new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Apr 14

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

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

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

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

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

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

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

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
·
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
·
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
·
Sep 29, 2024

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
·
Mar 24, 2025

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

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
·
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

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

Peakbagging the K2 KEYSTONE sample with PBjam: characterising the individual mode frequencies in solar-like oscillators

The pattern of individual mode frequencies in solar-like oscillators provides valuable insight into their properties and interior structures. The identification and characterisation of these modes requires high signal-to-noise and frequency resolution. The KEYSTONE project unlocks the asteroseismic potential of the K2 mission by providing individually reduced, high-quality time series data, global asteroseismic parameters, and spectroscopic analysis for 173 solar-like oscillators. In this work, we build on the KEYSTONE project and present the first analysis of the pattern of individual modes in the oscillation spectra for the K2 KEYSTONE stars. We perform a robust identification and characterisation of the modes through peakbagging methods in the open-source analysis tool PBjam. We present over 6000 mode frequencies, widths, and heights for 168 stars in the sample, covering the HR diagram from FGK dwarfs to sub-giants and the lower red giant branch, providing a significant increase in the number of individual mode frequency detections for main sequence and sub-giant oscillators. This study also presents sample-wide trends of oscillation patterns as a function of the fundamental stellar properties, and improves the precision of the global asteroseismic parameters. These measurements are part of the legacy of the K2 mission, and can be used to perform detailed modelling to improve the precision of fundamental properties of these stars. The results of this analysis provides evidence for the validity of using PBjam to identify and characterise the modes resulting from the observations of the future PLATO mission.

  • 8 authors
·
Oct 24, 2025

XRISM Observations of Cassiopeia A: Overview, Atomic Data, and Spectral Models

Cassiopeia A (Cas A) is the youngest known core-collapse supernova remnant (SNR) in the Galaxy and is perhaps the best-studied SNR in X-rays. Cas A has a line-rich spectrum dominated by thermal emission and given its high flux, it is an appealing target for high-resolution X-ray spectroscopy. Cas A was observed at two different locations during the Performance Verification phase of the XRISM mission, one location in the southeastern part (SE) of the remnant and one in the northwestern part (NW). This paper serves as an overview of these observations and discusses some of the issues relevant for the analysis of the data. We present maps of the so-called ``spatial-spectral mixing'' effect due to the fact that the XRISM point-spread function is larger than a pixel in the Resolve calorimeter array. We analyze spectra from two bright, on-axis regions such that the effects of spatial-spectral mixing are minimized. We find that it is critical to include redshifts/blueshifts and broadening of the emission lines in the two thermal components to achieve a reasonable fit given the high spectral resolution of the Resolve calorimeter. We fit the spectra with two versions of the AtomDB atomic database (3.0.9 and 3.1.0) and two versions of the SPEX (3.08.00 and 3.08.01*) spectral fitting software. Overall we find good agreement between AtomDB 3.1.0 and SPEX 3.08.01* for the spectral models considered in this paper. The most significant difference we found between AtomDB 3.0.9 and 3.1.0 and between AtomDB 3.1.0 and SPEX 3.08.01* is the Ni abundance, with the new atomic data favoring a considerably lower (up to a factor of 3) Ni abundance. Both regions exhibit significantly enhanced abundances compared to Solar values indicating that supernova ejecta dominate the emission in these regions. We find that the abundance ratios of Ti/Fe, Mn/Fe, \& Ni/Fe are significantly lower in the NW than the SE.

  • 17 authors
·
Aug 1, 2025

Arboretum: A Large Multimodal Dataset Enabling AI for Biodiversity

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

  • 15 authors
·
Jun 25, 2024 1

Euclid Quick Data Release (Q1): From images to multiwavelength catalogues: the Euclid MERge Processing Function

The Euclid satellite is an ESA mission that was launched in July 2023. \Euclid is working in its regular observing mode with the target of observing an area of 14,000~deg^2 with two instruments, the Visible Camera (VIS) and the Near IR Spectrometer and Photometer (NISP) down to I_{rm E} = 24.5~mag (10, sigma) in the Euclid Wide Survey. Ground-based imaging data in the ugriz bands complement the \Euclid data to enable photo-z determination and VIS PSF modeling for week lensing analysis. Euclid investigates the distance-redshift relation and the evolution of cosmic structures by measuring shapes and redshifts of galaxies and clusters of galaxies out to zsim 2. Generating the multi-wavelength catalogues from \Euclid and ground-based data is an essential part of the \Euclid data processing system. In the framework of the \Euclid Science Ground Segment (SGS), the aim of the MER Processing Function (PF) pipeline is to detect objects in the \Euclid imaging data, measure their properties, and MERge them into a single multi-wavelength catalogue. The MER PF pipeline performs source detection on both visible (VIS) and near-infrared (NIR) images and offers four different photometric measurements: Kron total flux, aperture photometry on PSF-matched images, template fitting photometry, and S\'ersic fitting photometry. Furthermore, the MER PF pipeline measures a set of ancillary quantities, spanning from morphology to quality flags, to better characterise all detected sources. In this paper, we show how the MER PF pipeline is designed, detailing its main steps, and we show that the pipeline products meet the tight requirements that Euclid aims to achieve on photometric accuracy. We also present the other measurements (e.g. morphology) that are included in the OU-MER output catalogues and we list all output products coming out of the MER PF pipeline.

  • 348 authors
·
Mar 19, 2025

DB-GPT: Empowering Database Interactions with Private Large Language Models

The recent breakthroughs in large language models (LLMs) are positioned to transition many areas of software. Database technologies particularly have an important entanglement with LLMs as efficient and intuitive database interactions are paramount. In this paper, we present DB-GPT, a revolutionary and production-ready project that integrates LLMs with traditional database systems to enhance user experience and accessibility. DB-GPT is designed to understand natural language queries, provide context-aware responses, and generate complex SQL queries with high accuracy, making it an indispensable tool for users ranging from novice to expert. The core innovation in DB-GPT lies in its private LLM technology, which is fine-tuned on domain-specific corpora to maintain user privacy and ensure data security while offering the benefits of state-of-the-art LLMs. We detail the architecture of DB-GPT, which includes a novel retrieval augmented generation (RAG) knowledge system, an adaptive learning mechanism to continuously improve performance based on user feedback and a service-oriented multi-model framework (SMMF) with powerful data-driven agents. Our extensive experiments and user studies confirm that DB-GPT represents a paradigm shift in database interactions, offering a more natural, efficient, and secure way to engage with data repositories. The paper concludes with a discussion of the implications of DB-GPT framework on the future of human-database interaction and outlines potential avenues for further enhancements and applications in the field. The project code is available at https://github.com/eosphoros-ai/DB-GPT. Experience DB-GPT for yourself by installing it with the instructions https://github.com/eosphoros-ai/DB-GPT#install and view a concise 10-minute video at https://www.youtube.com/watch?v=KYs4nTDzEhk.

  • 16 authors
·
Dec 28, 2023

Samanantar: The Largest Publicly Available Parallel Corpora Collection for 11 Indic Languages

We present Samanantar, the largest publicly available parallel corpora collection for Indic languages. The collection contains a total of 49.7 million sentence pairs between English and 11 Indic languages (from two language families). Specifically, we compile 12.4 million sentence pairs from existing, publicly-available parallel corpora, and additionally mine 37.4 million sentence pairs from the web, resulting in a 4x increase. We mine the parallel sentences from the web by combining many corpora, tools, and methods: (a) web-crawled monolingual corpora, (b) document OCR for extracting sentences from scanned documents, (c) multilingual representation models for aligning sentences, and (d) approximate nearest neighbor search for searching in a large collection of sentences. Human evaluation of samples from the newly mined corpora validate the high quality of the parallel sentences across 11 languages. Further, we extract 83.4 million sentence pairs between all 55 Indic language pairs from the English-centric parallel corpus using English as the pivot language. We trained multilingual NMT models spanning all these languages on Samanantar, which outperform existing models and baselines on publicly available benchmarks, such as FLORES, establishing the utility of Samanantar. Our data and models are available publicly at https://indicnlp.ai4bharat.org/samanantar/ and we hope they will help advance research in NMT and multilingual NLP for Indic languages.

  • 18 authors
·
Apr 12, 2021

AutoMIR: Effective Zero-Shot Medical Information Retrieval without Relevance Labels

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

  • 4 authors
·
Oct 25, 2024 2

Online Writer Retrieval with Chinese Handwritten Phrases: A Synergistic Temporal-Frequency Representation Learning Approach

Currently, the prevalence of online handwriting has spurred a critical need for effective retrieval systems to accurately search relevant handwriting instances from specific writers, known as online writer retrieval. Despite the growing demand, this field suffers from a scarcity of well-established methodologies and public large-scale datasets. This paper tackles these challenges with a focus on Chinese handwritten phrases. First, we propose DOLPHIN, a novel retrieval model designed to enhance handwriting representations through synergistic temporal-frequency analysis. For frequency feature learning, we propose the HFGA block, which performs gated cross-attention between the vanilla temporal handwriting sequence and its high-frequency sub-bands to amplify salient writing details. For temporal feature learning, we propose the CAIR block, tailored to promote channel interaction and reduce channel redundancy. Second, to address data deficit, we introduce OLIWER, a large-scale online writer retrieval dataset encompassing over 670,000 Chinese handwritten phrases from 1,731 individuals. Through extensive evaluations, we demonstrate the superior performance of DOLPHIN over existing methods. In addition, we explore cross-domain writer retrieval and reveal the pivotal role of increasing feature alignment in bridging the distributional gap between different handwriting data. Our findings emphasize the significance of point sampling frequency and pressure features in improving handwriting representation quality and retrieval performance. Code and dataset are available at https://github.com/SCUT-DLVCLab/DOLPHIN.

  • 2 authors
·
Dec 16, 2024

MeSH Suggester: A Library and System for MeSH Term Suggestion for Systematic Review Boolean Query Construction

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

  • 3 authors
·
Dec 18, 2022

GAIA Search: Hugging Face and Pyserini Interoperability for NLP Training Data Exploration

Noticing the urgent need to provide tools for fast and user-friendly qualitative analysis of large-scale textual corpora of the modern NLP, we propose to turn to the mature and well-tested methods from the domain of Information Retrieval (IR) - a research field with a long history of tackling TB-scale document collections. We discuss how Pyserini - a widely used toolkit for reproducible IR research can be integrated with the Hugging Face ecosystem of open-source AI libraries and artifacts. We leverage the existing functionalities of both platforms while proposing novel features further facilitating their integration. Our goal is to give NLP researchers tools that will allow them to develop retrieval-based instrumentation for their data analytics needs with ease and agility. We include a Jupyter Notebook-based walk through the core interoperability features, available on GitHub at https://github.com/huggingface/gaia. We then demonstrate how the ideas we present can be operationalized to create a powerful tool for qualitative data analysis in NLP. We present GAIA Search - a search engine built following previously laid out principles, giving access to four popular large-scale text collections. GAIA serves a dual purpose of illustrating the potential of methodologies we discuss but also as a standalone qualitative analysis tool that can be leveraged by NLP researchers aiming to understand datasets prior to using them in training. GAIA is hosted live on Hugging Face Spaces - https://huggingface.co/spaces/spacerini/gaia.

  • 9 authors
·
Jun 2, 2023

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

  • 11 authors
·
May 23, 2025 2

An open dataset for the evolution of oracle bone characters: EVOBC

The earliest extant Chinese characters originate from oracle bone inscriptions, which are closely related to other East Asian languages. These inscriptions hold immense value for anthropology and archaeology. However, deciphering oracle bone script remains a formidable challenge, with only approximately 1,600 of the over 4,500 extant characters elucidated to date. Further scholarly investigation is required to comprehensively understand this ancient writing system. Artificial Intelligence technology is a promising avenue for deciphering oracle bone characters, particularly concerning their evolution. However, one of the challenges is the lack of datasets mapping the evolution of these characters over time. In this study, we systematically collected ancient characters from authoritative texts and websites spanning six historical stages: Oracle Bone Characters - OBC (15th century B.C.), Bronze Inscriptions - BI (13th to 221 B.C.), Seal Script - SS (11th to 8th centuries B.C.), Spring and Autumn period Characters - SAC (770 to 476 B.C.), Warring States period Characters - WSC (475 B.C. to 221 B.C.), and Clerical Script - CS (221 B.C. to 220 A.D.). Subsequently, we constructed an extensive dataset, namely EVolution Oracle Bone Characters (EVOBC), consisting of 229,170 images representing 13,714 distinct character categories. We conducted validation and simulated deciphering on the constructed dataset, and the results demonstrate its high efficacy in aiding the study of oracle bone script. This openly accessible dataset aims to digitalize ancient Chinese scripts across multiple eras, facilitating the decipherment of oracle bone script by examining the evolution of glyph forms.

  • 9 authors
·
Jan 22, 2024

RePanda: Pandas-powered Tabular Verification and Reasoning

Fact-checking tabular data is essential for ensuring the accuracy of structured information. However, existing methods often rely on black-box models with opaque reasoning. We introduce RePanda, a structured fact verification approach that translates claims into executable pandas queries, enabling interpretable and verifiable reasoning. To train RePanda, we construct PanTabFact, a structured dataset derived from the TabFact train set, where claims are paired with executable queries generated using DeepSeek-Chat and refined through automated error correction. Fine-tuning DeepSeek-coder-7B-instruct-v1.5 on PanTabFact, RePanda achieves 84.09% accuracy on the TabFact test set. To evaluate Out-of-Distribution (OOD) generalization, we interpret question-answer pairs from WikiTableQuestions as factual claims and refer to this dataset as WikiFact. Without additional fine-tuning, RePanda achieves 84.72% accuracy on WikiFact, significantly outperforming all other baselines and demonstrating strong OOD robustness. Notably, these results closely match the zero-shot performance of DeepSeek-Chat (671B), indicating that our fine-tuning approach effectively distills structured reasoning from a much larger model into a compact, locally executable 7B model. Beyond fact verification, RePanda extends to tabular question answering by generating executable queries that retrieve precise answers. To support this, we introduce PanWiki, a dataset mapping WikiTableQuestions to pandas queries. Fine-tuning on PanWiki, RePanda achieves 75.1% accuracy in direct answer retrieval. These results highlight the effectiveness of structured execution-based reasoning for tabular verification and question answering. We have publicly released the dataset on Hugging Face at datasets/AtoosaChegini/PanTabFact.

  • 4 authors
·
Mar 14, 2025

Neural Databases

In recent years, neural networks have shown impressive performance gains on long-standing AI problems, and in particular, answering queries from natural language text. These advances raise the question of whether they can be extended to a point where we can relax the fundamental assumption of database management, namely, that our data is represented as fields of a pre-defined schema. This paper presents a first step in answering that question. We describe NeuralDB, a database system with no pre-defined schema, in which updates and queries are given in natural language. We develop query processing techniques that build on the primitives offered by the state of the art Natural Language Processing methods. We begin by demonstrating that at the core, recent NLP transformers, powered by pre-trained language models, can answer select-project-join queries if they are given the exact set of relevant facts. However, they cannot scale to non-trivial databases and cannot perform aggregation queries. Based on these findings, we describe a NeuralDB architecture that runs multiple Neural SPJ operators in parallel, each with a set of database sentences that can produce one of the answers to the query. The result of these operators is fed to an aggregation operator if needed. We describe an algorithm that learns how to create the appropriate sets of facts to be fed into each of the Neural SPJ operators. Importantly, this algorithm can be trained by the Neural SPJ operator itself. We experimentally validate the accuracy of NeuralDB and its components, showing that we can answer queries over thousands of sentences with very high accuracy.

  • 6 authors
·
Oct 14, 2020

Estimation of Classical Cepheid's Physical Parameters from NIR Light Curves

Recent space-borne and ground-based observations provide photometric measurements as time series. The effect of interstellar dust extinction in the near-infrared range is only 10% of that measured in the V band. However, the sensitivity of the light curve shape to the physical parameters in the near-infrared is much lower. So, interpreting these types of data sets requires new approaches like the different large-scale surveys, which create similar problems with big data. Using a selected data set, we provide a method for applying routines implemented in R to extract most information of measurements to determine physical parameters, which can also be used in automatic classification schemes and pipeline processing. We made a multivariate classification of 131 Cepheid light curves (LC) in J, H, and K colors, where all the LCs were represented in 20D parameter space in these colors separately. Performing a Principal Component Analysis (PCA), we got an orthogonal coordinate system and squared Euclidean distances between LCs, with 6 significant eigenvalues, reducing the 20-dimension to 6. We also estimated the optimal number of partitions of similar objects and found it to be equal to 7 in each color; their dependence on the period, absolute magnitude, amplitude, and metallicity are also discussed. We computed the Spearman rank correlations, showing that periods and absolute magnitudes correlate with the first three PCs significantly. The first two PC are also found to have a relationship with the amplitude, but the metallicity effects are only marginal. The method shown can be generalized and implemented in unsupervised classification schemes and analysis of mixed and biased samples. The analysis of our Classical Cepheid near-infrared LC sample showed that the J, H, K curves are insufficient for determination of stellar metallicity, with mass being the key factor shaping them.

  • 2 authors
·
Dec 9, 2024

Oracle Bone Inscriptions Multi-modal Dataset

Oracle bone inscriptions(OBI) is the earliest developed writing system in China, bearing invaluable written exemplifications of early Shang history and paleography. However, the task of deciphering OBI, in the current climate of the scholarship, can prove extremely challenging. Out of the 4,500 oracle bone characters excavated, only a third have been successfully identified. Therefore, leveraging the advantages of advanced AI technology to assist in the decipherment of OBI is a highly essential research topic. However, fully utilizing AI's capabilities in these matters is reliant on having a comprehensive and high-quality annotated OBI dataset at hand whereas most existing datasets are only annotated in just a single or a few dimensions, limiting the value of their potential application. For instance, the Oracle-MNIST dataset only offers 30k images classified into 10 categories. Therefore, this paper proposes an Oracle Bone Inscriptions Multi-modal Dataset(OBIMD), which includes annotation information for 10,077 pieces of oracle bones. Each piece has two modalities: pixel-level aligned rubbings and facsimiles. The dataset annotates the detection boxes, character categories, transcriptions, corresponding inscription groups, and reading sequences in the groups of each oracle bone character, providing a comprehensive and high-quality level of annotations. This dataset can be used for a variety of AI-related research tasks relevant to the field of OBI, such as OBI Character Detection and Recognition, Rubbing Denoising, Character Matching, Character Generation, Reading Sequence Prediction, Missing Characters Completion task and so on. We believe that the creation and publication of a dataset like this will help significantly advance the application of AI algorithms in the field of OBI research.

  • 20 authors
·
Jul 4, 2024

EgyBERT: A Large Language Model Pretrained on Egyptian Dialect Corpora

This study presents EgyBERT, an Arabic language model pretrained on 10.4 GB of Egyptian dialectal texts. We evaluated EgyBERT's performance by comparing it with five other multidialect Arabic language models across 10 evaluation datasets. EgyBERT achieved the highest average F1-score of 84.25% and an accuracy of 87.33%, significantly outperforming all other comparative models, with MARBERTv2 as the second best model achieving an F1-score 83.68% and an accuracy 87.19%. Additionally, we introduce two novel Egyptian dialectal corpora: the Egyptian Tweets Corpus (ETC), containing over 34.33 million tweets (24.89 million sentences) amounting to 2.5 GB of text, and the Egyptian Forums Corpus (EFC), comprising over 44.42 million sentences (7.9 GB of text) collected from various Egyptian online forums. Both corpora are used in pretraining the new model, and they are the largest Egyptian dialectal corpora to date reported in the literature. Furthermore, this is the first study to evaluate the performance of various language models on Egyptian dialect datasets, revealing significant differences in performance that highlight the need for more dialect-specific models. The results confirm the effectiveness of EgyBERT model in processing and analyzing Arabic text expressed in Egyptian dialect, surpassing other language models included in the study. EgyBERT model is publicly available on https://huggingface.co/faisalq/EgyBERT.

  • 1 authors
·
Aug 6, 2024

Ashaar: Automatic Analysis and Generation of Arabic Poetry Using Deep Learning Approaches

Poetry holds immense significance within the cultural and traditional fabric of any nation. It serves as a vehicle for poets to articulate their emotions, preserve customs, and convey the essence of their culture. Arabic poetry is no exception, having played a cherished role in the heritage of the Arabic community throughout history and maintaining its relevance in the present era. Typically, comprehending Arabic poetry necessitates the expertise of a linguist who can analyze its content and assess its quality. This paper presents the introduction of a framework called Ashaar https://github.com/ARBML/Ashaar, which encompasses a collection of datasets and pre-trained models designed specifically for the analysis and generation of Arabic poetry. The pipeline established within our proposed approach encompasses various aspects of poetry, such as meter, theme, and era classification. It also incorporates automatic poetry diacritization, enabling more intricate analyses like automated extraction of the Arudi style. Additionally, we explore the feasibility of generating conditional poetry through the pre-training of a character-based GPT model. Furthermore, as part of this endeavor, we provide four datasets: one for poetry generation, another for diacritization, and two for Arudi-style prediction. These datasets aim to facilitate research and development in the field of Arabic poetry by enabling researchers and enthusiasts to delve into the nuances of this rich literary tradition.

  • 3 authors
·
Jul 12, 2023

WebFAQ: A Multilingual Collection of Natural Q&A Datasets for Dense Retrieval

We present WebFAQ, a large-scale collection of open-domain question answering datasets derived from FAQ-style schema.org annotations. In total, the data collection consists of 96 million natural question-answer (QA) pairs across 75 languages, including 47 million (49%) non-English samples. WebFAQ further serves as the foundation for 20 monolingual retrieval benchmarks with a total size of 11.2 million QA pairs (5.9 million non-English). These datasets are carefully curated through refined filtering and near-duplicate detection, yielding high-quality resources for training and evaluating multilingual dense retrieval models. To empirically confirm WebFAQ's efficacy, we use the collected QAs to fine-tune an in-domain pretrained XLM-RoBERTa model. Through this process of dataset-specific fine-tuning, the model achieves significant retrieval performance gains, which generalize - beyond WebFAQ - to other multilingual retrieval benchmarks evaluated in zero-shot setting. Last but not least, we utilize WebFAQ to construct a set of QA-aligned bilingual corpora spanning over 1000 language pairs using state-of-the-art bitext mining and automated LLM-assessed translation evaluation. Due to our advanced, automated method of bitext dataset generation, the resulting bilingual corpora demonstrate higher translation quality compared to similar datasets. WebFAQ and all associated resources are publicly available on GitHub and HuggingFace.

  • 5 authors
·
Feb 28, 2025