Daily Papers

Data contamination poses a significant challenge to the fairness of LLM evaluations in natural language processing tasks by inadvertently exposing models to test data during training. Current studies attempt to mitigate this issue by modifying existing datasets or generating new ones from freshly collected information. However, these methods fall short of ensuring contamination-resilient evaluation, as they fail to fully eliminate pre-existing knowledge from models or preserve the semantic complexity of the original datasets. To address these limitations, we propose CoreEval, a Contamination-resilient Evaluation strategy for automatically updating data with real-world knowledge. This approach begins by extracting entity relationships from the original data and leveraging the GDELT database to retrieve relevant, up-to-date knowledge. The retrieved knowledge is then recontextualized and integrated with the original data, which is refined and restructured to ensure semantic coherence and enhanced task relevance. Ultimately, a robust data reflection mechanism is employed to iteratively verify and refine labels, ensuring consistency between the updated and original datasets. Extensive experiments on updated datasets validate the robustness of CoreEval, demonstrating its effectiveness in mitigating performance overestimation caused by data contamination.

Recent advancements in Large Language Models (LLMs) have empowered LLM agents to autonomously collect world information, over which to conduct reasoning to solve complex problems. Given this capability, increasing interests have been put into employing LLM agents for predicting international events, which can influence decision-making and shape policy development on an international scale. Despite such a growing interest, there is a lack of a rigorous benchmark of LLM agents' forecasting capability and reliability. To address this gap, we introduce MIRAI, a novel benchmark designed to systematically evaluate LLM agents as temporal forecasters in the context of international events. Our benchmark features an agentic environment with tools for accessing an extensive database of historical, structured events and textual news articles. We refine the GDELT event database with careful cleaning and parsing to curate a series of relational prediction tasks with varying forecasting horizons, assessing LLM agents' abilities from short-term to long-term forecasting. We further implement APIs to enable LLM agents to utilize different tools via a code-based interface. In summary, MIRAI comprehensively evaluates the agents' capabilities in three dimensions: 1) autonomously source and integrate critical information from large global databases; 2) write codes using domain-specific APIs and libraries for tool-use; and 3) jointly reason over historical knowledge from diverse formats and time to accurately predict future events. Through comprehensive benchmarking, we aim to establish a reliable framework for assessing the capabilities of LLM agents in forecasting international events, thereby contributing to the development of more accurate and trustworthy models for international relation analysis.

In this work we study various Retrieval Augmented Regeneration (RAG) approaches to gain an understanding of the strengths and weaknesses of each approach in a question-answering analysis. To gain this understanding we use a case-study subset of the Global Database of Events, Language, and Tone (GDELT) dataset as well as a corpus of raw text scraped from the online news articles. To retrieve information from the text corpus we implement a traditional vector store RAG as well as state-of-the-art large language model (LLM) based approaches for automatically constructing KGs and retrieving the relevant subgraphs. In addition to these corpus approaches, we develop a novel ontology-based framework for constructing knowledge graphs (KGs) from GDELT directly which leverages the underlying schema of GDELT to create structured representations of global events. For retrieving relevant information from the ontology-based KGs we implement both direct graph queries and state-of-the-art graph retrieval approaches. We compare the performance of each method in a question-answering task. We find that while our ontology-based KGs are valuable for question-answering, automated extraction of the relevant subgraphs is challenging. Conversely, LLM-generated KGs, while capturing event summaries, often lack consistency and interpretability. Our findings suggest benefits of a synergistic approach between ontology and LLM-based KG construction, with proposed avenues toward that end.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our larger model BioGPT-Large achieves 81.0% on PubMedQA. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

The success of ChatGPT has ignited an AI race, with researchers striving to develop new large language models (LLMs) that can match or surpass the language understanding and generation abilities of commercial ones. In recent times, a number of models have emerged, claiming performance near that of GPT-3.5 or GPT-4 through various instruction-tuning methods. As practitioners of Text-to-SQL parsing, we are grateful for their valuable contributions to open-source research. However, it is important to approach these claims with a sense of scrutiny and ascertain the actual effectiveness of these models. Therefore, we pit six popular large language models against each other, systematically evaluating their Text-to-SQL parsing capability on nine benchmark datasets with five different prompting strategies, covering both zero-shot and few-shot scenarios. Regrettably, the open-sourced models fell significantly short of the performance achieved by closed-source models like GPT-3.5, highlighting the need for further work to bridge the performance gap between these models.

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

Motivation: The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts through the graphical Cohort Builder, users (especially new ones) may struggle to find specific cohort descriptors across hundreds of possible fields and properties. However, users may be better able to describe their desired cohort in free-text natural language. Results: We introduce GDC Cohort Copilot, an open-source copilot tool for curating cohorts from the GDC. GDC Cohort Copilot automatically generates the GDC cohort filter corresponding to a user-input natural language description of their desired cohort, before exporting the cohort back to the GDC for further analysis. An interactive user interface allows users to further refine the generated cohort. We develop and evaluate multiple large language models (LLMs) for GDC Cohort Copilot and demonstrate that our locally-served, open-source GDC Cohort LLM achieves better results than GPT-4o prompting in generating GDC cohorts. Availability and implementation: The standalone docker image for GDC Cohort Copilot is available at https://quay.io/repository/cdis/gdc-cohort-copilot. Source code is available at https://github.com/uc-cdis/gdc-cohort-copilot. GDC Cohort LLM weights are available at https://huggingface.co/uc-ctds.

We introduce GLM-130B, a bilingual (English and Chinese) pre-trained language model with 130 billion parameters. It is an attempt to open-source a 100B-scale model at least as good as GPT-3 and unveil how models of such a scale can be successfully pre-trained. Over the course of this effort, we face numerous unexpected technical and engineering challenges, particularly on loss spikes and disconvergence. In this paper, we introduce the training process of GLM-130B including its design choices, training strategies for both efficiency and stability, and engineering efforts. The resultant GLM-130B model offers significant outperformance over GPT-3 175B on a wide range of popular English benchmarks while the performance advantage is not observed in OPT-175B and BLOOM-176B. It also consistently and significantly outperforms ERNIE TITAN 3.0 260B -- the largest Chinese language model -- across related benchmarks. Finally, we leverage a unique scaling property of GLM-130B to reach INT4 quantization, without quantization aware training and with almost no performance loss, making it the first among 100B-scale models. More importantly, the property allows its effective inference on 4timesRTX 3090 (24G) or 8timesRTX 2080 Ti (11G) GPUs, the most ever affordable GPUs required for using 100B-scale models. The GLM-130B model weights are publicly accessible and its code, training logs, related toolkit, and lessons learned are open-sourced at https://github.com/THUDM/GLM-130B .

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

We describe the JD Explore Academy's submission of the WMT 2022 shared general translation task. We participated in all high-resource tracks and one medium-resource track, including Chinese-English, German-English, Czech-English, Russian-English, and Japanese-English. We push the limit of our previous work -- bidirectional training for translation by scaling up two main factors, i.e. language pairs and model sizes, namely the Vega-MT system. As for language pairs, we scale the "bidirectional" up to the "multidirectional" settings, covering all participating languages, to exploit the common knowledge across languages, and transfer them to the downstream bilingual tasks. As for model sizes, we scale the Transformer-Big up to the extremely large model that owns nearly 4.7 Billion parameters, to fully enhance the model capacity for our Vega-MT. Also, we adopt the data augmentation strategies, e.g. cycle translation for monolingual data, and bidirectional self-training for bilingual and monolingual data, to comprehensively exploit the bilingual and monolingual data. To adapt our Vega-MT to the general domain test set, generalization tuning is designed. Based on the official automatic scores of constrained systems, in terms of the sacreBLEU shown in Figure-1, we got the 1st place on {Zh-En (33.5), En-Zh (49.7), De-En (33.7), En-De (37.8), Cs-En (54.9), En-Cs (41.4) and En-Ru (32.7)}, 2nd place on {Ru-En (45.1) and Ja-En (25.6)}, and 3rd place on {En-Ja(41.5)}, respectively; W.R.T the COMET, we got the 1st place on {Zh-En (45.1), En-Zh (61.7), De-En (58.0), En-De (63.2), Cs-En (74.7), Ru-En (64.9), En-Ru (69.6) and En-Ja (65.1)}, 2nd place on {En-Cs (95.3) and Ja-En (40.6)}, respectively.

As large language models (LLMs) have demonstrated their powerful capabilities in plenty of domains and tasks, including context understanding, code generation, language generation, data storytelling, etc., many data analysts may raise concerns if their jobs will be replaced by AI. This controversial topic has drawn a lot of attention in public. However, we are still at a stage of divergent opinions without any definitive conclusion. Motivated by this, we raise the research question of "is GPT-4 a good data analyst?" in this work and aim to answer it by conducting head-to-head comparative studies. In detail, we regard GPT-4 as a data analyst to perform end-to-end data analysis with databases from a wide range of domains. We propose a framework to tackle the problems by carefully designing the prompts for GPT-4 to conduct experiments. We also design several task-specific evaluation metrics to systematically compare the performance between several professional human data analysts and GPT-4. Experimental results show that GPT-4 can achieve comparable performance to humans. We also provide in-depth discussions about our results to shed light on further studies before we reach the conclusion that GPT-4 can replace data analysts.

We introduce ChatGLM, an evolving family of large language models that we have been developing over time. This report primarily focuses on the GLM-4 language series, which includes GLM-4, GLM-4-Air, and GLM-4-9B. They represent our most capable models that are trained with all the insights and lessons gained from the preceding three generations of ChatGLM. To date, the GLM-4 models are pre-trained on ten trillions of tokens mostly in Chinese and English, along with a small set of corpus from 24 languages, and aligned primarily for Chinese and English usage. The high-quality alignment is achieved via a multi-stage post-training process, which involves supervised fine-tuning and learning from human feedback. Evaluations show that GLM-4 1) closely rivals or outperforms GPT-4 in terms of general metrics such as MMLU, GSM8K, MATH, BBH, GPQA, and HumanEval, 2) gets close to GPT-4-Turbo in instruction following as measured by IFEval, 3) matches GPT-4 Turbo (128K) and Claude 3 for long context tasks, and 4) outperforms GPT-4 in Chinese alignments as measured by AlignBench. The GLM-4 All Tools model is further aligned to understand user intent and autonomously decide when and which tool(s) touse -- including web browser, Python interpreter, text-to-image model, and user-defined functions -- to effectively complete complex tasks. In practical applications, it matches and even surpasses GPT-4 All Tools in tasks like accessing online information via web browsing and solving math problems using Python interpreter. Over the course, we have open-sourced a series of models, including ChatGLM-6B (three generations), GLM-4-9B (128K, 1M), GLM-4V-9B, WebGLM, and CodeGeeX, attracting over 10 million downloads on Hugging face in the year 2023 alone. The open models can be accessed through https://github.com/THUDM and https://huggingface.co/THUDM.

Generative pre-trained transformer (GPT) models have revolutionized the field of natural language processing (NLP) with remarkable performance in various tasks and also extend their power to multimodal domains. Despite their success, large GPT models like GPT-4 face inherent limitations such as considerable size, high computational requirements, complex deployment processes, and closed development loops. These constraints restrict their widespread adoption and raise concerns regarding their responsible development and usage. The need for user-friendly, relatively small, and open-sourced alternative GPT models arises from the desire to overcome these limitations while retaining high performance. In this survey paper, we provide an examination of alternative open-sourced models of large GPTs, focusing on user-friendly and relatively small models that facilitate easier deployment and accessibility. Through this extensive survey, we aim to equip researchers, practitioners, and enthusiasts with a thorough understanding of user-friendly and relatively small open-sourced models of large GPTs, their current state, challenges, and future research directions, inspiring the development of more efficient, accessible, and versatile GPT models that cater to the broader scientific community and advance the field of general artificial intelligence. The source contents are continuously updating in https://github.com/GPT-Alternatives/gpt_alternatives.

Context: Test-driven development (TDD) is a widely employed software development practice that involves developing test cases based on requirements prior to writing the code. Although various methods for automated test case generation have been proposed, they are not specifically tailored for TDD, where requirements instead of code serve as input. Objective: In this paper, we introduce a text-to-testcase generation approach based on a large language model (GPT-3.5) that is fine-tuned on our curated dataset with an effective prompt design. Method: Our approach involves enhancing the capabilities of basic GPT-3.5 for text-to-testcase generation task that is fine-tuned on our curated dataset with an effective prompting design. We evaluated the effectiveness of our approach using a span of five large-scale open-source software projects. Results: Our approach generated 7k test cases for open source projects, achieving 78.5% syntactic correctness, 67.09% requirement alignment, and 61.7% code coverage, which substantially outperforms all other LLMs (basic GPT-3.5, Bloom, and CodeT5). In addition, our ablation study demonstrates the substantial performance improvement of the fine-tuning and prompting components of the GPT-3.5 model. Conclusions: These findings lead us to conclude that fine-tuning and prompting should be considered in the future when building a language model for the text-to-testcase generation task

Gender-neutral translation (GNT) that avoids biased and undue binary assumptions is a pivotal challenge for the creation of more inclusive translation technologies. Advancements for this task in Machine Translation (MT), however, are hindered by the lack of dedicated parallel data, which are necessary to adapt MT systems to satisfy neutral constraints. For such a scenario, large language models offer hitherto unforeseen possibilities, as they come with the distinct advantage of being versatile in various (sub)tasks when provided with explicit instructions. In this paper, we explore this potential to automate GNT by comparing MT with the popular GPT-4 model. Through extensive manual analyses, our study empirically reveals the inherent limitations of current MT systems in generating GNTs and provides valuable insights into the potential and challenges associated with prompting for neutrality.

Recent work has shown the immense potential of synthetically generated datasets for training large language models (LLMs), especially for acquiring targeted skills. Current large-scale math instruction tuning datasets such as MetaMathQA (Yu et al., 2024) and MAmmoTH (Yue et al., 2024) are constructed using outputs from closed-source LLMs with commercially restrictive licenses. A key reason limiting the use of open-source LLMs in these data generation pipelines has been the wide gap between the mathematical skills of the best closed-source LLMs, such as GPT-4, and the best open-source LLMs. Building on the recent progress in open-source LLMs, our proposed prompting novelty, and some brute-force scaling, we construct OpenMathInstruct-1, a math instruction tuning dataset with 1.8M problem-solution pairs. The dataset is constructed by synthesizing code-interpreter solutions for GSM8K and MATH, two popular math reasoning benchmarks, using the recently released and permissively licensed Mixtral model. Our best model, OpenMath-CodeLlama-70B, trained on a subset of OpenMathInstruct-1, achieves a score of 84.6% on GSM8K and 50.7% on MATH, which is competitive with the best gpt-distilled models. We release our code, models, and the OpenMathInstruct-1 dataset under a commercially permissive license.

Language models can serve as a valuable tool for software developers to increase productivity. Large generative models can be used for code generation and code completion, while smaller encoder-only models are capable of performing code search tasks using natural language queries.These capabilities are heavily influenced by the quality and diversity of the available training data. Source code datasets used for training usually focus on the most popular languages and testing is mostly conducted on the same distributions, often overlooking low-resource programming languages. Motivated by the NLP generalization taxonomy proposed by Hupkes et.\,al., we propose a new benchmark dataset called GenCodeSearchNet (GeCS) which builds upon existing natural language code search datasets to systemically evaluate the programming language understanding generalization capabilities of language models. As part of the full dataset, we introduce a new, manually curated subset StatCodeSearch that focuses on R, a popular but so far underrepresented programming language that is often used by researchers outside the field of computer science. For evaluation and comparison, we collect several baseline results using fine-tuned BERT-style models and GPT-style large language models in a zero-shot setting.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

We present our winning system for Task~B (generation with reference passages) in SemEval-2026 Task~8: MTRAGEval. Our method is a heterogeneous ensemble of seven LLMs with two prompting variants, where a GPT-4o-mini judge selects the best candidate per instance. We ranked 1st out of 26 teams, achieving a conditioned harmonic mean of 0.7827 and outperforming the strongest baseline (gpt-oss-120b, 0.6390). Ablations show that diversity in model families, scales, and prompting strategies is essential, with the ensemble consistently beating any single model. We also introduce Meno-Lite-0.1, a 7B domain-adapted model with a strong cost--performance trade-off, and analyse MTRAGEval, highlighting annotation limitations and directions for improvement. Our code is publicly available: https://github.com/RaguTeam/ragu_mtrag_semeval

Synthetic data generation has the potential to impact applications and domains with scarce data. However, before such data is used for sensitive tasks such as mental health, we need an understanding of how different demographics are represented in it. In our paper, we analyze the potential of producing synthetic data using GPT-3 by exploring the various stressors it attributes to different race and gender combinations, to provide insight for future researchers looking into using LLMs for data generation. Using GPT-3, we develop HEADROOM, a synthetic dataset of 3,120 posts about depression-triggering stressors, by controlling for race, gender, and time frame (before and after COVID-19). Using this dataset, we conduct semantic and lexical analyses to (1) identify the predominant stressors for each demographic group; and (2) compare our synthetic data to a human-generated dataset. We present the procedures to generate queries to develop depression data using GPT-3, and conduct analyzes to uncover the types of stressors it assigns to demographic groups, which could be used to test the limitations of LLMs for synthetic data generation for depression data. Our findings show that synthetic data mimics some of the human-generated data distribution for the predominant depression stressors across diverse demographics.

This paper presents a comprehensive overview of the data preparation pipeline developed for the OpenGPT-X project, a large-scale initiative aimed at creating open and high-performance multilingual large language models (LLMs). The project goal is to deliver models that cover all major European languages, with a particular focus on real-world applications within the European Union. We explain all data processing steps, starting with the data selection and requirement definition to the preparation of the final datasets for model training. We distinguish between curated data and web data, as each of these categories is handled by distinct pipelines, with curated data undergoing minimal filtering and web data requiring extensive filtering and deduplication. This distinction guided the development of specialized algorithmic solutions for both pipelines. In addition to describing the processing methodologies, we provide an in-depth analysis of the datasets, increasing transparency and alignment with European data regulations. Finally, we share key insights and challenges faced during the project, offering recommendations for future endeavors in large-scale multilingual data preparation for LLMs.

Recent work like GPT-3 has demonstrated excellent performance of Zero-Shot and Few-Shot learning on many natural language processing (NLP) tasks by scaling up model size, dataset size and the amount of computation. However, training a model like GPT-3 requires huge amount of computational resources which makes it challengeable to researchers. In this work, we propose a method that incorporates large-scale distributed training performance into model architecture design. With this method, Yuan 1.0, the current largest singleton language model with 245B parameters, achieves excellent performance on thousands GPUs during training, and the state-of-the-art results on NLP tasks. A data processing method is designed to efficiently filter massive amount of raw data. The current largest high-quality Chinese corpus with 5TB high quality texts is built based on this method. In addition, a calibration and label expansion method is proposed to improve the Zero-Shot and Few-Shot performance, and steady improvement is observed on the accuracy of various tasks. Yuan 1.0 presents strong capacity of natural language generation, and the generated articles are difficult to distinguish from the human-written ones.

Large language models have exhibited robust performance across diverse natural language processing tasks. This report introduces TechGPT-2.0, a project designed to enhance the capabilities of large language models specifically in knowledge graph construction tasks, including named entity recognition (NER) and relationship triple extraction (RTE) tasks in NLP applications. Additionally, it serves as a LLM accessible for research within the Chinese open-source model community. We offer two 7B large language model weights and a QLoRA weight specialized for processing lengthy texts.Notably, TechGPT-2.0 is trained on Huawei's Ascend server. Inheriting all functionalities from TechGPT-1.0, it exhibits robust text processing capabilities, particularly in the domains of medicine and law. Furthermore, we introduce new capabilities to the model, enabling it to process texts in various domains such as geographical areas, transportation, organizations, literary works, biology, natural sciences, astronomical objects, and architecture. These enhancements also fortified the model's adeptness in handling hallucinations, unanswerable queries, and lengthy texts. This report provides a comprehensive and detailed introduction to the full fine-tuning process on Huawei's Ascend servers, encompassing experiences in Ascend server debugging, instruction fine-tuning data processing, and model training. Our code is available at https://github.com/neukg/TechGPT-2.0

Training multi-billion to trillion-parameter language models efficiently on GPU clusters requires leveraging multiple parallelism strategies. We present Galvatron, a novel open-source framework (dubbed 'Optimus-Megatron' in the implementation) that dynamically combines data parallelism, tensor model parallelism, and pipeline parallelism to optimize training throughput. Built atop PyTorch and integrating NVIDIA's Megatron-LM and Microsoft's DeepSpeed, Galvatron automatically selects and adjusts parallelism strategies in real time based on model architecture, hardware, and training dynamics. This paper details Galvatron's key features -- automatic hybrid parallelism selection, layer-wise and phase-wise strategy optimization, and runtime adaptation -- and contrasts them with existing static frameworks. We describe the system's technical stack, including its use of DeepSpeed's ZeRO and NCCL communication, and provide an in-depth implementation overview of its core modules (profilers, strategy selector, parallelism manager). We then illustrate how Galvatron can be seamlessly integrated into existing training pipelines with minimal code modifications, providing companies a plug-and-play solution for efficient large-model training. Finally, we situate Galvatron in context with related efforts (NVIDIA Megatron-LM, Microsoft DeepSpeed, Google GShard, Meta FairScale, etc.), highlighting how it advances the state of the art in distributed deep learning. References to the GitHub repository and relevant literature are provided throughout.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.

Legal tasks and datasets are often used as benchmarks for the capabilities of language models. However, openly available annotated datasets are rare. In this paper, we introduce AGB-DE, a corpus of 3,764 clauses from German consumer contracts that have been annotated and legally assessed by legal experts. Together with the data, we present a first baseline for the task of detecting potentially void clauses, comparing the performance of an SVM baseline with three fine-tuned open language models and the performance of GPT-3.5. Our results show the challenging nature of the task, with no approach exceeding an F1-score of 0.54. While the fine-tuned models often performed better with regard to precision, GPT-3.5 outperformed the other approaches with regard to recall. An analysis of the errors indicates that one of the main challenges could be the correct interpretation of complex clauses, rather than the decision boundaries of what is permissible and what is not.

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Utilizing large language models (LLMs) for transforming natural language questions into SQL queries (text-to-SQL) is a promising yet challenging approach, particularly when applied to real-world databases with complex and extensive schemas. In particular, effectively incorporating data catalogs and database values for SQL generation remains an obstacle, leading to suboptimal solutions. We address this problem by proposing a new pipeline that effectively retrieves relevant data and context, selects an efficient schema, and synthesizes correct and efficient SQL queries. To increase retrieval precision, our pipeline introduces a hierarchical retrieval method leveraging model-generated keywords, locality-sensitive hashing indexing, and vector databases. Additionally, we have developed an adaptive schema pruning technique that adjusts based on the complexity of the problem and the model's context size. Our approach generalizes to both frontier proprietary models like GPT-4 and open-source models such as Llama-3-70B. Through a series of ablation studies, we demonstrate the effectiveness of each component of our pipeline and its impact on the end-to-end performance. Our method achieves new state-of-the-art performance on the cross-domain challenging BIRD dataset.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

We assessed the performance of commercial Large Language Models (LLMs) GPT-3.5-Turbo and GPT-4 on tasks from the 2023 BioASQ challenge. In Task 11b Phase B, which is focused on answer generation, both models demonstrated competitive abilities with leading systems. Remarkably, they achieved this with simple zero-shot learning, grounded with relevant snippets. Even without relevant snippets, their performance was decent, though not on par with the best systems. Interestingly, the older and cheaper GPT-3.5-Turbo system was able to compete with GPT-4 in the grounded Q&A setting on factoid and list answers. In Task 11b Phase A, focusing on retrieval, query expansion through zero-shot learning improved performance, but the models fell short compared to other systems. The code needed to rerun these experiments is available through GitHub.

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.

In this paper, we introduce SciGen, a new challenge dataset for the task of reasoning-aware data-to-text generation consisting of tables from scientific articles and their corresponding descriptions. Describing scientific tables goes beyond the surface realization of the table content and requires reasoning over table values. The unique properties of SciGen are that (1) tables mostly contain numerical values, and (2) the corresponding descriptions require arithmetic reasoning. SciGen is therefore the first dataset that assesses the arithmetic reasoning capabilities of generation models on complex input structures, i.e., tables from scientific articles. We study the effectiveness of state-of-the-art data-to-text generation models on SciGen and evaluate the results using common metrics as well as human evaluation. Our results and analyses show that (a) while humans like to reason for describing scientific tables, the ability of state-of-the-art models is severely limited on this task, (b) while adding more training data improves the results, it is not the solution for reasoning-aware text generation, and (c) one of the main bottlenecks for this task is the lack of proper automatic evaluation metrics. The data, code, and annotations for human evaluation will be available at https://github.com/UKPLab/SciGen. SciGen opens new avenues for future research in reasoning-aware text generation and evaluation.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

The recently released GPT-4 Code Interpreter has demonstrated remarkable proficiency in solving challenging math problems, primarily attributed to its ability to seamlessly reason with natural language, generate code, execute code, and continue reasoning based on the execution output. In this paper, we present a method to fine-tune open-source language models, enabling them to use code for modeling and deriving math equations and, consequently, enhancing their mathematical reasoning abilities. We propose a method of generating novel and high-quality datasets with math problems and their code-based solutions, referred to as MathCodeInstruct. Each solution interleaves natural language, code, and execution results. We also introduce a customized supervised fine-tuning and inference approach. This approach yields the MathCoder models, a family of models capable of generating code-based solutions for solving challenging math problems. Impressively, the MathCoder models achieve state-of-the-art scores among open-source LLMs on the MATH (45.2%) and GSM8K (83.9%) datasets, substantially outperforming other open-source alternatives. Notably, the MathCoder model not only surpasses ChatGPT-3.5 and PaLM-2 on GSM8K and MATH but also outperforms GPT-4 on the competition-level MATH dataset. The dataset and models will be released at https://github.com/mathllm/MathCoder.

This paper presents the system description of our entry for the COLING 2025 RegNLP RIRAG (Regulatory Information Retrieval and Answer Generation) challenge, focusing on leveraging advanced information retrieval and answer generation techniques in regulatory domains. We experimented with a combination of embedding models, including Stella, BGE, CDE, and Mpnet, and leveraged fine-tuning and reranking for retrieving relevant documents in top ranks. We utilized a novel approach, LeSeR, which achieved competitive results with a recall@10 of 0.8201 and map@10 of 0.6655 for retrievals. This work highlights the transformative potential of natural language processing techniques in regulatory applications, offering insights into their capabilities for implementing a retrieval augmented generation system while identifying areas for future improvement in robustness and domain adaptation.

We introduce TechQA, a domain-adaptation question answering dataset for the technical support domain. The TechQA corpus highlights two real-world issues from the automated customer support domain. First, it contains actual questions posed by users on a technical forum, rather than questions generated specifically for a competition or a task. Second, it has a real-world size -- 600 training, 310 dev, and 490 evaluation question/answer pairs -- thus reflecting the cost of creating large labeled datasets with actual data. Consequently, TechQA is meant to stimulate research in domain adaptation rather than being a resource to build QA systems from scratch. The dataset was obtained by crawling the IBM Developer and IBM DeveloperWorks forums for questions with accepted answers that appear in a published IBM Technote---a technical document that addresses a specific technical issue. We also release a collection of the 801,998 publicly available Technotes as of April 4, 2019 as a companion resource that might be used for pretraining, to learn representations of the IT domain language.

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

Constructing real-world data-to-insight pipelines often involves data extraction from data lakes, data integration across heterogeneous data sources, and diverse operations from data cleaning to analysis. The design and implementation of data science pipelines require domain knowledge, technical expertise, and even project-specific insights. AI systems have shown remarkable reasoning, coding, and understanding capabilities. However, it remains unclear to what extent these capabilities translate into successful design and execution of such complex pipelines. We introduce KRAMABENCH: a benchmark composed of 104 manually-curated real-world data science pipelines spanning 1700 data files from 24 data sources in 6 different domains. We show that these pipelines test the end-to-end capabilities of AI systems on data processing, requiring data discovery, wrangling and cleaning, efficient processing, statistical reasoning, and orchestrating data processing steps given a high-level task. Our evaluation tests 5 general models and 3 code generation models using our reference framework, DS-GURU, which instructs the AI model to decompose a question into a sequence of subtasks, reason through each step, and synthesize Python code that implements the proposed design. Our results on KRAMABENCH show that, although the models are sufficiently capable of solving well-specified data science code generation tasks, when extensive data processing and domain knowledge are required to construct real-world data science pipelines, existing out-of-box models fall short. Progress on KramaBench represents crucial steps towards developing autonomous data science agents for real-world applications. Our code, reference framework, and data are available at https://github.com/mitdbg/KramaBench.

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.

Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage biomedical tools, which clinical experts and biomedical researchers rely on extensively in daily workflows. While recent general-domain tool-calling datasets have substantially improved the capabilities of LLM agents, existing efforts in the biomedical domain largely rely on in-context learning and restrict models to a small set of tools. To address this gap, we introduce BioTool, a comprehensive biomedical tool-calling dataset designed for fine-tuning LLMs. BioTool comprises 34 frequently used tools collected from the NCBI, Ensembl, and UniProt databases, along with 7,040 high-quality, human-verified query-API call pairs spanning variation, genomics, proteomics, evolution, and general biology. Fine-tuning a 4-billion-parameter LLM on BioTool yields substantial improvements in biomedical tool-calling performance, outperforming cutting-edge commercial LLMs such as GPT-5.1. Furthermore, human expert evaluations demonstrate that integrating a BioTool-fine-tuned tool caller significantly improves downstream answer quality compared to the same LLM without tool usage, highlighting the effectiveness of BioTool in enhancing the biomedical capabilities of LLMs. The full dataset and evaluation code are available at https://github.com/gxx27/BioTool

Data-to-text (D2T) generation in the biomedical domain is a promising - yet mostly unexplored - field of research. Here, we apply neural models for D2T generation to a real-world dataset consisting of package leaflets of European medicines. We show that fine-tuned transformers are able to generate realistic, multisentence text from data in the biomedical domain, yet have important limitations. We also release a new dataset (BioLeaflets) for benchmarking D2T generation models in the biomedical domain.

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as "model hubs" support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult - there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing the data. We present an open-source dataset, PTMTorrent, to facilitate the evaluation and understanding of PTM packages. This paper describes the creation, structure, usage, and limitations of the dataset. The dataset includes a snapshot of 5 model hubs and a total of 15,913 PTM packages. These packages are represented in a uniform data schema for cross-hub mining. We describe prior uses of this data and suggest research opportunities for mining using our dataset. The PTMTorrent dataset (v1) is available at: https://app.globus.org/file-manager?origin_id=55e17a6e-9d8f-11ed-a2a2-8383522b48d9&origin_path=%2F~%2F. Our dataset generation tools are available on GitHub: https://doi.org/10.5281/zenodo.7570357.

We propose a new shared task for tactical data-to-text generation in the domain of source code libraries. Specifically, we focus on text generation of function descriptions from example software projects. Data is drawn from existing resources used for studying the related problem of semantic parser induction (Richardson and Kuhn, 2017b; Richardson and Kuhn, 2017a), and spans a wide variety of both natural languages and programming languages. In this paper, we describe these existing resources, which will serve as training and development data for the task, and discuss plans for building new independent test sets.

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

The recent success of general-domain large language models (LLMs) has significantly changed the natural language processing paradigm towards a unified foundation model across domains and applications. In this paper, we focus on assessing the performance of GPT-4, the most capable LLM so far, on the text-based applications for radiology reports, comparing against state-of-the-art (SOTA) radiology-specific models. Exploring various prompting strategies, we evaluated GPT-4 on a diverse range of common radiology tasks and we found GPT-4 either outperforms or is on par with current SOTA radiology models. With zero-shot prompting, GPT-4 already obtains substantial gains (approx 10% absolute improvement) over radiology models in temporal sentence similarity classification (accuracy) and natural language inference (F_1). For tasks that require learning dataset-specific style or schema (e.g. findings summarisation), GPT-4 improves with example-based prompting and matches supervised SOTA. Our extensive error analysis with a board-certified radiologist shows GPT-4 has a sufficient level of radiology knowledge with only occasional errors in complex context that require nuanced domain knowledge. For findings summarisation, GPT-4 outputs are found to be overall comparable with existing manually-written impressions.

Current research on generative language models (GLMs) for automated text scoring (ATS) has focused almost exclusively on querying proprietary models via Application Programming Interfaces (APIs). Yet such practices raise issues around transparency and security, and these methods offer little in the way of efficiency or customizability. With the recent proliferation of smaller, open-source models, there is the option to explore GLMs with computers equipped with modest, consumer-grade hardware, that is, for the "GPU poor." In this study, we analyze the performance and efficiency of open-source, small-scale GLMs for ATS. Results show that GLMs can be fine-tuned to achieve adequate, though not state-of-the-art, performance. In addition to ATS, we take small steps towards analyzing models' capacity for generating feedback by prompting GLMs to explain their scores. Model-generated feedback shows promise, but requires more rigorous evaluation focused on targeted use cases.

Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets poses a significant challenge for researchers aiming to apply these breakthroughs in engineering design. Synthetic datasets emerge as a viable alternative. However, practitioners are often uncertain about generating high-quality datasets that accurately represent real-world data and are suitable for the intended downstream applications. This study aims to fill this knowledge gap by proposing comprehensive guidelines for generating, annotating, and validating synthetic datasets. The trade-offs and methods associated with each of these aspects are elaborated upon. Further, the practical implications of these guidelines are illustrated through the creation of a turbo-compressors dataset. The study underscores the importance of thoughtful sampling methods to ensure the appropriate size, diversity, utility, and realism of a dataset. It also highlights that design diversity does not equate to performance diversity or realism. By employing test sets that represent uniform, real, or task-specific samples, the influence of sample size and sampling strategy is scrutinized. Overall, this paper offers valuable insights for researchers intending to create and publish synthetic datasets for engineering design, thereby paving the way for more effective applications of AI advancements in the field. The code and data for the dataset and methods are made publicly accessible at https://github.com/cyrilpic/radcomp .

In this study, we present a novel dataset for training machine learning models translating between OpenMP Fortran and C++ code. To ensure reliability and applicability, the dataset is created from a range of representative open-source OpenMP benchmarks. It is also refined using a meticulous code similarity test. The effectiveness of our dataset is assessed using both quantitative (CodeBLEU) and qualitative (human evaluation) methods. We showcase how this dataset significantly elevates the translation competencies of large language models (LLMs). Specifically, models without prior coding knowledge experienced a boost of times~5.1 in their CodeBLEU scores, while models with some coding familiarity saw an impressive times~9.9-fold increase. The best fine-tuned model using our dataset outperforms GPT-4. It is also reaching human-level accuracy. This work underscores the immense potential of our dataset in propelling advancements in the domain of code translation for high-performance computing. The dataset is accessible at https://github.com/bin123apple/Fortran-CPP-HPC-code-translation-dataset{OpenMP-Fortran-CPP-Translation}.

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

We introduce DIODE, a dataset that contains thousands of diverse high resolution color images with accurate, dense, long-range depth measurements. DIODE (Dense Indoor/Outdoor DEpth) is the first public dataset to include RGBD images of indoor and outdoor scenes obtained with one sensor suite. This is in contrast to existing datasets that focus on just one domain/scene type and employ different sensors, making generalization across domains difficult. The dataset is available for download at http://diode-dataset.org

We present HILGEN, a Hierarchically-Informed Data Generation approach that combines domain knowledge from the Unified Medical Language System (UMLS) with synthetic data generated by large language models (LLMs), specifically GPT-3.5. Our approach leverages UMLS's hierarchical structure to expand training data with related concepts, while incorporating contextual information from LLMs through targeted prompts aimed at automatically generating synthetic examples for sparsely occurring named entities. The performance of the HILGEN approach was evaluated across four biomedical NER datasets (MIMIC III, BC5CDR, NCBI-Disease, and Med-Mentions) using BERT-Large and DANN (Data Augmentation with Nearest Neighbor Classifier) models, applying various data generation strategies, including UMLS, GPT-3.5, and their best ensemble. For the BERT-Large model, incorporating UMLS led to an average F1 score improvement of 40.36%, while using GPT-3.5 resulted in a comparable average increase of 40.52%. The Best-Ensemble approach using BERT-Large achieved the highest improvement, with an average increase of 42.29%. DANN model's F1 score improved by 22.74% on average using the UMLS-only approach. The GPT-3.5-based method resulted in a 21.53% increase, and the Best-Ensemble DANN model showed a more notable improvement, with an average increase of 25.03%. Our proposed HILGEN approach improves NER performance in few-shot settings without requiring additional manually annotated data. Our experiments demonstrate that an effective strategy for optimizing biomedical NER is to combine biomedical knowledge curated in the past, such as the UMLS, and generative LLMs to create synthetic training instances. Our future research will focus on exploring additional innovative synthetic data generation strategies for further improving NER performance.

We introduce MTet, the largest publicly available parallel corpus for English-Vietnamese translation. MTet consists of 4.2M high-quality training sentence pairs and a multi-domain test set refined by the Vietnamese research community. Combining with previous works on English-Vietnamese translation, we grow the existing parallel dataset to 6.2M sentence pairs. We also release the first pretrained model EnViT5 for English and Vietnamese languages. Combining both resources, our model significantly outperforms previous state-of-the-art results by up to 2 points in translation BLEU score, while being 1.6 times smaller.

We present DART, an open domain structured DAta Record to Text generation dataset with over 82k instances (DARTs). Data-to-Text annotations can be a costly process, especially when dealing with tables which are the major source of structured data and contain nontrivial structures. To this end, we propose a procedure of extracting semantic triples from tables that encodes their structures by exploiting the semantic dependencies among table headers and the table title. Our dataset construction framework effectively merged heterogeneous sources from open domain semantic parsing and dialogue-act-based meaning representation tasks by utilizing techniques such as: tree ontology annotation, question-answer pair to declarative sentence conversion, and predicate unification, all with minimum post-editing. We present systematic evaluation on DART as well as new state-of-the-art results on WebNLG 2017 to show that DART (1) poses new challenges to existing data-to-text datasets and (2) facilitates out-of-domain generalization. Our data and code can be found at https://github.com/Yale-LILY/dart.

The need for large text corpora has increased with the advent of pretrained language models and, in particular, the discovery of scaling laws for these models. Most available corpora have sufficient data only for languages with large dominant communities. However, there is no corpus available that (i) covers a wide range of minority languages; (ii) is generated by an open-source reproducible pipeline; and (iii) is rigorously cleaned from noise, making it trustworthy to use. We present GlotCC, a clean, document-level, 2TB general domain corpus derived from CommonCrawl, covering more than 1000 languages. We make GlotCC and the system used to generate it - including the pipeline, language identification model, and filters - available to the research community. Corpus v. 1.0 https://huggingface.co/datasets/cis-lmu/GlotCC-v1, Pipeline v. 3.0 https://github.com/cisnlp/GlotCC.

Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model scale, architecture, tokenization, and pretraining data while explicitly exposing task-level trade-offs. Our analysis shows that aggregate leaderboards are unstable: model rankings vary sharply across task categories, scale provides only modest and inconsistent gains, and architectural and pretraining alignment frequently outweigh parameter count. These results highlight limitations of current evaluation practices and position GENEB as a reference framework for principled comparison and category-aware model selection in genomic machine learning.

This study investigates various approaches to using Large Language Models (LLMs) for Text-to-SQL program synthesis, focusing on the outcomes and insights derived. Employing the popular Text-to-SQL dataset, spider, the goal was to input a natural language question along with the database schema and output the correct SQL SELECT query. The initial approach was to fine-tune a local and open-source model to generate the SELECT query. After QLoRa fine-tuning WizardLM's WizardCoder-15B model on the spider dataset, the execution accuracy for generated queries rose to a high of 61%. With the second approach, using the fine-tuned gpt-3.5-turbo-16k (Few-shot) + gpt-4-turbo (Zero-shot error correction), the execution accuracy reached a high of 82.1%. Of all the incorrect queries, most can be categorized into a seven different categories of what went wrong: selecting the wrong columns or wrong order of columns, grouping by the wrong column, predicting the wrong values in conditionals, using different aggregates than the ground truth, extra or too few JOIN clauses, inconsistencies in the Spider dataset, and lastly completely incorrect query structure. Most if not all of the queries fall into these categories and it is insightful to understanding where the faults still lie with LLM program synthesis and where they can be improved.

Recently, neural techniques have been used to generate source code automatically. While promising for declarative languages, these approaches achieve much poorer performance on datasets for imperative languages. Since a declarative language is typically embedded in an imperative language (i.e., the turducken-style programming) in real-world software development, the promising results on declarative languages can hardly lead to significant reduction of manual software development efforts. In this paper, we define a new code generation task: given a natural language comment, this task aims to generate a program in a base imperative language with an embedded declarative language. To our knowledge, this is the first turducken-style code generation task. For this task, we present Lyra: a dataset in Python with embedded SQL. This dataset contains 2,000 carefully annotated database manipulation programs from real-world projects. Each program is paired with both a Chinese comment and an English comment. In our experiment, we adopted Transformer, BERT-style, and GPT-style models as baselines. In the best setting, the generation performance of GPT-style models is better than others, where the AST exact matching accuracy is 24% and 25.5% when using Chinese and English comments, respectively. Therefore, we believe that Lyra provides a new challenge for code generation. Yet, overcoming this challenge may significantly boost the applicability of code generation techniques for real-world software development.

This research delves into the construction and utilization of synthetic datasets, specifically within the telematics sphere, leveraging OpenAI's powerful language model, ChatGPT. Synthetic datasets present an effective solution to challenges pertaining to data privacy, scarcity, and control over variables - characteristics that make them particularly valuable for research pursuits. The utility of these datasets, however, largely depends on their quality, measured through the lenses of diversity, relevance, and coherence. To illustrate this data creation process, a hands-on case study is conducted, focusing on the generation of a synthetic telematics dataset. The experiment involved an iterative guidance of ChatGPT, progressively refining prompts and culminating in the creation of a comprehensive dataset for a hypothetical urban planning scenario in Columbus, Ohio. Upon generation, the synthetic dataset was subjected to an evaluation, focusing on the previously identified quality parameters and employing descriptive statistics and visualization techniques for a thorough analysis. Despite synthetic datasets not serving as perfect replacements for actual world data, their potential in specific use-cases, when executed with precision, is significant. This research underscores the potential of AI models like ChatGPT in enhancing data availability for complex sectors like telematics, thus paving the way for a myriad of new research opportunities.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

Large Language Models (LLMs) have demonstrated strong natural language processing and code synthesis capabilities, which has led to their rapid adoption in software engineering applications. However, details about LLM training data are often not made public, which has caused concern as to whether existing bug benchmarks are included. In lieu of the training data for the popular GPT models, we examine the training data of the open-source LLM StarCoder, and find it likely that data from the widely used Defects4J benchmark was included, raising the possibility of its inclusion in GPT training data as well. This makes it difficult to tell how well LLM-based results on Defects4J would generalize, as for any results it would be unclear whether a technique's performance is due to LLM generalization or memorization. To remedy this issue and facilitate continued research on LLM-based SE, we present the GitHub Recent Bugs (GHRB) dataset, which includes 76 real-world Java bugs that were gathered after the OpenAI data cut-off point.

Influence estimation analyzes how changes to the training data can lead to different model predictions; this analysis can help us better understand these predictions, the models making those predictions, and the data sets they're trained on. However, most influence-estimation techniques are designed for deep learning models with continuous parameters. Gradient-boosted decision trees (GBDTs) are a powerful and widely-used class of models; however, these models are black boxes with opaque decision-making processes. In the pursuit of better understanding GBDT predictions and generally improving these models, we adapt recent and popular influence-estimation methods designed for deep learning models to GBDTs. Specifically, we adapt representer-point methods and TracIn, denoting our new methods TREX and BoostIn, respectively; source code is available at https://github.com/jjbrophy47/tree_influence. We compare these methods to LeafInfluence and other baselines using 5 different evaluation measures on 22 real-world data sets with 4 popular GBDT implementations. These experiments give us a comprehensive overview of how different approaches to influence estimation work in GBDT models. We find BoostIn is an efficient influence-estimation method for GBDTs that performs equally well or better than existing work while being four orders of magnitude faster. Our evaluation also suggests the gold-standard approach of leave-one-out (LOO) retraining consistently identifies the single-most influential training example but performs poorly at finding the most influential set of training examples for a given target prediction.

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their rewards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search, which focuses on exploiting high-rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via backtracking and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme, which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: https://github.com/dbsxodud-11/ls_gfn.

Recent advances in reasoning with large language models (LLMs)has shown remarkable reasoning capabilities in domains such as mathematics and coding, yet their application to clinical diagnosis remains underexplored. Here, we introduce ClinicalGPT-R1, a reasoning enhanced generalist large language model for disease diagnosis. Trained on a dataset of 20,000 real-world clinical records, ClinicalGPT-R1 leverages diverse training strategies to enhance diagnostic reasoning. To benchmark performance, we curated MedBench-Hard, a challenging dataset spanning seven major medical specialties and representative diseases. Experimental results demonstrate that ClinicalGPT-R1 outperforms GPT-4o in Chinese diagnostic tasks and achieves comparable performance to GPT-4 in English settings. This comparative study effectively validates the superior performance of ClinicalGPT-R1 in disease diagnosis tasks. Resources are available at https://github.com/medfound/medfound.

The Land Matrix initiative (https://landmatrix.org) and its global observatory aim to provide reliable data on large-scale land acquisitions to inform debates and actions in sectors such as agriculture, extraction, or energy in low- and middle-income countries. Although these data are recognized in the academic world, they remain underutilized in public policy, mainly due to the complexity of access and exploitation, which requires technical expertise and a good understanding of the database schema. The objective of this work is to simplify access to data from different database systems. The methods proposed in this article are evaluated using data from the Land Matrix. This work presents various comparisons of Large Language Models (LLMs) as well as combinations of LLM adaptations (Prompt Engineering, RAG, Agents) to query different database systems (GraphQL and REST queries). The experiments are reproducible, and a demonstration is available online: https://github.com/tetis-nlp/landmatrix-graphql-python.

Language models have shown promising performance on the task of translating natural language questions into SQL queries (Text-to-SQL). However, most of the state-of-the-art (SOTA) approaches rely on powerful yet closed-source large language models (LLMs), such as ChatGPT and GPT-4, which may have the limitations of unclear model architectures, data privacy risks, and expensive inference overheads. To address the limitations, we introduce CodeS, a series of pre-trained language models with parameters ranging from 1B to 15B, specifically designed for the text-to-SQL task. CodeS is a fully open-source language model, which achieves superior accuracy with much smaller parameter sizes. This paper studies the research challenges in building CodeS. To enhance the SQL generation abilities of CodeS, we adopt an incremental pre-training approach using a specifically curated SQL-centric corpus. Based on this, we address the challenges of schema linking and rapid domain adaptation through strategic prompt construction and a bi-directional data augmentation technique. We conduct comprehensive evaluations on multiple datasets, including the widely used Spider benchmark, the newly released BIRD benchmark, robustness-diagnostic benchmarks such as Spider-DK, Spider-Syn, Spider-Realistic, and Dr.Spider, as well as two real-world datasets created for financial and academic applications. The experimental results show that our CodeS achieves new SOTA accuracy and robustness on nearly all challenging text-to-SQL benchmarks.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

The translation of natural language questions to SQL queries has attracted growing attention, in particular in connection with transformers and similar language models. A large number of techniques are geared towards the English language; in this work, we thus investigated translation to SQL when input questions are given in the Portuguese language. To do so, we properly adapted state-of-the-art tools and resources. We changed the RAT-SQL+GAP system by relying on a multilingual BART model (we report tests with other language models), and we produced a translated version of the Spider dataset. Our experiments expose interesting phenomena that arise when non-English languages are targeted; in particular, it is better to train with original and translated training datasets together, even if a single target language is desired. This multilingual BART model fine-tuned with a double-size training dataset (English and Portuguese) achieved 83% of the baseline, making inferences for the Portuguese test dataset. This investigation can help other researchers to produce results in Machine Learning in a language different from English. Our multilingual ready version of RAT-SQL+GAP and the data are available, open-sourced as mRAT-SQL+GAP at: https://github.com/C4AI/gap-text2sql

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

We introduce TeleQnA, the first benchmark dataset designed to evaluate the knowledge of Large Language Models (LLMs) in telecommunications. Comprising 10,000 questions and answers, this dataset draws from diverse sources, including standards and research articles. This paper outlines the automated question generation framework responsible for creating this dataset, along with how human input was integrated at various stages to ensure the quality of the questions. Afterwards, using the provided dataset, an evaluation is conducted to assess the capabilities of LLMs, including GPT-3.5 and GPT-4. The results highlight that these models struggle with complex standards related questions but exhibit proficiency in addressing general telecom-related inquiries. Additionally, our results showcase how incorporating telecom knowledge context significantly enhances their performance, thus shedding light on the need for a specialized telecom foundation model. Finally, the dataset is shared with active telecom professionals, whose performance is subsequently benchmarked against that of the LLMs. The findings illustrate that LLMs can rival the performance of active professionals in telecom knowledge, thanks to their capacity to process vast amounts of information, underscoring the potential of LLMs within this domain. The dataset has been made publicly accessible on GitHub.

Accurate diagnosis of Alzheimer's disease (AD) requires handling tabular biomarker data, yet such data are often small and incomplete, where deep learning models frequently fail to outperform classical methods. Pretrained large language models (LLMs) offer few-shot generalization, structured reasoning, and interpretable outputs, providing a powerful paradigm shift for clinical prediction. We propose TAP-GPT Tabular Alzheimer's Prediction GPT, a domain-adapted tabular LLM framework built on TableGPT2 and fine-tuned for few-shot AD classification using tabular prompts rather than plain texts. We evaluate TAP-GPT across four ADNI-derived datasets, including QT-PAD biomarkers and region-level structural MRI, amyloid PET, and tau PET for binary AD classification. Across multimodal and unimodal settings, TAP-GPT improves upon its backbone models and outperforms traditional machine learning baselines in the few-shot setting while remaining competitive with state-of-the-art general-purpose LLMs. We show that feature selection mitigates degradation in high-dimensional inputs and that TAP-GPT maintains stable performance under simulated and real-world missingness without imputation. Additionally, TAP-GPT produces structured, modality-aware reasoning aligned with established AD biology and shows greater stability under self-reflection, supporting its use in iterative multi-agent systems. To our knowledge, this is the first systematic application of a tabular-specialized LLM to multimodal biomarker-based AD prediction, demonstrating that such pretrained models can effectively address structured clinical prediction tasks and laying the foundation for tabular LLM-driven multi-agent clinical decision-support systems. The source code is publicly available on GitHub: https://github.com/sophie-kearney/TAP-GPT.

This paper presents the first comprehensive analysis of ChatGPT's Text-to-SQL ability. Given the recent emergence of large-scale conversational language model ChatGPT and its impressive capabilities in both conversational abilities and code generation, we sought to evaluate its Text-to-SQL performance. We conducted experiments on 12 benchmark datasets with different languages, settings, or scenarios, and the results demonstrate that ChatGPT has strong text-to-SQL abilities. Although there is still a gap from the current state-of-the-art (SOTA) model performance, considering that the experiment was conducted in a zero-shot scenario, ChatGPT's performance is still impressive. Notably, in the ADVETA (RPL) scenario, the zero-shot ChatGPT even outperforms the SOTA model that requires fine-tuning on the Spider dataset by 4.1\%, demonstrating its potential for use in practical applications. To support further research in related fields, we have made the data generated by ChatGPT publicly available at https://github.com/THU-BPM/chatgpt-sql.

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.

This paper presents EasyRAG, a simple, lightweight, and efficient retrieval-augmented generation framework for automated network operations. Our framework has three advantages. The first is accurate question answering. We designed a straightforward RAG scheme based on (1) a specific data processing workflow (2) dual-route sparse retrieval for coarse ranking (3) LLM Reranker for reranking (4) LLM answer generation and optimization. This approach achieved first place in the GLM4 track in the preliminary round and second place in the GLM4 track in the semifinals. The second is simple deployment. Our method primarily consists of BM25 retrieval and BGE-reranker reranking, requiring no fine-tuning of any models, occupying minimal VRAM, easy to deploy, and highly scalable; we provide a flexible code library with various search and generation strategies, facilitating custom process implementation. The last one is efficient inference. We designed an efficient inference acceleration scheme for the entire coarse ranking, reranking, and generation process that significantly reduces the inference latency of RAG while maintaining a good level of accuracy; each acceleration scheme can be plug-and-play into any component of the RAG process, consistently enhancing the efficiency of the RAG system. Our code and data are released at https://github.com/BUAADreamer/EasyRAG.

GPT series models, such as GPT-3, CodeX, InstructGPT, ChatGPT, and so on, have gained considerable attention due to their exceptional natural language processing capabilities. However, despite the abundance of research on the difference in capabilities between GPT series models and fine-tuned models, there has been limited attention given to the evolution of GPT series models' capabilities over time. To conduct a comprehensive analysis of the capabilities of GPT series models, we select six representative models, comprising two GPT-3 series models (i.e., davinci and text-davinci-001) and four GPT-3.5 series models (i.e., code-davinci-002, text-davinci-002, text-davinci-003, and gpt-3.5-turbo). We evaluate their performance on nine natural language understanding (NLU) tasks using 21 datasets. In particular, we compare the performance and robustness of different models for each task under zero-shot and few-shot scenarios. Our extensive experiments reveal that the overall ability of GPT series models on NLU tasks does not increase gradually as the models evolve, especially with the introduction of the RLHF training strategy. While this strategy enhances the models' ability to generate human-like responses, it also compromises their ability to solve some tasks. Furthermore, our findings indicate that there is still room for improvement in areas such as model robustness.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

In this paper, we present gfnx, a fast and scalable package for training and evaluating Generative Flow Networks (GFlowNets) written in JAX. gfnx provides an extensive set of environments and metrics for benchmarking, accompanied with single-file implementations of core objectives for training GFlowNets. We include synthetic hypergrids, multiple sequence generation environments with various editing regimes and particular reward designs for molecular generation, phylogenetic tree construction, Bayesian structure learning, and sampling from the Ising model energy. Across different tasks, gfnx achieves significant wall-clock speedups compared to Pytorch-based benchmarks (such as torchgfn library) and author implementations. For example, gfnx achieves up to 55 times speedup on CPU-based sequence generation environments, and up to 80 times speedup with the GPU-based Bayesian network structure learning setup. Our package provides a diverse set of benchmarks and aims to standardize empirical evaluation and accelerate research and applications of GFlowNets. The library is available on GitHub (https://github.com/d-tiapkin/gfnx) and on pypi (https://pypi.org/project/gfnx/). Documentation is available on https://gfnx.readthedocs.io.

Generative language models have shown significant potential in single-turn Text-to-SQL. However, their performance does not extend equivalently to multi-turn Text-to-SQL. This is primarily due to generative language models' inadequacy in handling the complexities of context information and dynamic schema linking in multi-turn interactions. In this paper, we propose a framework named Track-SQL, which enhances generative language models with dual-extractive modules designed to track schema and contextual changes in multi-turn Text-to-SQL. Specifically, Track-SQL incorporates a Semantic-enhanced Schema Extractor and a Schema-aware Context Extractor. Experimental results demonstrate that Track-SQL achieves state-of-the-art performance on the SparC and CoSQL datasets. Furthermore, detailed ablation studies reveal that Track-SQL significantly improves execution accuracy in multi-turn interactions by 7.1\% and 9.55\% on these datasets, respectively. Our implementation will be open-sourced at https://github.com/DMIRLAB-Group/Track-SQL.

Commercial large language models (LLMs), like OpenAI's GPT-4 powering ChatGPT and Anthropic's Claude 3 Opus, have dominated natural language processing (NLP) benchmarks across different domains. New competing Open-Source alternatives like Mixtral 8x7B or Llama 3 have emerged and seem to be closing the gap while often offering higher throughput and being less costly to use. Open-Source LLMs can also be self-hosted, which makes them interesting for enterprise and clinical use cases where sensitive data should not be processed by third parties. We participated in the 12th BioASQ challenge, which is a retrieval augmented generation (RAG) setting, and explored the performance of current GPT models Claude 3 Opus, GPT-3.5-turbo and Mixtral 8x7b with in-context learning (zero-shot, few-shot) and QLoRa fine-tuning. We also explored how additional relevant knowledge from Wikipedia added to the context-window of the LLM might improve their performance. Mixtral 8x7b was competitive in the 10-shot setting, both with and without fine-tuning, but failed to produce usable results in the zero-shot setting. QLoRa fine-tuning and Wikipedia context did not lead to measurable performance gains. Our results indicate that the performance gap between commercial and open-source models in RAG setups exists mainly in the zero-shot setting and can be closed by simply collecting few-shot examples for domain-specific use cases. The code needed to rerun these experiments is available through GitHub.

Large language models (LLMs) have seen considerable advancements in natural language understanding tasks, yet there remains a gap to bridge before attaining true artificial general intelligence, especially concerning shortcomings in mathematical reasoning capabilities. We postulate that the inherent nature of LLM training, which focuses on predicting probabilities of next token, presents challenges in effectively modeling mathematical reasoning that demands exact calculations, both from data-driven and theoretical standpoints. In this paper, we address this challenge by enriching the data landscape and introducing a novel math dataset, enhanced with a capability to utilize a Python code interpreter. This dataset is derived from GSM8K and MATH and has been further refined through a combination of GPT-4 annotations, human review, and self-training processes, where the errors in the original GSM8K training set have been fixed. Additionally, we propose a tentative, easily replicable protocol for the fine-tuning of math-specific LLMs, which has led to a significant improvement in the performance of a 7B-parameter LLM on the GSM8K and MATH datasets. We are committed to advancing the field of mathematical reasoning in LLMs and, to that end, we have made the model checkpoints and will make the dataset publicly available. We hope this will facilitate further research and development within the community.

Biomedical named entity recognition (NER) presents unique challenges due to specialized vocabularies, the sheer volume of entities, and the continuous emergence of novel entities. Traditional NER models, constrained by fixed taxonomies and human annotations, struggle to generalize beyond predefined entity types or efficiently adapt to emerging concepts. To address these issues, we introduce GLiNER-biomed, a domain-adapted suite of Generalist and Lightweight Model for NER (GLiNER) models specifically tailored for biomedical NER. In contrast to conventional approaches, GLiNER uses natural language descriptions to infer arbitrary entity types, enabling zero-shot recognition. Our approach first distills the annotation capabilities of large language models (LLMs) into a smaller, more efficient model, enabling the generation of high-coverage synthetic biomedical NER data. We subsequently train two GLiNER architectures, uni- and bi-encoder, at multiple scales to balance computational efficiency and recognition performance. Evaluations on several biomedical datasets demonstrate that GLiNER-biomed outperforms state-of-the-art GLiNER models in both zero- and few-shot scenarios, achieving 5.96% improvement in F1-score over the strongest baseline. Ablation studies highlight the effectiveness of our synthetic data generation strategy and emphasize the complementary benefits of synthetic biomedical pre-training combined with fine-tuning on high-quality general-domain annotations. All datasets, models, and training pipelines are publicly available at https://github.com/ds4dh/GLiNER-biomed.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

Long sequences of text are challenging in the context of transformers, due to quadratic memory increase in the self-attention mechanism. As this issue directly affects the translation from natural language to SQL queries (as techniques usually take as input a concatenated text with the question and the database schema), we present techniques that allow long text sequences to be handled by transformers with up to 512 input tokens. We propose a training process with database schema pruning (removal of tables and columns names that are useless for the query of interest). In addition, we used a multilingual approach with the mT5-large model fine-tuned with a data-augmented Spider dataset in four languages simultaneously: English, Portuguese, Spanish, and French. Our proposed technique used the Spider dataset and increased the exact set match accuracy results from 0.718 to 0.736 in a validation dataset (Dev). Source code, evaluations, and checkpoints are available at: https://github.com/C4AI/gap-text2sql.

Synthesizing high-quality reasoning data for continual training has been proven to be effective in enhancing the performance of Large Language Models (LLMs). However, previous synthetic approaches struggle to easily scale up data and incur high costs in the pursuit of high quality. In this paper, we propose the Graph-based Synthetic Data Pipeline (GSDP), an economical and scalable framework for high-quality reasoning data synthesis. Inspired by knowledge graphs, we extracted knowledge points from seed data and constructed a knowledge point relationships graph to explore their interconnections. By exploring the implicit relationships among knowledge, our method achieves times255 data expansion. Furthermore, GSDP led by open-source models, achieves synthesis quality comparable to GPT-4-0613 while maintaining times100 lower costs. To tackle the most challenging mathematical reasoning task, we present the GSDP-MATH dataset comprising over 1.91 million pairs of math problems and answers. After fine-tuning on GSDP-MATH, GSDP-7B based on Mistral-7B achieves 37.7% accuracy on MATH and 78.4% on GSM8K, demonstrating the effectiveness of our method. The dataset and models trained in this paper will be available.

This work presents a new dataset for the Martian digital elevation model prediction task, ready for machine learning applications called MCTED. The dataset has been generated using a comprehensive pipeline designed to process high-resolution Mars orthoimage and DEM pairs from Day et al., yielding a dataset consisting of 80,898 data samples. The source images are data gathered by the Mars Reconnaissance Orbiter using the CTX instrument, providing a very diverse and comprehensive coverage of the Martian surface. Given the complexity of the processing pipelines used in large-scale DEMs, there are often artefacts and missing data points in the original data, for which we developed tools to solve or mitigate their impact. We divide the processed samples into training and validation splits, ensuring samples in both splits cover no mutual areas to avoid data leakage. Every sample in the dataset is represented by the optical image patch, DEM patch, and two mask patches, indicating values that were originally missing or were altered by us. This allows future users of the dataset to handle altered elevation regions as they please. We provide statistical insights of the generated dataset, including the spatial distribution of samples, the distributions of elevation values, slopes and more. Finally, we train a small U-Net architecture on the MCTED dataset and compare its performance to a monocular depth estimation foundation model, DepthAnythingV2, on the task of elevation prediction. We find that even a very small architecture trained on this dataset specifically, beats a zero-shot performance of a depth estimation foundation model like DepthAnythingV2. We make the dataset and code used for its generation completely open source in public repositories.

Neural Machine Translation (NMT) models are typically trained on datasets with limited exposure to Scientific, Technical and Educational domains. Translation models thus, in general, struggle with tasks that involve scientific understanding or technical jargon. Their performance is found to be even worse for low-resource Indian languages. Finding a translation dataset that tends to these domains in particular, poses a difficult challenge. In this paper, we address this by creating a multilingual parallel corpus containing more than 2.8 million rows of English-to-Indic and Indic-to-Indic high-quality translation pairs across 8 Indian languages. We achieve this by bitext mining human-translated transcriptions of NPTEL video lectures. We also finetune and evaluate NMT models using this corpus and surpass all other publicly available models at in-domain tasks. We also demonstrate the potential for generalizing to out-of-domain translation tasks by improving the baseline by over 2 BLEU on average for these Indian languages on the Flores+ benchmark. We are pleased to release our model and dataset via this link: https://huggingface.co/SPRINGLab.

This paper presents FormationEval, an open multiple-choice question benchmark for evaluating language models on petroleum geoscience and subsurface disciplines. The dataset contains 505 questions across seven domains including petrophysics, petroleum geology and reservoir engineering, derived from three authoritative sources using a reasoning model with detailed instructions and a concept-based approach that avoids verbatim copying of copyrighted text. Each question includes source metadata to support traceability and audit. The evaluation covers 72 models from major providers including OpenAI, Anthropic, Google, Meta and open-weight alternatives. The top performers achieve over 97\% accuracy, with Gemini 3 Pro Preview reaching 99.8\%, while tier and domain gaps persist. Among open-weight models, GLM-4.7 leads at 98.6\%, with several DeepSeek, Llama, Qwen and Mistral models also exceeding 93\%. The performance gap between open-weight and closed models is narrower than expected, with several lower-cost open-weight models exceeding 90\% accuracy. Petrophysics emerges as the most challenging domain across all models, while smaller models show wider performance variance. Residual length bias in the dataset (correct answers tend to be longer) is documented along with bias mitigation strategies applied during construction. The benchmark, evaluation code and results are publicly available.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

The increasingly popular adoption of deep learning models in many critical source code tasks motivates the development of data augmentation (DA) techniques to enhance training data and improve various capabilities (e.g., robustness and generalizability) of these models. Although a series of DA methods have been proposed and tailored for source code models, there lacks a comprehensive survey and examination to understand their effectiveness and implications. This paper fills this gap by conducting a comprehensive and integrative survey of data augmentation for source code, wherein we systematically compile and encapsulate existing literature to provide a comprehensive overview of the field. We start with an introduction of data augmentation in source code and then provide a discussion on major representative approaches. Next, we highlight the general strategies and techniques to optimize the DA quality. Subsequently, we underscore techniques useful in real-world source code scenarios and downstream tasks. Finally, we outline the prevailing challenges and potential opportunities for future research. In essence, we aim to demystify the corpus of existing literature on source code DA for deep learning, and foster further exploration in this sphere. Complementing this, we present a continually updated GitHub repository that hosts a list of update-to-date papers on DA for source code modeling, accessible at https://github.com/terryyz/DataAug4Code.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

Recent text-to-SQL systems powered by large language models (LLMs) have demonstrated remarkable performance in translating natural language queries into SQL. However, these systems often struggle with complex database structures and domain-specific queries, as they primarily focus on enhancing logical reasoning and SQL syntax while overlooking the critical need for comprehensive database understanding. To address this limitation, we propose DB-Explore, a novel framework that systematically aligns LLMs with database knowledge through automated exploration and instruction synthesis. DB-Explore constructs database graphs to capture complex relational schemas, leverages GPT-4 to systematically mine structural patterns and semantic knowledge, and synthesizes instructions to distill this knowledge for efficient fine-tuning of LLMs. Our framework enables comprehensive database understanding through diverse sampling strategies and automated instruction generation, bridging the gap between database structures and language models. Experiments conducted on the SPIDER and BIRD benchmarks validate the effectiveness of DB-Explore, achieving an execution accuracy of 52.1% on BIRD and 84.0% on SPIDER. Notably, our open-source implementation, based on the Qwen2.5-coder-7B model, outperforms multiple GPT-4-driven text-to-SQL systems in comparative evaluations, and achieves near state-of-the-art performance with minimal computational cost.

There has been an influx of biomedical domain-specific language models, showing language models pre-trained on biomedical text perform better on biomedical domain benchmarks than those trained on general domain text corpora such as Wikipedia and Books. Yet, most works do not study the factors affecting each domain language application deeply. Additionally, the study of model size on domain-specific models has been mostly missing. We empirically study and evaluate several factors that can affect performance on domain language applications, such as the sub-word vocabulary set, model size, pre-training corpus, and domain transfer. We show consistent improvements on benchmarks with our larger BioMegatron model trained on a larger domain corpus, contributing to our understanding of domain language model applications. We demonstrate noticeable improvements over the previous state-of-the-art (SOTA) on standard biomedical NLP benchmarks of named entity recognition, relation extraction, and question answering. Model checkpoints and code are available at [https://ngc.nvidia.com] and [https://github.com/NVIDIA/NeMo].

Tabular data, a prevalent data type across various domains, presents unique challenges due to its heterogeneous nature and complex structural relationships. Achieving high predictive performance and robustness in tabular data analysis holds significant promise for numerous applications. Influenced by recent advancements in natural language processing, particularly transformer architectures, new methods for tabular data modeling have emerged. Early techniques concentrated on pre-training transformers from scratch, often encountering scalability issues. Subsequently, methods leveraging pre-trained language models like BERT have been developed, which require less data and yield enhanced performance. The recent advent of large language models, such as GPT and LLaMA, has further revolutionized the field, facilitating more advanced and diverse applications with minimal fine-tuning. Despite the growing interest, a comprehensive survey of language modeling techniques for tabular data remains absent. This paper fills this gap by providing a systematic review of the development of language modeling for tabular data, encompassing: (1) a categorization of different tabular data structures and data types; (2) a review of key datasets used in model training and tasks used for evaluation; (3) a summary of modeling techniques including widely-adopted data processing methods, popular architectures, and training objectives; (4) the evolution from adapting traditional Pre-training/Pre-trained language models to the utilization of large language models; (5) an identification of persistent challenges and potential future research directions in language modeling for tabular data analysis. GitHub page associated with this survey is available at: https://github.com/lanxiang1017/Language-Modeling-on-Tabular-Data-Survey.git.

Large language models (LLMs) typically utilize the top-k contexts from a retriever in retrieval-augmented generation (RAG). In this work, we propose a novel instruction fine-tuning framework RankRAG, which instruction-tunes a single LLM for the dual purpose of context ranking and answer generation in RAG. In particular, the instruction-tuned LLMs work surprisingly well by adding a small fraction of ranking data into the training blend, and outperform existing expert ranking models, including the same LLM exclusively fine-tuned on a large amount of ranking data. For generation, we compare our model with many strong baselines, including GPT-4-0613, GPT-4-turbo-2024-0409, and ChatQA-1.5, an open-sourced model with the state-of-the-art performance on RAG benchmarks. Specifically, our Llama3-RankRAG significantly outperforms Llama3-ChatQA-1.5 and GPT-4 models on nine knowledge-intensive benchmarks. In addition, it also performs comparably to GPT-4 on five RAG benchmarks in the biomedical domain without instruction fine-tuning on biomedical data, demonstrating its superb capability for generalization to new domains.

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

Large Language Models (LLMs) have demonstrated impressive zero shot performance on a wide range of NLP tasks, demonstrating the ability to reason and apply commonsense. A relevant application is to use them for creating high quality synthetic datasets for downstream tasks. In this work, we probe whether GPT-4 can be used to augment existing extractive reading comprehension datasets. Automating data annotation processes has the potential to save large amounts of time, money and effort that goes into manually labelling datasets. In this paper, we evaluate the performance of GPT-4 as a replacement for human annotators for low resource reading comprehension tasks, by comparing performance after fine tuning, and the cost associated with annotation. This work serves to be the first analysis of LLMs as synthetic data augmenters for QA systems, highlighting the unique opportunities and challenges. Additionally, we release augmented versions of low resource datasets, that will allow the research community to create further benchmarks for evaluation of generated datasets.

The objective of Classic Referring Expression Comprehension (REC) is to produce a bounding box corresponding to the object mentioned in a given textual description. Commonly, existing datasets and techniques in classic REC are tailored for expressions that pertain to a single target, meaning a sole expression is linked to one specific object. Expressions that refer to multiple targets or involve no specific target have not been taken into account. This constraint hinders the practical applicability of REC. This study introduces a new benchmark termed as Generalized Referring Expression Comprehension (GREC). This benchmark extends the classic REC by permitting expressions to describe any number of target objects. To achieve this goal, we have built the first large-scale GREC dataset named gRefCOCO. This dataset encompasses a range of expressions: those referring to multiple targets, expressions with no specific target, and the single-target expressions. The design of GREC and gRefCOCO ensures smooth compatibility with classic REC. The proposed gRefCOCO dataset, a GREC method implementation code, and GREC evaluation code are available at https://github.com/henghuiding/gRefCOCO.

As large language models (LLMs) advance, the ultimate vision for their role in science is emerging: we could build an AI collaborator to effectively assist human beings throughout the entire scientific research process. We refer to this envisioned system as ResearchGPT. Given that scientific research progresses through multiple interdependent phases, achieving this vision requires rigorous benchmarks that evaluate the end-to-end workflow rather than isolated sub-tasks. To this end, we contribute CS-54k, a high-quality corpus of scientific Q&A pairs in computer science, built from 14k CC-licensed papers. It is constructed through a scalable, paper-grounded pipeline that combines retrieval-augmented generation (RAG) with multi-stage quality control to ensure factual grounding. From this unified corpus, we derive two complementary subsets: CS-4k, a carefully curated benchmark for evaluating AI's ability to assist scientific research, and CS-50k, a large-scale training dataset. Extensive experiments demonstrate that CS-4k stratifies state-of-the-art LLMs into distinct capability tiers. Open models trained on CS-50k with supervised training and reinforcement learning demonstrate substantial improvements. Even 7B-scale models, when properly trained, outperform many larger proprietary systems, such as GPT-4.1, GPT-4o, and Gemini 2.5 Pro. This indicates that making AI models better research assistants relies more on domain-aligned training with high-quality data than on pretraining scale or general benchmark performance. We release CS-4k and CS-50k in the hope of fostering AI systems as reliable collaborators in CS research.

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.

Relational databases often suffer from uninformative descriptors of table contents, such as ambiguous columns and hard-to-interpret values, impacting both human users and Text-to-SQL models. This paper explores the use of large language models (LLMs) to generate informative column descriptions as a semantic layer for relational databases. Using the BIRD-Bench development set, we created ColSQL, a dataset with gold-standard column descriptions generated and refined by LLMs and human annotators. We evaluated several instruction-tuned models, finding that GPT-4o and Command R+ excelled in generating high-quality descriptions. Additionally, we applied an LLM-as-a-judge to evaluate model performance. Although this method does not align well with human evaluations, we included it to explore its potential and to identify areas for improvement. More work is needed to improve the reliability of automatic evaluations for this task. We also find that detailed column descriptions significantly improve Text-to-SQL execution accuracy, especially when columns are uninformative. This study establishes LLMs as effective tools for generating detailed metadata, enhancing the usability of relational databases.

The emergence of models like GPTs, Claude, LLaMA, and Qwen has reshaped AI applications, presenting vast new opportunities across industries. Yet, the integration of tabular data remains notably underdeveloped, despite its foundational role in numerous real-world domains. This gap is critical for three main reasons. First, database or data warehouse data integration is essential for advanced applications; second, the vast and largely untapped resource of tabular data offers immense potential for analysis; and third, the business intelligence domain specifically demands adaptable, precise solutions that many current LLMs may struggle to provide. In response, we introduce TableGPT2, a model rigorously pre-trained and fine-tuned with over 593.8K tables and 2.36M high-quality query-table-output tuples, a scale of table-related data unprecedented in prior research. This extensive training enables TableGPT2 to excel in table-centric tasks while maintaining strong general language and coding abilities. One of TableGPT2's key innovations is its novel table encoder, specifically designed to capture schema-level and cell-level information. This encoder strengthens the model's ability to handle ambiguous queries, missing column names, and irregular tables commonly encountered in real-world applications. Similar to visual language models, this pioneering approach integrates with the decoder to form a robust large multimodal model. We believe the results are compelling: over 23 benchmarking metrics, TableGPT2 achieves an average performance improvement of 35.20% in the 7B model and 49.32% in the 72B model over prior benchmark-neutral LLMs, with robust general-purpose capabilities intact.

We present Gyan AI Paramanu ("atom"), a family of novel language models for Indian languages. It is a collection of auto-regressive monolingual, bilingual, and multilingual Indic language models pretrained from scratch on a single GPU for 10 Indian languages (Assamese, Bangla, Hindi, Konkani, Maithili, Marathi, Odia, Sanskrit, Tamil, Telugu) across 5 scripts (Bangla, Devanagari, Odia, Tamil, Telugu) of varying sizes ranging from 13.29M to 367.5M.The models are pretrained with a context size of 1024 on a single GPU. The models are very efficient, small, fast, and powerful. We have also developed an efficient most advanced Indic tokenizer that can even tokenize unseen languages. In order to avoid the "curse of multi-linguality" in our multilingual mParamanu model, we pretrained on comparable corpora by typological grouping using the same script. We performed human evaluation of our pretrained models for open end text generation on grammar, coherence, creativity, and factuality metrics for Bangla, Hindi, and Sanskrit. Our Bangla, Hindi, and Sanskrit models outperformed GPT-3.5-Turbo (ChatGPT), Bloom 7B, LLaMa-2 7B, OPT 6.7B, GPT-J 6B, GPTNeo 1.3B, GPT2-XL large language models (LLMs) by a large margin despite being smaller in size by 66 to 20 times compared to standard 7B LLMs. To run inference on our pretrained models, CPU is enough, and GPU is not needed. We also instruction-tuned our pretrained Bangla, Hindi, Marathi, Tamil, and Telugu models on 23k instructions in respective languages. Our pretrained and instruction-tuned models which are first of its kind, most powerful efficient small generative language models ever developed for Indic languages, and the various results lead to the conclusion that high quality generative language models are possible without high amount of compute power and humongous number of parameters. We plan to release our models at https://www.bharatgpts.com.

This paper presents an empirical study to build relation extraction systems in low-resource settings. Based upon recent pre-trained language models, we comprehensively investigate three schemes to evaluate the performance in low-resource settings: (i) different types of prompt-based methods with few-shot labeled data; (ii) diverse balancing methods to address the long-tailed distribution issue; (iii) data augmentation technologies and self-training to generate more labeled in-domain data. We create a benchmark with 8 relation extraction (RE) datasets covering different languages, domains and contexts and perform extensive comparisons over the proposed schemes with combinations. Our experiments illustrate: (i) Though prompt-based tuning is beneficial in low-resource RE, there is still much potential for improvement, especially in extracting relations from cross-sentence contexts with multiple relational triples; (ii) Balancing methods are not always helpful for RE with long-tailed distribution; (iii) Data augmentation complements existing baselines and can bring much performance gain, while self-training may not consistently achieve advancement to low-resource RE. Code and datasets are in https://github.com/zjunlp/LREBench.

With the future striving toward data-centric decision-making, seamless access to databases is of utmost importance. There is extensive research on creating an efficient text-to-sql (TEXT2SQL) model to access data from the database. Using a Natural language is one of the best interfaces that can bridge the gap between the data and results by accessing the database efficiently, especially for non-technical users. It will open the doors and create tremendous interest among users who are well versed in technical skills or not very skilled in query languages. Even if numerous deep learning-based algorithms are proposed or studied, there still is very challenging to have a generic model to solve the data query issues using natural language in a real-work scenario. The reason is the use of different datasets in different studies, which comes with its limitations and assumptions. At the same time, we do lack a thorough understanding of these proposed models and their limitations with the specific dataset it is trained on. In this paper, we try to present a holistic overview of 24 recent neural network models studied in the last couple of years, including their architectures involving convolutional neural networks, recurrent neural networks, pointer networks, reinforcement learning, generative models, etc. We also give an overview of the 11 datasets that are widely used to train the models for TEXT2SQL technologies. We also discuss the future application possibilities of TEXT2SQL technologies for seamless data queries.

Text-to-SQL benchmarks play a crucial role in evaluating the progress made in the field and the ranking of different models. However, accurately matching a model-generated SQL query to a reference SQL query in a benchmark fails for various reasons, such as underspecified natural language queries, inherent assumptions in both model-generated and reference queries, and the non-deterministic nature of SQL output under certain conditions. In this paper, we conduct an extensive study of several prominent cross-domain text-to-SQL benchmarks and re-evaluate some of the top-performing models within these benchmarks, by both manually evaluating the SQL queries and rewriting them in equivalent expressions. Our evaluation reveals that attaining a perfect performance on these benchmarks is unfeasible due to the multiple interpretations that can be derived from the provided samples. Furthermore, we find that the true performance of the models is underestimated and their relative performance changes after a re-evaluation. Most notably, our evaluation reveals a surprising discovery: a recent GPT4-based model surpasses the gold standard reference queries in the Spider benchmark in our human evaluation. This finding highlights the importance of interpreting benchmark evaluations cautiously, while also acknowledging the critical role of additional independent evaluations in driving advancements in the field.

Large Language Models (LLMs) have displayed massive improvements in reasoning and decision-making skills and can hold natural conversations with users. Recently, many tool-use benchmark datasets have been proposed. However, existing datasets have the following limitations: (1). Insufficient evaluation scenarios (e.g., only cover limited tool-use scenes). (2). Extensive evaluation costs (e.g., GPT API costs). To address these limitations, in this work, we propose a multi-granularity tool-use benchmark for large language models called MTU-Bench. For the "multi-granularity" property, our MTU-Bench covers five tool usage scenes (i.e., single-turn and single-tool, single-turn and multiple-tool, multiple-turn and single-tool, multiple-turn and multiple-tool, and out-of-distribution tasks). Besides, all evaluation metrics of our MTU-Bench are based on the prediction results and the ground truth without using any GPT or human evaluation metrics. Moreover, our MTU-Bench is collected by transforming existing high-quality datasets to simulate real-world tool usage scenarios, and we also propose an instruction dataset called MTU-Instruct data to enhance the tool-use abilities of existing LLMs. Comprehensive experimental results demonstrate the effectiveness of our MTU-Bench. Code and data will be released at https: //github.com/MTU-Bench-Team/MTU-Bench.git.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

This paper details the process of developing the first native large generative language model for the Nordic languages, GPT-SW3. We cover all parts of the development process, from data collection and processing, training configuration and instruction finetuning, to evaluation and considerations for release strategies. We hope that this paper can serve as a guide and reference for other researchers that undertake the development of large generative models for smaller languages.

In recent years,Text-to-SQL, the problem of automatically converting questions posed in natural language to formal SQL queries, has emerged as an important problem at the intersection of natural language processing and data management research. Large language models (LLMs) have delivered impressive performance when used in an off-the-shelf performance, but still fall significantly short of expected expert-level performance. Errors are especially probable when a nuanced understanding is needed of database schemas, questions, and SQL clauses to do proper Text-to-SQL conversion. We introduce SelECT-SQL, a novel in-context learning solution that uses an algorithmic combination of chain-of-thought (CoT) prompting, self-correction, and ensemble methods to yield a new state-of-the-art result on challenging Text-to-SQL benchmarks. Specifically, when configured using GPT-3.5-Turbo as the base LLM, SelECT-SQL achieves 84.2% execution accuracy on the Spider leaderboard's development set, exceeding both the best results of other baseline GPT-3.5-Turbo-based solutions (81.1%), and the peak performance (83.5%) of the GPT-4 result reported on the leaderboard.

Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection methods lags behind the rapid evolution of LLMs. Conventional training-based methods have limitations in flexibility, particularly when adapting to new domains, and they often lack explanatory power. To address this gap, we propose a novel training-free detection strategy called Divergent N-Gram Analysis (DNA-GPT). Given a text, we first truncate it in the middle and then use only the preceding portion as input to the LLMs to regenerate the new remaining parts. By analyzing the differences between the original and new remaining parts through N-gram analysis in black-box or probability divergence in white-box, we can clearly illustrate significant discrepancies between machine-generated and human-written text. We conducted extensive experiments on the most advanced LLMs from OpenAI, including text-davinci-003, GPT-3.5-turbo, and GPT-4, as well as open-source models such as GPT-NeoX-20B and LLaMa-13B. Results show that our zero-shot approach exhibits state-of-the-art performance in distinguishing between human and GPT-generated text on four English and one German dataset, outperforming OpenAI's own classifier, which is trained on millions of text. Additionally, our methods provide reasonable explanations and evidence to support our claim, which is a unique feature of explainable detection. Our method is also robust under the revised text attack and can additionally solve model sourcing. Codes are available at https://github.com/Xianjun-Yang/DNA-GPT.

The NLP community has mainly focused on scaling Large Language Models (LLMs) vertically, i.e., making them better for about 100 languages. We instead scale LLMs horizontally: we create, through continued pretraining, Glot500-m, an LLM that covers 511 languages, almost all of them low-resource. An important part of this effort is to collect and clean Glot500-c, a corpus that covers these 511 languages and allows us to train Glot500-m. We evaluate Glot500-m on five diverse tasks across these languages. We observe large improvements for both high-resource and lowresource languages compared to an XLM-R baseline. Our analysis shows that no single factor explains the quality of multilingual LLM representations. Rather, a combination of factors determines quality including corpus size, script, "help" from related languages and the total capacity of the model. Our work addresses an important goal of NLP research: we should not limit NLP to a small fraction of the world's languages and instead strive to support as many languages as possible to bring the benefits of NLP technology to all languages and cultures. Code, data and models are available at https://github.com/cisnlp/Glot500.

Generative Pre-trained Transformer (GPT) architectures are the most popular design for language modeling. Energy-based modeling is a different paradigm that views inference as a dynamical process operating on an energy landscape. We propose a minimal modification of the GPT setting to unify it with the EBM framework. The inference step of our model, which we call eNeRgy-GPT (NRGPT), is conceptualized as an exploration of the tokens on the energy landscape. We prove, and verify empirically, that under certain circumstances this exploration becomes gradient descent, although they don't necessarily lead to the best performing models. We demonstrate that our model performs well for simple language (Shakespeare dataset), algebraic ListOPS tasks, and richer settings such as OpenWebText language modeling. We also observe that our models may be more resistant to overfitting, doing so only during very long training.

Large language models (LLMs) have recently achieved human-level performance on a range of professional and academic benchmarks. The accessibility of these models has lagged behind their performance. State-of-the-art LLMs require costly infrastructure; are only accessible via rate-limited, geo-locked, and censored web interfaces; and lack publicly available code and technical reports. In this paper, we tell the story of GPT4All, a popular open source repository that aims to democratize access to LLMs. We outline the technical details of the original GPT4All model family, as well as the evolution of the GPT4All project from a single model into a fully fledged open source ecosystem. It is our hope that this paper acts as both a technical overview of the original GPT4All models as well as a case study on the subsequent growth of the GPT4All open source ecosystem.

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

We present the GPT-NL Public Corpus, the biggest permissively licensed corpus of Dutch language resources. The GPT-NL Public Corpus contains 21 Dutch-only collections totalling 36B preprocessed Dutch tokens not present in any other LLM pretraining corpus. Additionally, the corpus includes roughly 207B English, 232B Code, and 48B German/Danish tokens taken from existing sets which we further curated for compliance. This corpus includes curated data from large existing corpora like Common Corpus and Common Crawl, as well as newly created Dutch-specific collections. Most newly created Dutch collections consist of content collected in collaboration with organisations or synthetically augmented content. All data is collected and evaluated with the aim of facilitating the creation of (commercial) language models that are lawful, useful and non-harmful. All data included in the GPT-NL Public Corpus is sourced from datasets with permissive licensing and is curated and redistributed under a CC-BY license. The full dataset is publicly available on the Hugging Face Hub.

The Generative Pre-trained Transformer (GPT) represents a notable breakthrough in the domain of natural language processing, which is propelling us toward the development of machines that can understand and communicate using language in a manner that closely resembles that of humans. GPT is based on the transformer architecture, a deep neural network designed for natural language processing tasks. Due to their impressive performance on natural language processing tasks and ability to effectively converse, GPT have gained significant popularity among researchers and industrial communities, making them one of the most widely used and effective models in natural language processing and related fields, which motivated to conduct this review. This review provides a detailed overview of the GPT, including its architecture, working process, training procedures, enabling technologies, and its impact on various applications. In this review, we also explored the potential challenges and limitations of a GPT. Furthermore, we discuss potential solutions and future directions. Overall, this paper aims to provide a comprehensive understanding of GPT, enabling technologies, their impact on various applications, emerging challenges, and potential solutions.

Language models, such as GPT-3.5 and ChatGPT, demonstrate remarkable abilities to follow diverse human instructions and perform a wide range of tasks. However, when probing language models using a range of basic table-understanding tasks, we observe that today's language models are still sub-optimal in many table-related tasks, likely because they are pre-trained predominantly on one-dimensional natural-language texts, whereas relational tables are two-dimensional objects. In this work, we propose a new "table-tuning" paradigm, where we continue to train/fine-tune language models like GPT-3.5 and ChatGPT, using diverse table-tasks synthesized from real tables as training data, with the goal of enhancing language models' ability to understand tables and perform table tasks. We show that our resulting Table-GPT models demonstrate (1) better table-understanding capabilities, by consistently outperforming the vanilla GPT-3.5 and ChatGPT, on a wide-range of table tasks, including holdout unseen tasks, and (2) strong generalizability, in its ability to respond to diverse human instructions to perform new table-tasks, in a manner similar to GPT-3.5 and ChatGPT.

Large Language Models (LLMs), typified by OpenAI's GPT series and Meta's LLaMA variants, have marked a significant advancement in artificial intelligence. Trained on vast amounts of text data, LLMs are capable of understanding and generating human-like text across a diverse range of topics. This study expands on the applications of LLMs, exploring their potential in data preprocessing, a critical stage in data mining and analytics applications. We delve into the applicability of state-of-the-art LLMs such as GPT-3.5, GPT-4, and Vicuna-13B for error detection, data imputation, schema matching, and entity matching tasks. Alongside showcasing the inherent capabilities of LLMs, we highlight their limitations, particularly in terms of computational expense and inefficiency. We propose an LLM-based framework for data preprocessing, which integrates cutting-edge prompt engineering techniques, coupled with traditional methods like contextualization and feature selection, to improve the performance and efficiency of these models. The effectiveness of LLMs in data preprocessing is evaluated through an experimental study spanning 12 datasets. GPT-4 emerged as a standout, achieving 100\% accuracy or F1 score on 4 datasets, suggesting LLMs' immense potential in these tasks. Despite certain limitations, our study underscores the promise of LLMs in this domain and anticipates future developments to overcome current hurdles.