. Experiments on ImageNet demonstrate that, compared to the pretrained VAR-d30 (FID 1.95), VARiant-d16 and VARiant-d8 achieve nearly equivalent quality (FID 2.05/2.12) while reducing memory consumption by 40-65%. VARiant-d2 achieves 3.5 times speedup and 80% memory reduction at moderate quality cost (FID 2.97). In terms of deployment, VARiant's single-model architecture supports zero-cost runtime depth switching and provides flexible deployment options from high quality to extreme efficiency, catering to diverse application scenarios.

Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.

Neural posterior estimation has emerged as a powerful tool for amortized inference, with growing adoption across scientific and applied domains. In many of these applications, the conditioning variable is a set of observations whose elements depend not only on the target but also on unknown factors shared across the set. Optimal inference therefore requires treating the set jointly, which in turn requires training the estimator at the deployment set size -- a regime where memory and compute quickly become prohibitive. We introduce a simple, theoretically grounded strategy that decouples representation learning from posterior modeling. Our method trains a mean-pool Deep Set on sets of size at most two, producing an encoder that generalizes to arbitrary set sizes. The inference head is then finetuned on pre-aggregated embeddings, making training cost essentially independent of the deployment set size N. Across scalar, image, multi-view 3D, molecular, and high-dimensional conditional generation benchmarks with N in the thousands, our approach matches or outperforms standard baselines at a fraction of the compute.

Benchmarks measure whether a model is correct. They do not measure whether a model is reliable. This distinction is largely academic for single-shot inference, but becomes critical for agentic AI systems, where a single rephrased prompt can trigger cascading failures in multi-step execution. Yet this form of instability is not captured by existing evaluations. Hallucinations live in variance: they arise when semantically equivalent prompts activate inconsistent internal pathways, producing divergent outputs. Consistent but incorrect outputs reflect bias or missing knowledge; confident guessing reflects calibration failure. Neither constitutes hallucination under this definition. When error is variance-dominated, reducing redundant pathways improves reliability without adding knowledge. We formalize this through Semantic Stability (SS), measured via Paraphrase Consistency (PC@k): generate k paraphrases, greedy decode each, compute mode agreement. SS is a diagnostic for variance-driven unreliability, not a method for improving correctness. We show that a dense Qwen3-0.6B agrees with itself only 23.8% of the time; at 32% sparsity, agreement jumps to 55.9%. A phase diagram reveals the sweet spot where variance reduction outpaces bias accumulation, and regimes where stability collapses onto wrong answers.

Causal discovery, i.e., inferring underlying cause-effect relationships from observations of a scene or system, is an inherent mechanism in human cognition, but has been shown to be highly challenging to automate. The majority of approaches in the literature aiming for this task consider constrained scenarios with fully observed variables or data from stationary time-series. In this work we aim for causal discovery in a more general class of scenarios, scenes with non-stationary behavior over time. For our purposes we here regard a scene as a composition objects interacting with each other over time. Non-stationarity is modeled as stationarity conditioned on an underlying variable, a state, which can be of varying dimension, more or less hidden given observations of the scene, and also depend more or less directly on these observations. We propose a probabilistic deep learning approach called State-Dependent Causal Inference (SDCI) for causal discovery in such conditionally stationary time-series data. Results in two different synthetic scenarios show that this method is able to recover the underlying causal dependencies with high accuracy even in cases with hidden states.

We propose a statistical framework built on latent variable modeling for scaling laws of large language models (LLMs). Our work is motivated by the rapid emergence of numerous new LLM families with distinct architectures and training strategies, evaluated on an increasing number of benchmarks. This heterogeneity makes a single global scaling curve inadequate for capturing how performance varies across families and benchmarks. To address this, we propose a latent variable modeling framework in which each LLM family is associated with a latent variable that captures the common underlying features in that family. An LLM's performance on different benchmarks is then driven by its latent skills, which are jointly determined by the latent variable and the model's own observable features. We develop an estimation procedure for this latent variable model and establish its statistical properties. We also design efficient numerical algorithms that support estimation and various downstream tasks. Empirically, we evaluate the approach on 12 widely used benchmarks from the Open LLM Leaderboard (v1/v2).

Powerful generative models, particularly in Natural Language Modelling, are commonly trained by maximizing a variational lower bound on the data log likelihood. These models often suffer from poor use of their latent variable, with ad-hoc annealing factors used to encourage retention of information in the latent variable. We discuss an alternative and general approach to latent variable modelling, based on an objective that combines the data log likelihood as well as the likelihood of a perfect reconstruction through an autoencoder. Tying these together ensures by design that the latent variable captures information about the observations, whilst retaining the ability to generate well. Interestingly, though this approach is a priori unrelated to VAEs, the lower bound attained is identical to the standard VAE bound but with the addition of a simple pre-factor; thus, providing a formal interpretation of the commonly used, ad-hoc pre-factors in training VAEs.

The variational autoencoder (VAE; Kingma, Welling (2014)) is a recently proposed generative model pairing a top-down generative network with a bottom-up recognition network which approximates posterior inference. It typically makes strong assumptions about posterior inference, for instance that the posterior distribution is approximately factorial, and that its parameters can be approximated with nonlinear regression from the observations. As we show empirically, the VAE objective can lead to overly simplified representations which fail to use the network's entire modeling capacity. We present the importance weighted autoencoder (IWAE), a generative model with the same architecture as the VAE, but which uses a strictly tighter log-likelihood lower bound derived from importance weighting. In the IWAE, the recognition network uses multiple samples to approximate the posterior, giving it increased flexibility to model complex posteriors which do not fit the VAE modeling assumptions. We show empirically that IWAEs learn richer latent space representations than VAEs, leading to improved test log-likelihood on density estimation benchmarks.

Python type inference is challenging in practice. Due to its dynamic properties and extensive dependencies on third-party libraries without type annotations, the performance of traditional static analysis techniques is limited. Although semantics in source code can help manifest intended usage for variables (thus help infer types), they are usually ignored by existing tools. In this paper, we propose PYInfer, an end-to-end learning-based type inference tool that automatically generates type annotations for Python variables. The key insight is that contextual code semantics is critical in inferring the type for a variable. For each use of a variable, we collect a few tokens within its contextual scope, and design a neural network to predict its type. One challenge is that it is difficult to collect a high-quality human-labeled training dataset for this purpose. To address this issue, we apply an existing static analyzer to generate the ground truth for variables in source code. Our main contribution is a novel approach to statically infer variable types effectively and efficiently. Formulating the type inference as a classification problem, we can handle user-defined types and predict type probabilities for each variable. Our model achieves 91.2% accuracy on classifying 11 basic types in Python and 81.2% accuracy on classifying 500 most common types. Our results substantially outperform the state-of-the-art type annotators. Moreover, PYInfer achieves 5.2X more code coverage and is 187X faster than a state-of-the-art learning-based tool. With similar time consumption, our model annotates 5X more variables than a state-of-the-art static analysis tool. Our model also outperforms a learning-based function-level annotator on annotating types for variables and function arguments. All our tools and datasets are publicly available to facilitate future research in this direction.

The increasing frequency of extreme weather events due to global climate change urges accurate weather prediction. Recently, great advances have been made by the end-to-end methods, thanks to deep learning techniques, but they face limitations of representation inconsistency in multivariable integration and struggle to effectively capture the dependency between variables, which is required in complex weather systems. Treating different variables as distinct modalities and applying a two-stage training approach from multimodal models can partially alleviate this issue, but due to the inconformity in training tasks between the two stages, the results are often suboptimal. To address these challenges, we propose an implicit two-stage training method, configuring separate encoders and decoders for each variable. In detailed, in the first stage, the Translator is frozen while the Encoders and Decoders learn a shared latent space, in the second stage, the Encoders and Decoders are frozen, and the Translator captures inter-variable interactions for prediction. Besides, by introducing a self-attention mechanism for multivariable fusion in the latent space, the performance achieves further improvements. Empirically, extensive experiments show the state-of-the-art performance of our method. Specifically, it reduces the MSE for near-surface air temperature and relative humidity predictions by 28.82\% and 23.39\%, respectively. The source code is available at https://github.com/ShremG/Met2Net.

The development of generative language models that can create long and coherent textual outputs via autoregression has lead to a proliferation of uses and a corresponding sweep of analyses as researches work to determine the limitations of this new paradigm. Unlike humans, these 'Large Language Models' (LLMs) are highly sensitive to small changes in their inputs, leading to unwanted inconsistency in their behavior. One problematic inconsistency when LLMs are used to answer multiple-choice questions or analyze multiple inputs is order dependency: the output of an LLM can (and often does) change significantly when sub-sequences are swapped, despite both orderings being semantically identical. In this paper we present , a technique that guarantees the output of an LLM will not have order dependence on a specified set of sub-sequences. We show that this method provably eliminates order dependency, and that it can be applied to any transformer-based LLM to enable text generation that is unaffected by re-orderings. Delving into the implications of our method, we show that, despite our inputs being out of distribution, the impact on expected accuracy is small, where the expectation is over the order of uniformly chosen shuffling of the candidate responses, and usually significantly less in practice. Thus, can be used as a 'dropped-in' method on fully trained models. Finally, we discuss how our method's success suggests that other strong guarantees can be obtained on LLM performance via modifying the input representations.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

Predicting program behavior without execution is an essential and challenging task in software engineering. Traditional models often struggle to capture dynamic dependencies and interactions within code. This paper introduces a novel machine learning-based framework called CodeFlowrepresents, which predicts code coverage and detects runtime errors through Dynamic Dependencies Learning. Utilizing control flow graphs (CFGs), CodeFlowrepresents all possible execution paths and the relationships between different statements, offering a comprehensive understanding of program behavior. It constructs CFGs to depict execution paths and learns vector representations for CFG nodes, capturing static control-flow dependencies. Additionally, it learns dynamic dependencies through execution traces, which reflect the impacts among statements during execution. This approach enables accurate prediction of code coverage and identification of runtime errors. Empirical evaluations show significant improvements in code coverage prediction accuracy and effective localization of runtime errors, surpassing current models.

Deep latent variable models (DLVMs) are designed to learn meaningful representations in an unsupervised manner, such that the hidden explanatory factors are interpretable by independent latent variables (aka disentanglement). The variational autoencoder (VAE) is a popular DLVM widely studied in disentanglement analysis due to the modeling of the posterior distribution using a factorized Gaussian distribution that encourages the alignment of the latent factors with the latent axes. Several metrics have been proposed recently, assuming that the latent variables explaining the variation in data are aligned with the latent axes (cardinal directions). However, there are other DLVMs, such as the AAE and WAE-MMD (matching the aggregate posterior to the prior), where the latent variables might not be aligned with the latent axes. In this work, we propose a statistical method to evaluate disentanglement for any DLVMs in general. The proposed technique discovers the latent vectors representing the generative factors of a dataset that can be different from the cardinal latent axes. We empirically demonstrate the advantage of the method on two datasets.

Understanding the abilities of LLMs to reason about natural language plans, such as instructional text and recipes, is critical to reliably using them in decision-making systems. A fundamental aspect of plans is the temporal order in which their steps needs to be executed, which reflects the underlying causal dependencies between them. We introduce CaT-Bench, a benchmark of Step Order Prediction questions, which test whether a step must necessarily occur before or after another in cooking recipe plans. We use this to evaluate how well frontier LLMs understand causal and temporal dependencies. We find that SOTA LLMs are underwhelming (best zero-shot is only 0.59 in F1), and are biased towards predicting dependence more often, perhaps relying on temporal order of steps as a heuristic. While prompting for explanations and using few-shot examples improve performance, the best F1 result is only 0.73. Further, human evaluation of explanations along with answer correctness show that, on average, humans do not agree with model reasoning. Surprisingly, we also find that explaining after answering leads to better performance than normal chain-of-thought prompting, and LLM answers are not consistent across questions about the same step pairs. Overall, results show that LLMs' ability to detect dependence between steps has significant room for improvement.

Multivariate time series forecasting tasks are usually conducted in a channel-dependent (CD) way since it can incorporate more variable-relevant information. However, it may also involve a lot of irrelevant variables, and this even leads to worse performance than the channel-independent (CI) strategy. This paper combines the strengths of both strategies and proposes the Deep Graph Clustering Transformer (DGCformer) for multivariate time series forecasting. Specifically, it first groups these relevant variables by a graph convolutional network integrated with an autoencoder, and a former-latter masked self-attention mechanism is then considered with the CD strategy being applied to each group of variables while the CI one for different groups. Extensive experimental results on eight datasets demonstrate the superiority of our method against state-of-the-art models, and our code will be publicly available upon acceptance.

Inference tasks such as answer sentence selection (AS2) or fact verification are typically solved by fine-tuning transformer-based models as individual sentence-pair classifiers. Recent studies show that these tasks benefit from modeling dependencies across multiple candidate sentences jointly. In this paper, we first show that popular pre-trained transformers perform poorly when used for fine-tuning on multi-candidate inference tasks. We then propose a new pre-training objective that models the paragraph-level semantics across multiple input sentences. Our evaluation on three AS2 and one fact verification datasets demonstrates the superiority of our pre-training technique over the traditional ones for transformers used as joint models for multi-candidate inference tasks, as well as when used as cross-encoders for sentence-pair formulations of these tasks. Our code and pre-trained models are released at https://github.com/amazon-research/wqa-multi-sentence-inference .

Large Language Models (LLMs) have shown strong potential for tabular data generation by modeling textualized feature-value pairs. However, tabular data inherently exhibits sparse feature-level dependencies, where many feature interactions are structurally insignificant. This creates a fundamental mismatch as LLMs' self-attention mechanism inevitably distributes focus across all pairs, diluting attention on critical relationships, particularly in datasets with complex dependencies or semantically ambiguous features. To address this limitation, we propose GraDe (Graph-Guided Dependency Learning), a novel method that explicitly integrates sparse dependency graphs into LLMs' attention mechanism. GraDe employs a lightweight dynamic graph learning module guided by externally extracted functional dependencies, prioritizing key feature interactions while suppressing irrelevant ones. Our experiments across diverse real-world datasets demonstrate that GraDe outperforms existing LLM-based approaches by up to 12% on complex datasets while achieving competitive results with state-of-the-art approaches in synthetic data quality. Our method is minimally intrusive yet effective, offering a practical solution for structure-aware tabular data modeling with LLMs.

Tabular machine learning presents a paradox: modern models achieve state-of-the-art performance using high-dimensional (high-D), collinear, error-prone data, defying the "Garbage In, Garbage Out" mantra. To help resolve this, we synthesize principles from Information Theory, Latent Factor Models, and Psychometrics, clarifying that predictive robustness arises not solely from data cleanliness, but from the synergy between data architecture and model capacity. Partitioning predictor-space "noise" into "Predictor Error" and "Structural Uncertainty" (informational deficits from stochastic generative mappings), we prove that leveraging high-D sets of error-prone predictors asymptotically overcomes both types of noise, whereas cleaning a low-D set is fundamentally bounded by Structural Uncertainty. We demonstrate why "Informative Collinearity" (dependencies from shared latent causes) enhances reliability and convergence efficiency, and explain why increased dimensionality reduces the latent inference burden, enabling feasibility with finite samples. To address practical constraints, we propose "Proactive Data-Centric AI" to identify predictors that enable robustness efficiently. We also derive boundaries for Systematic Error Regimes and show why models that absorb "rogue" dependencies can mitigate assumption violations. Linking latent architecture to Benign Overfitting, we offer a first step towards a unified view of robustness to Outcome Error and predictor-space noise, while also delineating when traditional DCAI's focus on label cleaning remains powerful. By redefining data quality from item-level perfection to portfolio-level architecture, we provide a theoretical rationale for "Local Factories" -- learning from live, uncurated enterprise "data swamps" -- supporting a deployment paradigm shift from "Model Transfer" to "Methodology Transfer'' to overcome static generalizability limitations.

We propose a novel interpretation technique to explain the behavior of structured output models, which learn mappings between an input vector to a set of output variables simultaneously. Because of the complex relationship between the computational path of output variables in structured models, a feature can affect the value of output through other ones. We focus on one of the outputs as the target and try to find the most important features utilized by the structured model to decide on the target in each locality of the input space. In this paper, we assume an arbitrary structured output model is available as a black box and argue how considering the correlations between output variables can improve the explanation performance. The goal is to train a function as an interpreter for the target output variable over the input space. We introduce an energy-based training process for the interpreter function, which effectively considers the structural information incorporated into the model to be explained. The effectiveness of the proposed method is confirmed using a variety of simulated and real data sets.

In Open Source Software, the source code and any other resources available in a project can be viewed or reused by anyone subject to often permissive licensing restrictions. In contrast to some studies of dependency-based reuse supported via package managers, no studies of OSS-wide copy-based reuse exist. This dataset seeks to encourage the studies of OSS-wide copy-based reuse by providing copying activity data that captures whole-file reuse in nearly all OSS. To accomplish that, we develop approaches to detect copy-based reuse by developing an efficient algorithm that exploits World of Code infrastructure: a curated and cross referenced collection of nearly all open source repositories. We expect this data to enable future research and tool development that support such reuse and minimize associated risks.

The technique of data augmentation (DA) is often used in machine learning for regularization purposes to better generalize under i.i.d. settings. In this work, we present a unifying framework with topics in causal inference to make a case for the use of DA beyond just the i.i.d. setting, but for generalization across interventions as well. Specifically, we argue that when the outcome generating mechanism is invariant to our choice of DA, then such augmentations can effectively be thought of as interventions on the treatment generating mechanism itself. This can potentially help to reduce bias in causal effect estimation arising from hidden confounders. In the presence of such unobserved confounding we typically make use of instrumental variables (IVs) -- sources of treatment randomization that are conditionally independent of the outcome. However, IVs may not be as readily available as DA for many applications, which is the main motivation behind this work. By appropriately regularizing IV based estimators, we introduce the concept of IV-like (IVL) regression for mitigating confounding bias and improving predictive performance across interventions even when certain IV properties are relaxed. Finally, we cast parameterized DA as an IVL regression problem and show that when used in composition can simulate a worst-case application of such DA, further improving performance on causal estimation and generalization tasks beyond what simple DA may offer. This is shown both theoretically for the population case and via simulation experiments for the finite sample case using a simple linear example. We also present real data experiments to support our case.

Open-Source Software (OSS) vulnerabilities bring great challenges to the software security and pose potential risks to our society. Enormous efforts have been devoted into automated vulnerability detection, among which deep learning (DL)-based approaches have proven to be the most effective. However, the current labeled data present the following limitations: (1) Tangled Patches: Developers may submit code changes unrelated to vulnerability fixes within patches, leading to tangled patches. (2) Lacking Inter-procedural Vulnerabilities: The existing vulnerability datasets typically contain function-level and file-level vulnerabilities, ignoring the relations between functions, thus rendering the approaches unable to detect the inter-procedural vulnerabilities. (3) Outdated Patches: The existing datasets usually contain outdated patches, which may bias the model during training. To address the above limitations, in this paper, we propose an automated data collection framework and construct the first repository-level high-quality vulnerability dataset named ReposVul. The proposed framework mainly contains three modules: (1) A vulnerability untangling module, aiming at distinguishing vulnerability-fixing related code changes from tangled patches, in which the Large Language Models (LLMs) and static analysis tools are jointly employed. (2) A multi-granularity dependency extraction module, aiming at capturing the inter-procedural call relationships of vulnerabilities, in which we construct multiple-granularity information for each vulnerability patch, including repository-level, file-level, function-level, and line-level. (3) A trace-based filtering module, aiming at filtering the outdated patches, which leverages the file path trace-based filter and commit time trace-based filter to construct an up-to-date dataset.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Deep models have demonstrated remarkable performance in time series forecasting. However, due to the partially-observed nature of real-world applications, solely focusing on the target of interest, so-called endogenous variables, is usually insufficient to guarantee accurate forecasting. Notably, a system is often recorded into multiple variables, where the exogenous variables can provide valuable external information for endogenous variables. Thus, unlike well-established multivariate or univariate forecasting paradigms that either treat all the variables equally or ignore exogenous information, this paper focuses on a more practical setting: time series forecasting with exogenous variables. We propose a novel approach, TimeXer, to ingest external information to enhance the forecasting of endogenous variables. With deftly designed embedding layers, TimeXer empowers the canonical Transformer with the ability to reconcile endogenous and exogenous information, where patch-wise self-attention and variate-wise cross-attention are used simultaneously. Moreover, global endogenous tokens are learned to effectively bridge the causal information underlying exogenous series into endogenous temporal patches. Experimentally, TimeXer achieves consistent state-of-the-art performance on twelve real-world forecasting benchmarks and exhibits notable generality and scalability. Code is available at this repository: https://github.com/thuml/TimeXer.

Advances in neural recording present increasing opportunities to study neural activity in unprecedented detail. Latent variable models (LVMs) are promising tools for analyzing this rich activity across diverse neural systems and behaviors, as LVMs do not depend on known relationships between the activity and external experimental variables. However, progress with LVMs for neuronal population activity is currently impeded by a lack of standardization, resulting in methods being developed and compared in an ad hoc manner. To coordinate these modeling efforts, we introduce a benchmark suite for latent variable modeling of neural population activity. We curate four datasets of neural spiking activity from cognitive, sensory, and motor areas to promote models that apply to the wide variety of activity seen across these areas. We identify unsupervised evaluation as a common framework for evaluating models across datasets, and apply several baselines that demonstrate benchmark diversity. We release this benchmark through EvalAI. http://neurallatents.github.io

Dependency graph, as a heterogeneous graph representing the intrinsic relationships between different pairs of system entities, is essential to many data analysis applications, such as root cause diagnosis, intrusion detection, etc. Given a well-trained dependency graph from a source domain and an immature dependency graph from a target domain, how can we extract the entity and dependency knowledge from the source to enhance the target? One way is to directly apply a mature dependency graph learned from a source domain to the target domain. But due to the domain variety problem, directly using the source dependency graph often can not achieve good performance. Traditional transfer learning methods mainly focus on numerical data and are not applicable. In this paper, we propose ACRET, a knowledge transfer based model for accelerating dependency graph learning from heterogeneous categorical event streams. In particular, we first propose an entity estimation model to filter out irrelevant entities from the source domain based on entity embedding and manifold learning. Only the entities with statistically high correlations are transferred to the target domain. On the surviving entities, we propose a dependency construction model for constructing the unbiased dependency relationships by solving a two-constraint optimization problem. The experimental results on synthetic and real-world datasets demonstrate the effectiveness and efficiency of ACRET. We also apply ACRET to a real enterprise security system for intrusion detection. Our method is able to achieve superior detection performance at least 20 days lead lag time in advance with more than 70% accuracy.

LLM agents excel when environments are mostly static and the needed information fits in a model's context window, but they often fail in open-ended investigations where explanations must be constructed by iteratively mining evidence from massive, heterogeneous operational data. These investigations exhibit hidden dependency structure: entities interact, signals co-vary, and the importance of a fact may only become clear after other evidence is discovered. Because the context window is bounded, agents must summarize intermediate findings before their significance is known, increasing the risk of discarding key evidence. ReAct-style agents are especially brittle in this regime. Their retrieve-summarize-reason loop makes conclusions sensitive to exploration order and introduces run-to-run non-determinism, producing a reliability gap where Pass-at-k may be high but Majority-at-k remains low. Simply sampling more rollouts or generating longer reasoning traces does not reliably stabilize results, since hypotheses cannot be autonomously checked as new evidence arrives and there is no explicit mechanism for belief bookkeeping and revision. In addition, ReAct entangles semantic reasoning with controller duties such as tool orchestration and state tracking, so execution errors and plan drift degrade reasoning while consuming scarce context. We address these issues by formulating investigation as abductive reasoning over a dependency graph and proposing EoG (Explanations over Graphs), a disaggregated framework in which an LLM performs bounded local evidence mining and labeling (cause vs symptom) while a deterministic controller manages traversal, state, and belief propagation to compute a minimal explanatory frontier. On a representative ITBench diagnostics task, EoG improves both accuracy and run-to-run consistency over ReAct baselines, including a 7x average gain in Majority-at-k entity F1.

Supervised learning datasets may contain multiple cues that explain the training set equally well, i.e., learning any of them would lead to the correct predictions on the training data. However, many of them can be spurious, i.e., lose their predictive power under a distribution shift and consequently fail to generalize to out-of-distribution (OOD) data. Recently developed "diversification" methods (Lee et al., 2023; Pagliardini et al., 2023) approach this problem by finding multiple diverse hypotheses that rely on different features. This paper aims to study this class of methods and identify the key components contributing to their OOD generalization abilities. We show that (1) diversification methods are highly sensitive to the distribution of the unlabeled data used for diversification and can underperform significantly when away from a method-specific sweet spot. (2) Diversification alone is insufficient for OOD generalization. The choice of the used learning algorithm, e.g., the model's architecture and pretraining, is crucial. In standard experiments (classification on Waterbirds and Office-Home datasets), using the second-best choice leads to an up to 20\% absolute drop in accuracy. (3) The optimal choice of learning algorithm depends on the unlabeled data and vice versa i.e. they are co-dependent. (4) Finally, we show that, in practice, the above pitfalls cannot be alleviated by increasing the number of diverse hypotheses, the major feature of diversification methods. These findings provide a clearer understanding of the critical design factors influencing the OOD generalization abilities of diversification methods. They can guide practitioners in how to use the existing methods best and guide researchers in developing new, better ones.

In image generation, Multiple Latent Variable Generative Models (MLVGMs) employ multiple latent variables to gradually shape the final images, from global characteristics to finer and local details (e.g., StyleGAN, NVAE), emerging as powerful tools for diverse applications. Yet their generative dynamics remain only empirically observed, without a systematic understanding of each latent variable's impact. In this work, we propose a novel framework that quantifies the contribution of each latent variable using Mutual Information (MI) as a metric. Our analysis reveals that current MLVGMs often underutilize some latent variables, and provides actionable insights for their use in downstream applications. With this foundation, we introduce a method for generating synthetic data for Self-Supervised Contrastive Representation Learning (SSCRL). By leveraging the hierarchical and disentangled variables of MLVGMs, our approach produces diverse and semantically meaningful views without the need for real image data. Additionally, we introduce a Continuous Sampling (CS) strategy, where the generator dynamically creates new samples during SSCRL training, greatly increasing data variability. Our comprehensive experiments demonstrate the effectiveness of these contributions, showing that MLVGMs' generated views compete on par with or even surpass views generated from real data. This work establishes a principled approach to understanding and exploiting MLVGMs, advancing both generative modeling and self-supervised learning. Code and pre-trained models at: https://github.com/SerezD/mi_ml_gen.

Large Language Models (LLMs) have emerged as powerful sources of evidence for linguists seeking to develop theories of syntax. In this paper, we argue that causal interpretability methods, applied to LLMs, can greatly enhance the value of such evidence by helping us characterize the abstract mechanisms that LLMs learn to use. Our empirical focus is a set of English filler-gap dependency constructions (e.g., questions, relative clauses). Linguistic theories largely agree that these constructions share many properties. Using experiments based in Distributed Interchange Interventions, we show that LLMs converge on similar abstract analyses of these constructions. These analyses also reveal previously overlooked factors -- relating to frequency, filler type, and surrounding context -- that could motivate changes to standard linguistic theory. Overall, these results suggest that mechanistic, internal analyses of LLMs can push linguistic theory forward.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Variable-order Markov models generate sequences over a finite alphabet by conditioning each symbol on the longest available suffix of the generated history. Regular constraints, by contrast, describe finite-horizon control requirements by an automaton: fixed positions, forced endings, metrical patterns, and forbidden copied fragments are all special cases. Existing exact methods already handle regular constraints with belief propagation for first-order Markov chains. The contribution here is the variable-order extension: identifying the state space on which the existing BP-regular machinery must be run when the generator is a variable-order/backoff model. A first-order constraint layer can enforce useful support conditions, but it computes future mass after merging histories that a variable-order generator deliberately keeps distinct. We formalize this mismatch and give the sparse construction obtained by replacing the first-order Markov state with the observed context state, then taking the standard product with the regular constraint automaton. For a fixed trained context graph and automaton, inference is linear in the sequence horizon; in general it is polynomial in the number of reachable product edges. This gives the correct variable-order distribution conditioned on regular constraints without expanding to all K-tuples. The same finite-source interface supports reversible data augmentation by inverse count lookup, matching materialized transposition augmentation without storing transformed corpora. We also separate exact BP inference from generation-time backoff policies, such as singleton avoidance, whose stochastic semantics must be made explicit if exactness is claimed.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

Automated detection of software vulnerabilities is a fundamental problem in software security. Existing program analysis techniques either suffer from high false positives or false negatives. Recent progress in Deep Learning (DL) has resulted in a surge of interest in applying DL for automated vulnerability detection. Several recent studies have demonstrated promising results achieving an accuracy of up to 95% at detecting vulnerabilities. In this paper, we ask, "how well do the state-of-the-art DL-based techniques perform in a real-world vulnerability prediction scenario?". To our surprise, we find that their performance drops by more than 50%. A systematic investigation of what causes such precipitous performance drop reveals that existing DL-based vulnerability prediction approaches suffer from challenges with the training data (e.g., data duplication, unrealistic distribution of vulnerable classes, etc.) and with the model choices (e.g., simple token-based models). As a result, these approaches often do not learn features related to the actual cause of the vulnerabilities. Instead, they learn unrelated artifacts from the dataset (e.g., specific variable/function names, etc.). Leveraging these empirical findings, we demonstrate how a more principled approach to data collection and model design, based on realistic settings of vulnerability prediction, can lead to better solutions. The resulting tools perform significantly better than the studied baseline: up to 33.57% boost in precision and 128.38% boost in recall compared to the best performing model in the literature. Overall, this paper elucidates existing DL-based vulnerability prediction systems' potential issues and draws a roadmap for future DL-based vulnerability prediction research. In that spirit, we make available all the artifacts supporting our results: https://git.io/Jf6IA.

Large Language Models (LLMs) can interact with the real world by connecting with versatile external APIs, resulting in better problem-solving and task automation capabilities. Previous research primarily focuses on APIs with limited arguments from a single source or overlooks the complex dependency relationship between different APIs. However, it is essential to utilize multiple APIs collaboratively from various sources (e.g., different Apps in the iPhone), especially for complex user instructions. In this paper, we introduce AppBench, the first benchmark to evaluate LLMs' ability to plan and execute multiple APIs from various sources in order to complete the user's task. Specifically, we consider two significant challenges in multiple APIs: 1) graph structures: some APIs can be executed independently while others need to be executed one by one, resulting in graph-like execution order; and 2) permission constraints: which source is authorized to execute the API call. We have experimental results on 9 distinct LLMs; e.g., GPT-4o achieves only a 2.0\% success rate at the most complex instruction, revealing that the existing state-of-the-art LLMs still cannot perform well in this situation even with the help of in-context learning and finetuning. Our code and data are publicly available at https://github.com/ruleGreen/AppBench.

Autoregressive models excel in modeling sequential dependencies by enforcing causal constraints, yet they struggle to capture complex bidirectional patterns due to their unidirectional nature. In contrast, mask-based models leverage bidirectional context, enabling richer dependency modeling. However, they often assume token independence during prediction, which undermines the modeling of sequential dependencies. Additionally, the corruption of sequences through masking or absorption can introduce unnatural distortions, complicating the learning process. To address these issues, we propose Bidirectional Autoregressive Diffusion (BAD), a novel approach that unifies the strengths of autoregressive and mask-based generative models. BAD utilizes a permutation-based corruption technique that preserves the natural sequence structure while enforcing causal dependencies through randomized ordering, enabling the effective capture of both sequential and bidirectional relationships. Comprehensive experiments show that BAD outperforms autoregressive and mask-based models in text-to-motion generation, suggesting a novel pre-training strategy for sequence modeling. The codebase for BAD is available on https://github.com/RohollahHS/BAD.