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Jul 9

AGBD: A Global-scale Biomass Dataset

Accurate estimates of Above Ground Biomass (AGB) are essential in addressing two of humanity's biggest challenges, climate change and biodiversity loss. Existing datasets for AGB estimation from satellite imagery are limited. Either they focus on specific, local regions at high resolution, or they offer global coverage at low resolution. There is a need for a machine learning-ready, globally representative, high-resolution benchmark. Our findings indicate significant variability in biomass estimates across different vegetation types, emphasizing the necessity for a dataset that accurately captures global diversity. To address these gaps, we introduce a comprehensive new dataset that is globally distributed, covers a range of vegetation types, and spans several years. This dataset combines AGB reference data from the GEDI mission with data from Sentinel-2 and PALSAR-2 imagery. Additionally, it includes pre-processed high-level features such as a dense canopy height map, an elevation map, and a land-cover classification map. We also produce a dense, high-resolution (10m) map of AGB predictions for the entire area covered by the dataset. Rigorously tested, our dataset is accompanied by several benchmark models and is publicly available. It can be easily accessed using a single line of code, offering a solid basis for efforts towards global AGB estimation. The GitHub repository github.com/ghjuliasialelli/AGBD serves as a one-stop shop for all code and data.

  • 4 authors
·
Jun 7, 2024

Fanar-Sadiq: A Multi-Agent Architecture for Grounded Islamic QA

Large language models (LLMs) can answer religious knowledge queries fluently, yet they often hallucinate and misattribute sources, which is especially consequential in Islamic settings where users expect grounding in canonical texts (Qur'an and Hadith) and jurisprudential (fiqh) nuance. Retrieval-augmented generation (RAG) reduces some of these limitations by grounding generation in external evidence. However, a single ``retrieve-then-generate'' pipeline is limited to deal with the diversity of Islamic queries. Users may request verbatim scripture, fatwa-style guidance with citations or rule-constrained computations such as zakat and inheritance that require strict arithmetic and legal invariants. In this work, we present a bilingual (Arabic/English) multi-agent Islamic assistant, called Fanar-Sadiq, which is a core component of the Fanar AI platform. Fanar-Sadiq routes Islamic-related queries to specialized modules within an agentic, tool-using architecture. The system supports intent-aware routing, retrieval-grounded fiqh answers with deterministic citation normalization and verification traces, exact verse lookup with quotation validation, and deterministic calculators for Sunni zakat and inheritance with madhhab-sensitive branching. We evaluate the complete end-to-end system on public Islamic QA benchmarks and demonstrate effectiveness and efficiency. Our system is currently publicly and freely accessible through API and a Web application, and has been accessed approx1.9M times in less than a year.

Bayesian Deep Learning for Exoplanet Atmospheric Retrieval

Over the past decade, the study of extrasolar planets has evolved rapidly from plain detection and identification to comprehensive categorization and characterization of exoplanet systems and their atmospheres. Atmospheric retrieval, the inverse modeling technique used to determine an exoplanetary atmosphere's temperature structure and composition from an observed spectrum, is both time-consuming and compute-intensive, requiring complex algorithms that compare thousands to millions of atmospheric models to the observational data to find the most probable values and associated uncertainties for each model parameter. For rocky, terrestrial planets, the retrieved atmospheric composition can give insight into the surface fluxes of gaseous species necessary to maintain the stability of that atmosphere, which may in turn provide insight into the geological and/or biological processes active on the planet. These atmospheres contain many molecules, some of them biosignatures, spectral fingerprints indicative of biological activity, which will become observable with the next generation of telescopes. Runtimes of traditional retrieval models scale with the number of model parameters, so as more molecular species are considered, runtimes can become prohibitively long. Recent advances in machine learning (ML) and computer vision offer new ways to reduce the time to perform a retrieval by orders of magnitude, given a sufficient data set to train with. Here we present an ML-based retrieval framework called Intelligent exoplaNet Atmospheric RetrievAl (INARA) that consists of a Bayesian deep learning model for retrieval and a data set of 3,000,000 synthetic rocky exoplanetary spectra generated using the NASA Planetary Spectrum Generator. Our work represents the first ML retrieval model for rocky, terrestrial exoplanets and the first synthetic data set of terrestrial spectra generated at this scale.

  • 11 authors
·
Nov 8, 2018

HumBugDB: A Large-scale Acoustic Mosquito Dataset

This paper presents the first large-scale multi-species dataset of acoustic recordings of mosquitoes tracked continuously in free flight. We present 20 hours of audio recordings that we have expertly labelled and tagged precisely in time. Significantly, 18 hours of recordings contain annotations from 36 different species. Mosquitoes are well-known carriers of diseases such as malaria, dengue and yellow fever. Collecting this dataset is motivated by the need to assist applications which utilise mosquito acoustics to conduct surveys to help predict outbreaks and inform intervention policy. The task of detecting mosquitoes from the sound of their wingbeats is challenging due to the difficulty in collecting recordings from realistic scenarios. To address this, as part of the HumBug project, we conducted global experiments to record mosquitoes ranging from those bred in culture cages to mosquitoes captured in the wild. Consequently, the audio recordings vary in signal-to-noise ratio and contain a broad range of indoor and outdoor background environments from Tanzania, Thailand, Kenya, the USA and the UK. In this paper we describe in detail how we collected, labelled and curated the data. The data is provided from a PostgreSQL database, which contains important metadata such as the capture method, age, feeding status and gender of the mosquitoes. Additionally, we provide code to extract features and train Bayesian convolutional neural networks for two key tasks: the identification of mosquitoes from their corresponding background environments, and the classification of detected mosquitoes into species. Our extensive dataset is both challenging to machine learning researchers focusing on acoustic identification, and critical to entomologists, geo-spatial modellers and other domain experts to understand mosquito behaviour, model their distribution, and manage the threat they pose to humans.

  • 16 authors
·
Oct 14, 2021

vstash: Local-First Hybrid Retrieval with Adaptive Fusion for LLM Agents

We present **vstash**, a local-first document memory system that combines vector similarity search with full-text keyword matching via Reciprocal Rank Fusion (RRF) and adaptive per-query IDF weighting. All data resides in a single SQLite file using sqlite-vec for approximate nearest neighbor search and FTS5 for keyword matching. We make four primary contributions. **(1)** Self-supervised embedding refinement via hybrid retrieval disagreement: across 753 BEIR queries on SciFact, NFCorpus, and FiQA, 74.5% produce top-10 disagreement between vector-heavy (vec=0.95, fts=0.05) and FTS-heavy (vec=0.05, fts=0.95) search (per-dataset rates 63.4% / 73.4% / 86.7%, Section 5.2), providing a free training signal without human labels. Fine-tuning BGE-small (33M params) with MultipleNegativesRankingLoss on 76K disagreement triples improves NDCG@10 on all 5 BEIR datasets (up to +19.5% on NFCorpus vs. BGE-small base RRF, Table 6). On 3 of 5 datasets, under different preprocessing, the tuned 33M-parameter pipeline matches or exceeds published ColBERTv2 results (110M params) and an untrained BGE-base (110M); on FiQA and ArguAna it underperforms ColBERTv2 (Section 5.5). **(2)** Adaptive RRF with per-query IDF weighting improves NDCG@10 on all 5 BEIR datasets versus fixed weights (up to +21.4% on ArguAna), achieving 0.7263 on SciFact with BGE-small. **(3)** A negative result on post-RRF scoring: frequency+decay, history-augmented recall, and cross-encoder reranking all failed to improve NDCG. **(4)** A production-grade substrate with integrity checking, schema versioning, ranking diagnostics, and a distance-based relevance signal validated on 50,425 relevance-judged queries across the 5 BEIR datasets. Search latency remains 20.9 ms median at 50K chunks with stable NDCG. The fine-tuned model is published as `Stffens/bge-small-rrf-v2` on HuggingFace. All code, data, and experiments are open-source.

  • 1 authors
·
Apr 15

Gaia Data Release 3: Summary of the content and survey properties

We present the third data release of the European Space Agency's Gaia mission, GDR3. The GDR3 catalogue is the outcome of the processing of raw data collected with the Gaia instruments during the first 34 months of the mission by the Gaia Data Processing and Analysis Consortium. The GDR3 catalogue contains the same source list, celestial positions, proper motions, parallaxes, and broad band photometry in the G, G_{BP}, and G_{RP} pass-bands already present in the Early Third Data Release. GDR3 introduces an impressive wealth of new data products. More than 33 million objects in the ranges G_{rvs} < 14 and 3100 <T_{eff} <14500 , have new determinations of their mean radial velocities based on data collected by Gaia. We provide G_{rvs} magnitudes for most sources with radial velocities, and a line broadening parameter is listed for a subset of these. Mean Gaia spectra are made available to the community. The GDR3 catalogue includes about 1 million mean spectra from the radial velocity spectrometer, and about 220 million low-resolution blue and red prism photometer BPRP mean spectra. The results of the analysis of epoch photometry are provided for some 10 million sources across 24 variability types. GDR3 includes astrophysical parameters and source class probabilities for about 470 million and 1500 million sources, respectively, including stars, galaxies, and quasars. Orbital elements and trend parameters are provided for some 800,000 astrometric, spectroscopic and eclipsing binaries. More than 150,000 Solar System objects, including new discoveries, with preliminary orbital solutions and individual epoch observations are part of this release. Reflectance spectra derived from the epoch BPRP spectral data are published for about 60\,000 asteroids. Finally, an additional data set is provided, namely the Gaia Andromeda Photometric Survey (abridged)

  • 456 authors
·
Jul 30, 2022

Advancing Retrieval-Augmented Generation for Persian: Development of Language Models, Comprehensive Benchmarks, and Best Practices for Optimization

This paper examines the specific obstacles of constructing Retrieval-Augmented Generation(RAG) systems in low-resource languages, with a focus on Persian's complicated morphology and versatile syntax. The research aims to improve retrieval and generation accuracy by introducing Persian-specific models, namely MatinaRoberta(a masked language model) and MatinaSRoberta(a fine-tuned Sentence-BERT), along with a comprehensive benchmarking framework. Three datasets-general knowledge(PQuad), scientifically specialized texts, and organizational reports, were used to assess these models after they were trained on a varied corpus of 73.11 billion Persian tokens. The methodology involved extensive pretraining, fine-tuning with tailored loss functions, and systematic evaluations using both traditional metrics and the Retrieval-Augmented Generation Assessment framework. The results show that MatinaSRoberta outperformed previous embeddings, achieving superior contextual relevance and retrieval accuracy across datasets. Temperature tweaking, chunk size modifications, and document summary indexing were explored to enhance RAG setups. Larger models like Llama-3.1 (70B) consistently demonstrated the highest generation accuracy, while smaller models faced challenges with domain-specific and formal contexts. The findings underscore the potential for developing RAG systems in Persian through customized embeddings and retrieval-generation settings and highlight the enhancement of NLP applications such as search engines and legal document analysis in low-resource languages.

  • 5 authors
·
Jan 8, 2025

The Science Data Lake: A Unified Open Infrastructure Integrating 293 Million Papers Across Eight Scholarly Sources with Embedding-Based Ontology Alignment

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

  • 1 authors
·
Mar 3

Open High-Resolution Satellite Imagery: The WorldStrat Dataset -- With Application to Super-Resolution

Analyzing the planet at scale with satellite imagery and machine learning is a dream that has been constantly hindered by the cost of difficult-to-access highly-representative high-resolution imagery. To remediate this, we introduce here the WorldStrat dataset. The largest and most varied such publicly available dataset, at Airbus SPOT 6/7 satellites' high resolution of up to 1.5 m/pixel, empowered by European Space Agency's Phi-Lab as part of the ESA-funded QueryPlanet project, we curate nearly 10,000 sqkm of unique locations to ensure stratified representation of all types of land-use across the world: from agriculture to ice caps, from forests to multiple urbanization densities. We also enrich those with locations typically under-represented in ML datasets: sites of humanitarian interest, illegal mining sites, and settlements of persons at risk. We temporally-match each high-resolution image with multiple low-resolution images from the freely accessible lower-resolution Sentinel-2 satellites at 10 m/pixel. We accompany this dataset with an open-source Python package to: rebuild or extend the WorldStrat dataset, train and infer baseline algorithms, and learn with abundant tutorials, all compatible with the popular EO-learn toolbox. We hereby hope to foster broad-spectrum applications of ML to satellite imagery, and possibly develop from free public low-resolution Sentinel2 imagery the same power of analysis allowed by costly private high-resolution imagery. We illustrate this specific point by training and releasing several highly compute-efficient baselines on the task of Multi-Frame Super-Resolution. High-resolution Airbus imagery is CC BY-NC, while the labels and Sentinel2 imagery are CC BY, and the source code and pre-trained models under BSD. The dataset is available at https://zenodo.org/record/6810791 and the software package at https://github.com/worldstrat/worldstrat .

  • 3 authors
·
May 30, 2025

INQUIRE: A Natural World Text-to-Image Retrieval Benchmark

We introduce INQUIRE, a text-to-image retrieval benchmark designed to challenge multimodal vision-language models on expert-level queries. INQUIRE includes iNaturalist 2024 (iNat24), a new dataset of five million natural world images, along with 250 expert-level retrieval queries. These queries are paired with all relevant images comprehensively labeled within iNat24, comprising 33,000 total matches. Queries span categories such as species identification, context, behavior, and appearance, emphasizing tasks that require nuanced image understanding and domain expertise. Our benchmark evaluates two core retrieval tasks: (1) INQUIRE-Fullrank, a full dataset ranking task, and (2) INQUIRE-Rerank, a reranking task for refining top-100 retrievals. Detailed evaluation of a range of recent multimodal models demonstrates that INQUIRE poses a significant challenge, with the best models failing to achieve an mAP@50 above 50%. In addition, we show that reranking with more powerful multimodal models can enhance retrieval performance, yet there remains a significant margin for improvement. By focusing on scientifically-motivated ecological challenges, INQUIRE aims to bridge the gap between AI capabilities and the needs of real-world scientific inquiry, encouraging the development of retrieval systems that can assist with accelerating ecological and biodiversity research. Our dataset and code are available at https://inquire-benchmark.github.io

  • 8 authors
·
Nov 4, 2024

Presenting an extensive lab- and field-image dataset of crops and weeds for computer vision tasks in agriculture

We present two large datasets of labelled plant-images that are suited towards the training of machine learning and computer vision models. The first dataset encompasses as the day of writing over 1.2 million images of indoor-grown crops and weeds common to the Canadian Prairies and many US states. The second dataset consists of over 540,000 images of plants imaged in farmland. All indoor plant images are labelled by species and we provide rich etadata on the level of individual images. This comprehensive database allows to filter the datasets under user-defined specifications such as for example the crop-type or the age of the plant. Furthermore, the indoor dataset contains images of plants taken from a wide variety of angles, including profile shots, top-down shots, and angled perspectives. The images taken from plants in fields are all from a top-down perspective and contain usually multiple plants per image. For these images metadata is also available. In this paper we describe both datasets' characteristics with respect to plant variety, plant age, and number of images. We further introduce an open-access sample of the indoor-dataset that contains 1,000 images of each species covered in our dataset. These, in total 14,000 images, had been selected, such that they form a representative sample with respect to plant age and ndividual plants per species. This sample serves as a quick entry point for new users to the dataset, allowing them to explore the data on a small scale and find the parameters of data most useful for their application without having to deal with hundreds of thousands of individual images.

  • 6 authors
·
Aug 12, 2021

Deep Synoptic Array Science: Searching for Long Duration Radio Transients with the DSA-110

We describe the design and commissioning tests for the DSA-110 Not-So-Fast Radio Burst (NSFRB) search pipeline, a 1.4 GHz image-plane single-pulse search sensitive to 134 ms-160.8 s radio bursts. Extending the pulse width range of the Fast Radio Burst (FRB) search by 3 orders of magnitude, the NSFRB search is sensitive to the recently-discovered Galactic Long Period Radio Transients (LPRTs). The NSFRB search operates in real-time, utilizing a custom GPU-accelerated search code, cerberus, implemented in Python with JAX. We summarize successful commissioning sensitivity tests with continuum sources and pulsar B0329+54, estimating the 6sigma flux (fluence) threshold to be ~290 mJy (~40 Jy ms). Future tests of recovery of longer timescale transients, e.g. CHIME J1634+44, are planned to supplement injection testing and B0329+54 observations. An offline DSA-110 NSFRB Galactic Plane Survey was conducted to search for LPRTs, covering -3.5^circ<b<5.7^circ and 141^circ<l<225^circ (~770 square degrees) in Galactic coordinates. We estimate an upper limit Poissonian burst rate ~1 hr^{-1} per square degree (~7 hr^{-1} per 3^circtimes3^circ survey grid cell) maximized across the inner |b|<0.25^circ of the surveyed region. By imposing the ~290 mJy flux limit on two representative models (the magnetar plastic flow model and the White Dwarf-M Dwarf binary model), we reject with 95% confidence the presence of White Dwarf-M Dwarf binary LPRTs with periods between ~10-70s within ~95% of the surveyed region. Combined with the prevalence of LPRTs in the Galactic Plane, our results motivate further consideration of both White Dwarf-M Dwarf binary models and isolated magnetar models. We will continue to explore novel LPRT search strategies during real-time operations, such as triggered periodicity searches and additional targeted surveys.

  • 13 authors
·
Oct 20, 2025

MAWARITH: A Dataset and Benchmark for Legal Inheritance Reasoning with LLMs

Islamic inheritance law ('ilm al-mawarith) is challenging for large language models because solving inheritance cases requires complex, structured multi-step reasoning and the correct application of juristic rules to compute heirs' shares. We introduce MAWARITH, a large-scale annotated dataset of 12,500 Arabic inheritance cases for training and evaluating models on the full reasoning chain: (i) identifying eligible heirs, (ii) applying blocking (hajb) and allocation rules, and (iii) computing exact inheritance shares. Unlike prior datasets that restrict inheritance case solving to multiple-choice questions, MAWARITH supports the full reasoning chain and provides step-by-step solutions, including intermediate legal decisions and justifications based on classical juristic sources and established inheritance rules, as well as exact share calculations. To evaluate models beyond final-answer accuracy, we propose MIR-E (Mawarith Inheritance Reasoning Evaluation), a weighted multi-stage metric that scores key reasoning stages and captures error propagation across the pipeline. We evaluate six LLMs in a zero-shot setting. Gemini-2.5-flash achieves about 90% MIR-E on both validation and test, while Fanar-C, Fanar-Sadiq, LLaMA 3, and Qwen 3 remain below 50%. Our error analysis identifies recurring failure patterns, including scenario misinterpretation, errors in heir identification, errors in share allocation, and missing or incorrect application of key inheritance rules such as 'awl and radd. The MAWARITH dataset is publicly available at https://gitlab.com/islamgpt1/qias_shared_task_2026.

  • 8 authors
·
Mar 15

Demo of the Linguistic Field Data Management and Analysis System -- LiFE

In the proposed demo, we will present a new software - Linguistic Field Data Management and Analysis System - LiFE (https://github.com/kmi-linguistics/life) - an open-source, web-based linguistic data management and analysis application that allows for systematic storage, management, sharing and usage of linguistic data collected from the field. The application allows users to store lexical items, sentences, paragraphs, audio-visual content with rich glossing / annotation; generate interactive and print dictionaries; and also train and use natural language processing tools and models for various purposes using this data. Since its a web-based application, it also allows for seamless collaboration among multiple persons and sharing the data, models, etc with each other. The system uses the Python-based Flask framework and MongoDB in the backend and HTML, CSS and Javascript at the frontend. The interface allows creation of multiple projects that could be shared with the other users. At the backend, the application stores the data in RDF format so as to allow its release as Linked Data over the web using semantic web technologies - as of now it makes use of the OntoLex-Lemon for storing the lexical data and Ligt for storing the interlinear glossed text and then internally linking it to the other linked lexicons and databases such as DBpedia and WordNet. Furthermore it provides support for training the NLP systems using scikit-learn and HuggingFace Transformers libraries as well as make use of any model trained using these libraries - while the user interface itself provides limited options for tuning the system, an externally-trained model could be easily incorporated within the application; similarly the dataset itself could be easily exported into a standard machine-readable format like JSON or CSV that could be consumed by other programs and pipelines.

  • 4 authors
·
Mar 21, 2022

A Dataset for Greek Traditional and Folk Music: Lyra

Studying under-represented music traditions under the MIR scope is crucial, not only for developing novel analysis tools, but also for unveiling musical functions that might prove useful in studying world musics. This paper presents a dataset for Greek Traditional and Folk music that includes 1570 pieces, summing in around 80 hours of data. The dataset incorporates YouTube timestamped links for retrieving audio and video, along with rich metadata information with regards to instrumentation, geography and genre, among others. The content has been collected from a Greek documentary series that is available online, where academics present music traditions of Greece with live music and dance performance during the show, along with discussions about social, cultural and musicological aspects of the presented music. Therefore, this procedure has resulted in a significant wealth of descriptions regarding a variety of aspects, such as musical genre, places of origin and musical instruments. In addition, the audio recordings were performed under strict production-level specifications, in terms of recording equipment, leading to very clean and homogeneous audio content. In this work, apart from presenting the dataset in detail, we propose a baseline deep-learning classification approach to recognize the involved musicological attributes. The dataset, the baseline classification methods and the models are provided in public repositories. Future directions for further refining the dataset are also discussed.

  • 5 authors
·
Nov 21, 2022

ScIRGen: Synthesize Realistic and Large-Scale RAG Dataset for Scientific Research

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

  • 10 authors
·
Jun 9, 2025

IndoToxic2024: A Demographically-Enriched Dataset of Hate Speech and Toxicity Types for Indonesian Language

Hate speech poses a significant threat to social harmony. Over the past two years, Indonesia has seen a ten-fold increase in the online hate speech ratio, underscoring the urgent need for effective detection mechanisms. However, progress is hindered by the limited availability of labeled data for Indonesian texts. The condition is even worse for marginalized minorities, such as Shia, LGBTQ, and other ethnic minorities because hate speech is underreported and less understood by detection tools. Furthermore, the lack of accommodation for subjectivity in current datasets compounds this issue. To address this, we introduce IndoToxic2024, a comprehensive Indonesian hate speech and toxicity classification dataset. Comprising 43,692 entries annotated by 19 diverse individuals, the dataset focuses on texts targeting vulnerable groups in Indonesia, specifically during the hottest political event in the country: the presidential election. We establish baselines for seven binary classification tasks, achieving a macro-F1 score of 0.78 with a BERT model (IndoBERTweet) fine-tuned for hate speech classification. Furthermore, we demonstrate how incorporating demographic information can enhance the zero-shot performance of the large language model, gpt-3.5-turbo. However, we also caution that an overemphasis on demographic information can negatively impact the fine-tuned model performance due to data fragmentation.

  • 7 authors
·
Jun 27, 2024

MAG-SQL: Multi-Agent Generative Approach with Soft Schema Linking and Iterative Sub-SQL Refinement for Text-to-SQL

Recent In-Context Learning based methods have achieved remarkable success in Text-to-SQL task. However, there is still a large gap between the performance of these models and human performance on datasets with complex database schema and difficult questions, such as BIRD. Besides, existing work has neglected to supervise intermediate steps when solving questions iteratively with question decomposition methods, and the schema linking methods used in these works are very rudimentary. To address these issues, we propose MAG-SQL, a multi-agent generative approach with soft schema linking and iterative Sub-SQL refinement. In our framework, an entity-based method with tables' summary is used to select the columns in database, and a novel targets-conditions decomposition method is introduced to decompose those complex questions. Additionally, we build a iterative generating module which includes a Sub-SQL Generator and Sub-SQL Refiner, introducing external oversight for each step of generation. Through a series of ablation studies, the effectiveness of each agent in our framework has been demonstrated. When evaluated on the BIRD benchmark with GPT-4, MAG-SQL achieves an execution accuracy of 61.08\%, compared to the baseline accuracy of 46.35\% for vanilla GPT-4 and the baseline accuracy of 57.56\% for MAC-SQL. Besides, our approach makes similar progress on Spider.

  • 3 authors
·
Aug 15, 2024

Benchmarking Filtered Approximate Nearest Neighbor Search Algorithms on Transformer-based Embedding Vectors

Advances in embedding models for text, image, audio, and video drive progress across multiple domains, including retrieval-augmented generation, recommendation systems, vehicle/person reidentification, and face recognition. Many applications in these domains require an efficient method to retrieve items that are close to a given query in the embedding space while satisfying a filter condition based on the item's attributes, a problem known as Filtered Approximate Nearest Neighbor Search (FANNS). In this work, we present a comprehensive survey and taxonomy of FANNS methods and analyze how they are benchmarked in the literature. By doing so, we identify a key challenge in the current FANNS landscape: the lack of diverse and realistic datasets, particularly ones derived from the latest transformer-based text embedding models. To address this, we introduce a novel dataset consisting of embedding vectors for the abstracts of over 2.7 million research articles from the arXiv repository, accompanied by 11 real-world attributes such as authors and categories. We benchmark a wide range of FANNS methods on our novel dataset and find that each method has distinct strengths and limitations; no single approach performs best across all scenarios. ACORN, for example, supports various filter types and performs reliably across dataset scales but is often outperformed by more specialized methods. SeRF shows excellent performance for range filtering on ordered attributes but cannot handle categorical attributes. Filtered-DiskANN and UNG excel on the medium-scale dataset but fail on the large-scale dataset, highlighting the challenge posed by transformer-based embeddings, which are often more than an order of magnitude larger than earlier embeddings. We conclude that no universally best method exists.

  • 5 authors
·
Jul 29, 2025

CNN based Cuneiform Sign Detection Learned from Annotated 3D Renderings and Mapped Photographs with Illumination Augmentation

Motivated by the challenges of the Digital Ancient Near Eastern Studies (DANES) community, we develop digital tools for processing cuneiform script being a 3D script imprinted into clay tablets used for more than three millennia and at least eight major languages. It consists of thousands of characters that have changed over time and space. Photographs are the most common representations usable for machine learning, while ink drawings are prone to interpretation. Best suited 3D datasets that are becoming available. We created and used the HeiCuBeDa and MaiCuBeDa datasets, which consist of around 500 annotated tablets. For our novel OCR-like approach to mixed image data, we provide an additional mapping tool for transferring annotations between 3D renderings and photographs. Our sign localization uses a RepPoints detector to predict the locations of characters as bounding boxes. We use image data from GigaMesh's MSII (curvature, see https://gigamesh.eu) based rendering, Phong-shaded 3D models, and photographs as well as illumination augmentation. The results show that using rendered 3D images for sign detection performs better than other work on photographs. In addition, our approach gives reasonably good results for photographs only, while it is best used for mixed datasets. More importantly, the Phong renderings, and especially the MSII renderings, improve the results on photographs, which is the largest dataset on a global scale.

  • 3 authors
·
Aug 22, 2023

Euclid Quick Data Release (Q1) Exploring galaxy properties with a multi-modal foundation model

Modern astronomical surveys, such as the Euclid mission, produce high-dimensional, multi-modal data sets that include imaging and spectroscopic information for millions of galaxies. These data serve as an ideal benchmark for large, pre-trained multi-modal models, which can leverage vast amounts of unlabelled data. In this work, we present the first exploration of Euclid data with AstroPT, an autoregressive multi-modal foundation model trained on approximately 300 000 optical and infrared Euclid images and spectral energy distributions (SEDs) from the first Euclid Quick Data Release. We compare self-supervised pre-training with baseline fully supervised training across several tasks: galaxy morphology classification; redshift estimation; similarity searches; and outlier detection. Our results show that: (a) AstroPT embeddings are highly informative, correlating with morphology and effectively isolating outliers; (b) including infrared data helps to isolate stars, but degrades the identification of edge-on galaxies, which are better captured by optical images; (c) simple fine-tuning of these embeddings for photometric redshift and stellar mass estimation outperforms a fully supervised approach, even when using only 1% of the training labels; and (d) incorporating SED data into AstroPT via a straightforward multi-modal token-chaining method improves photo-z predictions, and allow us to identify potentially more interesting anomalies (such as ringed or interacting galaxies) compared to a model pre-trained solely on imaging data.

  • 324 authors
·
Mar 19, 2025

AFRILANGTUTOR: Advancing Language Tutoring and Culture Education in Low-Resource Languages with Large Language Models

How can language learning systems be developed for languages that lack sufficient training resources? This challenge is increasingly faced by developers across the African continent who aim to build AI systems capable of understanding and responding in local languages. To address this gap, we introduce AFRILANGDICT, a collection of 194.7K African language-English dictionary entries designed as seed resources for generating language-learning materials, enabling us to automatically construct large-scale, diverse, and verifiable student-tutor question-answer interactions suitable for training AI-assisted language tutors. Using AFRILANGDICT, we build AFRILANGEDU, a dataset of 78.9K multi-turn training examples for Supervised Fine-Tuning (SFT) and Direct Preference Optimization (DPO). Using AFRILANGEDU, we train language tutoring models collectively referred to as AFRILANGTUTOR. We fine-tune two multilingual LLMs: Llama-3-8B-IT and Gemma-3-12B-IT on AFRILANGEDU across 10 African languages and evaluate their performance. Our results show that models trained on AFRILANGEDU consistently outperform their base counterparts, and combining SFT and DPO yields substantial improvements, with gains ranging from 1.8% to 15.5% under LLM-as-a-judge evaluations across four criteria. To facilitate further research on low-resource languages -- all resources are available at https://huggingface.co/afrilang-edu.

  • 7 authors
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Apr 21

A Reproducible Universal Dependencies-Style Pipeline for Katharevousa Greek Parliamentary Text

Katharevousa Greek remains poorly served by contemporary NLP pipelines despite its importance for legal, administrative, and parliamentary archives. We present a reproducible workflow for building and evaluating a Universal Dependencies-style parsing resource for Katharevousa parliamentary questions from Greece's early post-junta period. The pipeline links OCR-aware reconstruction, schema-constrained LLM-assisted annotation, automatic validation, deterministic CoNLL-U snapshotting, fixed-split evaluation, and model-family comparison. The frozen automatically validated reference set contains 1{,}697 sentences, split into 1{,}357 training sentences and 340 held-out test sentences. We compare off-the-shelf Greek and Ancient Greek parsers, a feature-based parser, mBERT, XLM-R, and custom Stanza training under the same scoring protocol. Off-the-shelf systems show substantial register mismatch: the strongest external baseline, spaCy Greek, reaches 0.4183 LAS. The best structural parser, an XLM-R model, reaches 0.8893 UPOS accuracy, 0.7250 dependency-relation F1, 0.6098 UAS, and 0.5162 LAS, an absolute LAS gain of 0.0980 over the best external baseline. The feature-based model remains competitive for UPOS and relation labeling, indicating that transparent lexical-context features still matter at this data scale. Beyond scores, the paper contributes an auditable methodology for turning difficult historical parliamentary OCR into reusable syntactic NLP infrastructure. The entire pipeline -- code, schema, frozen reference annotations, fixed train/test split, and per-model benchmark reports -- is released as an open-access companion to this paper.

  • 2 authors
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May 21

An inorganic ABX3 perovskite materials dataset for target property prediction and classification using machine learning

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

  • 2 authors
·
Dec 18, 2023

Understanding of the properties of neural network approaches for transient light curve approximations

Modern-day time-domain photometric surveys collect a lot of observations of various astronomical objects and the coming era of large-scale surveys will provide even more information on their properties. Spectroscopic follow-ups are especially crucial for transients such as supernovae and most of these objects have not been subject to such studies. }{Flux time series are actively used as an affordable alternative for photometric classification and characterization, for instance, peak identifications and luminosity decline estimations. However, the collected time series are multidimensional and irregularly sampled, while also containing outliers and without any well-defined systematic uncertainties. This paper presents a search for the best-performing methods to approximate the observed light curves over time and wavelength for the purpose of generating time series with regular time steps in each passband.}{We examined several light curve approximation methods based on neural networks such as multilayer perceptrons, Bayesian neural networks, and normalizing flows to approximate observations of a single light curve. Test datasets include simulated PLAsTiCC and real Zwicky Transient Facility Bright Transient Survey light curves of transients.}{The tests demonstrate that even just a few observations are enough to fit the networks and improve the quality of approximation, compared to state-of-the-art models. The methods described in this work have a low computational complexity and are significantly faster than Gaussian processes. Additionally, we analyzed the performance of the approximation techniques from the perspective of further peak identification and transients classification. The study results have been released in an open and user-friendly Fulu Python library available on GitHub for the scientific community.

  • 7 authors
·
Sep 15, 2022

DFIN-SQL: Integrating Focused Schema with DIN-SQL for Superior Accuracy in Large-Scale Databases

The task of converting natural language queries into SQL queries is intricate, necessitating a blend of precise techniques for an accurate translation. The DIN-SQL (Decomposed-In-Context SQL) methodology represents a significant development in this domain. This paper introduces DFIN (Decomposed Focused-In-Context), an innovative extension of DIN-SQL that enhances Text-to-SQL conversion by addressing schema linking errors, which are a major source of inaccuracies. DFIN uniquely alternates between prompting techniques and Retrieval-Augmented Generation (RAG), adapting to the size and complexity of the database schema. A preprocessing phase embeds database definitions and leverages annotated files, akin to those in the BIRD dataset, facilitating the runtime retrieval of pertinent schema information. This strategy significantly reduces the token count for schema linking prompts, enabling the use of a standard GPT-4 model over its larger context variant, thus handling large-scale databases more effectively and economically. Our evaluation on the BIRD dataset, a challenging real-world benchmark, demonstrates that DFIN not only scales efficiently but also improves accuracy, achieving a score of 51.69. This improvement surpasses DIN-SQL method (the current third-place), which is the highest-ranked model employing in-context learning rather than fine-tuning, previously scoring 50.72. The advancement of DFIN underscores the evolving capabilities of in-context learning methodologies combined with advanced language models, offering a promising avenue for future research in complex Text-to-SQL conversion tasks.

  • 3 authors
·
Mar 1, 2024

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

  • 17 authors
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Oct 8, 2024

HoneyBee: Progressive Instruction Finetuning of Large Language Models for Materials Science

We propose an instruction-based process for trustworthy data curation in materials science (MatSci-Instruct), which we then apply to finetune a LLaMa-based language model targeted for materials science (HoneyBee). MatSci-Instruct helps alleviate the scarcity of relevant, high-quality materials science textual data available in the open literature, and HoneyBee is the first billion-parameter language model specialized to materials science. In MatSci-Instruct we improve the trustworthiness of generated data by prompting multiple commercially available large language models for generation with an Instructor module (e.g. Chat-GPT) and verification from an independent Verifier module (e.g. Claude). Using MatSci-Instruct, we construct a dataset of multiple tasks and measure the quality of our dataset along multiple dimensions, including accuracy against known facts, relevance to materials science, as well as completeness and reasonableness of the data. Moreover, we iteratively generate more targeted instructions and instruction-data in a finetuning-evaluation-feedback loop leading to progressively better performance for our finetuned HoneyBee models. Our evaluation on the MatSci-NLP benchmark shows HoneyBee's outperformance of existing language models on materials science tasks and iterative improvement in successive stages of instruction-data refinement. We study the quality of HoneyBee's language modeling through automatic evaluation and analyze case studies to further understand the model's capabilities and limitations. Our code and relevant datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-HoneyBee.

  • 4 authors
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Oct 12, 2023

The GALAH Survey: Data Release 4

The stars of the Milky Way carry the chemical history of our Galaxy in their atmospheres as they journey through its vast expanse. Like barcodes, we can extract the chemical fingerprints of stars from high-resolution spectroscopy. The fourth data release (DR4) of the Galactic Archaeology with HERMES (GALAH) Survey, based on a decade of observations, provides the chemical abundances of up to 32 elements for 917 588 stars that also have exquisite astrometric data from the Gaia satellite. For the first time, these elements include life-essential nitrogen to complement carbon, and oxygen as well as more measurements of rare-earth elements critical to modern-life electronics, offering unparalleled insights into the chemical composition of the Milky Way. For this release, we use neural networks to simultaneously fit stellar parameters and abundances across the whole wavelength range, leveraging synthetic grids computed with Spectroscopy Made Easy. These grids account for atomic line formation in non-local thermodynamic equilibrium for 14 elements. In a two-iteration process, we first fit stellar labels to all 1 085 520 spectra, then co-add repeated observations and refine these labels using astrometric data from Gaia and 2MASS photometry, improving the accuracy and precision of stellar parameters and abundances. Our validation thoroughly assesses the reliability of spectroscopic measurements and highlights key caveats. GALAH DR4 represents yet another milestone in Galactic archaeology, combining detailed chemical compositions from multiple nucleosynthetic channels with kinematic information and age estimates. The resulting dataset, covering nearly a million stars, opens new avenues for understanding not only the chemical and dynamical history of the Milky Way, but also the broader questions of the origin of elements and the evolution of planets, stars, and galaxies.

  • 39 authors
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Sep 29, 2024

Parsed Categoric Encodings with Automunge

The Automunge open source python library platform for tabular data pre-processing automates feature engineering data transformations of numerical encoding and missing data infill to received tidy data on bases fit to properties of columns in a designated train set for consistent and efficient application to subsequent data pipelines such as for inference, where transformations may be applied to distinct columns in "family tree" sets with generations and branches of derivations. Included in the library of transformations are methods to extract structure from bounded categorical string sets by way of automated string parsing, in which comparisons between entries in the set of unique values are parsed to identify character subset overlaps which may be encoded by appended columns of boolean overlap detection activations or by replacing string entries with identified overlap partitions. Further string parsing options, which may also be applied to unbounded categoric sets, include extraction of numeric substring partitions from entries or search functions to identify presence of specified substring partitions. The aggregation of these methods into "family tree" sets of transformations are demonstrated for use to automatically extract structure from categoric string compositions in relation to the set of entries in a column, such as may be applied to prepare categoric string set encodings for machine learning without human intervention.

  • 1 authors
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Feb 18, 2022

Darshana Graph: A Parallel Commentary Corpus for Comparative Indian Philosophy, with Stylometric and Exploratory Graph Analyses

We introduce Darshana Graph, a corpus of over 125,000 text records spanning classical Hindu, Buddhist, and Jain philosophical traditions, drawn from public-domain and openly licensed translations of sources including the Bhagavad Gita, Brahma Sutras, principal Upanishads, the Pali Canon, and core Jain texts. Its distinctive contribution lies in a structurally unique subset of roughly 8,500 Hindu and Jain records in which the same root verse or sutra is aligned across eighteen historical commentators representing five schools of Vedanta and other darshanas, enabling direct comparison of how independent interpretive traditions read identical source material. To our knowledge, no publicly available resource provides comparable cross-commentator alignment at this scale. We present two analyses built on this corpus. First, a transparent stylometric comparison requiring no machine learning measures argumentative style through scriptural citation density, explicit refutation rate, and sentence complexity. It finds a moderate negative correlation between citation density and refutation rate, a marked increase in refutation rate across three commentators in a related doctrinal lineage, and measurable genre-level differences within the Pali Canon itself. Second, we describe a constrained large language model pipeline that extracts typed philosophical relationships between concepts using a predefined relation vocabulary and deterministic post-hoc validation. The resulting graph surfaces cross-school disagreement patterns while also revealing important extraction limitations, including cases where an independent embedding-based analysis disagrees with the graph-derived findings. We release the full corpus, extracted relationship graph, and all source code.

  • 1 authors
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Jun 15

LinkAlign: Scalable Schema Linking for Real-World Large-Scale Multi-Database Text-to-SQL

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

  • 2 authors
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Mar 24, 2025

BIRDNet: Mining and Encoding Boolean Implication Knowledge Graphs as Interpretable Deep Neural Networks

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most 2/d of the weights in each BIR layer are active, where d is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to 96times fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

  • 1 authors
·
May 27

Question Answering on Patient Medical Records with Private Fine-Tuned LLMs

Healthcare systems continuously generate vast amounts of electronic health records (EHRs), commonly stored in the Fast Healthcare Interoperability Resources (FHIR) standard. Despite the wealth of information in these records, their complexity and volume make it difficult for users to retrieve and interpret crucial health insights. Recent advances in Large Language Models (LLMs) offer a solution, enabling semantic question answering (QA) over medical data, allowing users to interact with their health records more effectively. However, ensuring privacy and compliance requires edge and private deployments of LLMs. This paper proposes a novel approach to semantic QA over EHRs by first identifying the most relevant FHIR resources for a user query (Task1) and subsequently answering the query based on these resources (Task2). We explore the performance of privately hosted, fine-tuned LLMs, evaluating them against benchmark models such as GPT-4 and GPT-4o. Our results demonstrate that fine-tuned LLMs, while 250x smaller in size, outperform GPT-4 family models by 0.55% in F1 score on Task1 and 42% on Meteor Task in Task2. Additionally, we examine advanced aspects of LLM usage, including sequential fine-tuning, model self-evaluation (narcissistic evaluation), and the impact of training data size on performance. The models and datasets are available here: https://huggingface.co/genloop

  • 2 authors
·
Jan 23, 2025 2

EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical Text

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

  • 11 authors
·
Apr 16, 2023

Harnessing the Hubble Space Telescope Archives: A Catalogue of 21,926 Interacting Galaxies

Mergers play a complex role in galaxy formation and evolution. Continuing to improve our understanding of these systems require ever larger samples, which can be difficult (even impossible) to select from individual surveys. We use the new platform ESA Datalabs to assemble a catalogue of interacting galaxies from the Hubble Space Telescope science archives; this catalogue is larger than previously published catalogues by nearly an order of magnitude. In particular, we apply the Zoobot convolutional neural network directly to the entire public archive of HST F814W images and make probabilistic interaction predictions for 126 million sources from the Hubble Source Catalogue. We employ a combination of automated visual representation and visual analysis to identify a clean sample of 21,926 interacting galaxy systems, mostly with z < 1. Sixty five percent of these systems have no previous references in either the NASA Extragalactic Database or Simbad. In the process of removing contamination, we also discover many other objects of interest, such as gravitational lenses, edge-on protoplanetary disks, and `backlit' overlapping galaxies. We briefly investigate the basic properties of this sample, and we make our catalogue publicly available for use by the community. In addition to providing a new catalogue of scientifically interesting objects imaged by HST, this work also demonstrates the power of the ESA Datalabs tool to facilitate substantial archival analysis without placing a high computational or storage burden on the end user.

  • 16 authors
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Mar 1, 2023

OmniSQL: Synthesizing High-quality Text-to-SQL Data at Scale

Text-to-SQL, the task of translating natural language questions into SQL queries, plays a crucial role in enabling non-experts to interact with databases. While recent advancements in large language models (LLMs) have significantly enhanced text-to-SQL performance, existing approaches face notable limitations in real-world text-to-SQL applications. Prompting-based methods often depend on closed-source LLMs, which are expensive, raise privacy concerns, and lack customization. Fine-tuning-based methods, on the other hand, suffer from poor generalizability due to the limited coverage of publicly available training data. To overcome these challenges, we propose a novel and scalable text-to-SQL data synthesis framework for automatically synthesizing large-scale, high-quality, and diverse datasets without extensive human intervention. Using this framework, we introduce SynSQL-2.5M, the first million-scale text-to-SQL dataset, containing 2.5 million samples spanning over 16,000 synthetic databases. Each sample includes a database, SQL query, natural language question, and chain-of-thought (CoT) solution. Leveraging SynSQL-2.5M, we develop OmniSQL, a powerful open-source text-to-SQL model available in three sizes: 7B, 14B, and 32B. Extensive evaluations across nine datasets demonstrate that OmniSQL achieves state-of-the-art performance, matching or surpassing leading closed-source and open-source LLMs, including GPT-4o and DeepSeek-V3, despite its smaller size. We release all code, datasets, and models to support further research.

  • 12 authors
·
Mar 3, 2025 1

Instruct-Tuning Pretrained Causal Language Models for Ancient Greek Papyrology and Epigraphy

This article presents an experiment in fine-tuning a pretrained causal language model (Meta's Llama 3.1 8B Instruct) for aiding in three fundamental tasks of philological research: chronological and geographic attribution as well as text restoration in ancient Greek inscriptions and documentary papyri. Using a prompt-based instruct approach, the fine-tuned models surpass the state of the art in key metrics. For inscriptions, the models achieve a lower average character error rate (CER) of 22.5% (vs. 26.3%), while closely matching top-1 accuracy (60.9% vs. 61.8%) and top-20 accuracy (77.5% vs. 78.3%) for sequences up to 10 characters. They also provide a practical advantage by ignoring spaces during reconstruction, aligning better with the scriptio continua typically used in ancient written artifacts. In geographic attribution, the model outperforms previous benchmarks with a top-1 accuracy of 75.0% (vs. 70.8%) and a top-3 accuracy of 83.7% (vs. 82.1%). For dating, it achieves an average deviation of 26.2 years (vs. 29.3) and a median deviation of 1 year (vs. 3) from the actual date range. The models also set new baselines for documentary papyri, with a CER of 16.3%, a top-1 accuracy of 71.3%, and top-20 of 85.0% in text reconstruction; a top-1 accuracy of 66.4% and top-3 of 79.9% in geographic attribution; and, in chronological attribution, a deviation of 21.7 years from the actual termini post/ante quem, with a median deviation of 0 years.

  • 1 authors
·
Sep 20, 2024

CoIR: A Comprehensive Benchmark for Code Information Retrieval Models

Despite the substantial success of Information Retrieval (IR) in various NLP tasks, most IR systems predominantly handle queries and corpora in natural language, neglecting the domain of code retrieval. Code retrieval is critically important yet remains under-explored, with existing methods and benchmarks inadequately representing the diversity of code in various domains and tasks. Addressing this gap, we present \name (Code Information Retrieval Benchmark), a robust and comprehensive benchmark specifically designed to assess code retrieval capabilities. \name comprises ten meticulously curated code datasets, spanning eight distinctive retrieval tasks across seven diverse domains. We first discuss the construction of \name and its diverse dataset composition. Further, we evaluate nine widely used retrieval models using \name, uncovering significant difficulties in performing code retrieval tasks even with state-of-the-art systems. To facilitate easy adoption and integration within existing research workflows, \name has been developed as a user-friendly Python framework, readily installable via pip. It shares same data schema as other popular benchmarks like MTEB and BEIR, enabling seamless cross-benchmark evaluations. Through \name, we aim to invigorate research in the code retrieval domain, providing a versatile benchmarking tool that encourages further development and exploration of code retrieval systems\url{ https://github.com/CoIR-team/coir}.

  • 9 authors
·
Jul 3, 2024

p-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines p-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a p-adic distance on k-mer prefixes, which captures hierarchical positional structure, and a compositional L_1 distance on k-mer frequencies, which captures local sequence content. The two distances jointly parameterise a bi-filtered Vietoris--Rips complex, and per-sequence topological summaries from this bi-filtration serve as features for standard machine learning classifiers. We establish theoretical guarantees for the construction: stability under metric perturbations and invariance to the choice of prime, alongside a result that explains why a single p-adic axis is topologically uninformative and why the bi-filtration recovers nontrivial homology. On twelve genomic benchmarks (28 to 500 sequences, 3 to 7 classes), pVR outperforms four established alignment-free baselines on three of six low-sample datasets, with gains of up to 21 percentage points; it underperforms only on a SARS-CoV-2 variant benchmark whose point-mutation divergence violates the hierarchical assumption, and all methods saturate in the large-sample regime. pVR also outperforms zero-shot frozen embeddings from the 500M-parameter Nucleotide Transformer v2 by 6.7 to 11.4 percentage points on three low-sample benchmarks. The pVR codebase is publicly available at https://github.com/MAHI-Group/pVR.

  • 2 authors
·
Jun 4

Automatic Synthetic Data and Fine-grained Adaptive Feature Alignment for Composed Person Retrieval

Person retrieval has attracted rising attention. Existing methods are mainly divided into two retrieval modes, namely image-only and text-only. However, they are unable to make full use of the available information and are difficult to meet diverse application requirements. To address the above limitations, we propose a new Composed Person Retrieval (CPR) task, which combines visual and textual queries to identify individuals of interest from large-scale person image databases. Nevertheless, the foremost difficulty of the CPR task is the lack of available annotated datasets. Therefore, we first introduce a scalable automatic data synthesis pipeline, which decomposes complex multimodal data generation into the creation of textual quadruples followed by identity-consistent image synthesis using fine-tuned generative models. Meanwhile, a multimodal filtering method is designed to ensure the resulting SynCPR dataset retains 1.15 million high-quality and fully synthetic triplets. Additionally, to improve the representation of composed person queries, we propose a novel Fine-grained Adaptive Feature Alignment (FAFA) framework through fine-grained dynamic alignment and masked feature reasoning. Moreover, for objective evaluation, we manually annotate the Image-Text Composed Person Retrieval (ITCPR) test set. The extensive experiments demonstrate the effectiveness of the SynCPR dataset and the superiority of the proposed FAFA framework when compared with the state-of-the-art methods. All code and data will be provided at https://github.com/Delong-liu-bupt/Composed_Person_Retrieval.

  • 6 authors
·
Nov 25, 2023

Characterizing WASP-43b's interior structure: unveiling tidal decay and apsidal motion

Context. Recent developments in exoplanetary research highlight the importance of Love numbers in understanding their internal dynamics, formation, migration history and their potential habitability. Love numbers represent crucial parameters that gauge how exoplanets respond to external forces such as tidal interactions and rotational effects. By measuring these responses, we can gain insights into the internal structure, composition, and density distribution of exoplanets. The rate of apsidal precession of a planetary orbit is directly linked to the second-order fluid Love number, thus we can gain valuable insights into the mass distribution of the planet. Aims. In this context, we aim to re-determine the orbital parameters of WASP-43b-in particular, orbital period, eccentricity, and argument of the periastron-and its orbital evolution. We study the outcomes of the tidal interaction with the host star:whether tidal decay and periastron precession are occurring in the system. Method. We observed the system with HARPS, whose data we present for the first time, and we also analyse the newly acquired JWST full-phase light curve. We fit jointly archival and new radial velocity and transit and occultation mid-times, including tidal decay, periastron precession and long-term acceleration in the system. Results. We detected a tidal decay rate of \dotP_a=(-1.99pm0.50) and a periastron precession rate of \dotomega=(0.1851+0.0070-0.0077)=(0.1727+0.0083-0.0089)deg/d=(621.72+29.88-32.04)arcsec/d. This is the first time that both periastron precession and tidal decay are simultaneously detected in an exoplanetary system. The observed tidal interactions can neither be explained by the tidal contribution to apsidal motion of a non-aligned stellar or planetary rotation axis nor by assuming non-synchronous rotation for the planet, and a value for the planetary Love number cannot be derived. [...]

  • 11 authors
·
Jan 7, 2025

IndicDB -- Benchmarking Multilingual Text-to-SQL Capabilities in Indian Languages

While Large Language Models (LLMs) have significantly advanced Text-to-SQL performance, existing benchmarks predominantly focus on Western contexts and simplified schemas, leaving a gap in real-world, non-Western applications. We present IndicDB, a multilingual Text-to-SQL benchmark for evaluating cross-lingual semantic parsing across diverse Indic languages. The relational schemas are sourced from open-data platforms, including the National Data and Analytics Platform (NDAP) and the India Data Portal (IDP), ensuring realistic administrative data complexity. IndicDB comprises 20 databases across 237 tables. To convert denormalized government data into rich relational structures, we employ an iterative three-agent framework (Architect, Auditor, Refiner) to ensure structural rigor and high relational density (11.85 tables per database; join depths up to six). Our pipeline is value-aware, difficulty-calibrated, and join-enforced, generating 15,617 tasks across English, Hindi, and five Indic languages. We evaluate cross-lingual semantic parsing performance of state-of-the-art models (DeepSeek v3.2, MiniMax 2.7, LLaMA 3.3, Qwen3) across seven linguistic variants. Results show a 9.00% performance drop from English to Indic languages, revealing an "Indic Gap" driven by harder schema linking, increased structural ambiguity, and limited external knowledge. IndicDB serves as a rigorous benchmark for multilingual Text-to-SQL. Code and data: https://anonymous.4open.science/r/multilingualText2Sql-Indic--DDCC/

  • 4 authors
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Apr 14