Daily Papers

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Recent advancements in language models have started a new era of superior information retrieval and content generation, with embedding models playing an important role in optimizing data representation efficiency and performance. While benchmarks like the Massive Text Embedding Benchmark (MTEB) have standardized the evaluation of general domain embedding models, a gap remains in specialized fields such as chemistry, which require tailored approaches due to domain-specific challenges. This paper introduces a novel benchmark, the Chemical Text Embedding Benchmark (ChemTEB), designed specifically for the chemical sciences. ChemTEB addresses the unique linguistic and semantic complexities of chemical literature and data, offering a comprehensive suite of tasks on chemical domain data. Through the evaluation of 34 open-source and proprietary models using this benchmark, we illuminate the strengths and weaknesses of current methodologies in processing and understanding chemical information. Our work aims to equip the research community with a standardized, domain-specific evaluation framework, promoting the development of more precise and efficient NLP models for chemistry-related applications. Furthermore, it provides insights into the performance of generic models in a domain-specific context. ChemTEB comes with open-source code and data, contributing further to its accessibility and utility.

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

Large language models (LLMs) have established great success in the general domain of natural language processing. Their emerging task generalization and free-form dialogue capabilities can greatly help to design Chemical General Intelligence (CGI) to assist real-world research in chemistry. However, the existence of specialized language and knowledge in the field of chemistry, such as the highly informative SMILES notation, hinders the performance of general-domain LLMs in chemistry. To this end, we develop ChemDFM, the first LLM towards CGI. ChemDFM-13B is trained on 34B tokens from chemical literature, textbooks, and instructions as well as various data from the general domain. Therefore, it can store, understand, and reason over chemical knowledge and languages while still possessing advanced free-form language comprehension capabilities. Extensive quantitative evaluation shows that ChemDFM can significantly outperform the representative open-sourced LLMs. Moreover, ChemDFM can also surpass GPT-4 on a great portion of chemical tasks, despite the significant size difference. Further qualitative evaluations demonstrate the efficiency and effectiveness of ChemDFM in real-world research scenarios. We will open-source the ChemDFM model soon.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies typically treat molecular captioning (molecule-to-text) and text-based molecular design (text-to-molecule) as separate tasks, relying on supervised fine-tuning or contrastive learning pipelines. These approaches face three key limitations: (i) conventional metrics like BLEU prioritize linguistic fluency over chemical accuracy, (ii) training datasets frequently contain chemically ambiguous narratives with incomplete specifications, and (iii) independent optimization of generation directions leads to bidirectional inconsistency. To address these issues, we propose RTMol, a bidirectional alignment framework that unifies molecular captioning and text-to-SMILES generation through self-supervised round-trip learning. The framework introduces novel round-trip evaluation metrics and enables unsupervised training for molecular captioning without requiring paired molecule-text corpora. Experiments demonstrate that RTMol enhances bidirectional alignment performance by up to 47% across various LLMs, establishing an effective paradigm for joint molecule-text understanding and generation.

Large-scale chemical reaction datasets are crucial for AI research in chemistry. However, existing chemical reaction data often exist as images within papers, making them not machine-readable and unusable for training machine learning models. In response to this challenge, we propose the RxnCaption framework for the task of chemical Reaction Diagram Parsing (RxnDP). Our framework reformulates the traditional coordinate prediction driven parsing process into an image captioning problem, which Large Vision Language Models (LVLMs) handle naturally. We introduce a strategy termed BBox and Index as Visual Prompt (BIVP), which uses our state-of-the-art molecular detector, MolYOLO, to pre-draw molecular bounding boxes and indices directly onto the input image. This turns the downstream parsing into a natural-language description problem. Extensive experiments show that the BIVP strategy significantly improves structural extraction quality while simplifying model design. We further construct the RxnCaption-15k dataset, an order of magnitude larger than prior real-world literature benchmarks, with a balanced test subset across four layout archetypes. Experiments demonstrate that RxnCaption-VL achieves state-of-the-art performance on multiple metrics. We believe our method, dataset, and models will advance structured information extraction from chemical literature and catalyze broader AI applications in chemistry. We will release data, models, and code on GitHub.

The blue bottle experiment was first introduced to the chemical education literature as a simple demonstration on kinetics. Its original formulation contains only glucose, NaOH and small amount of methylene blue. The solution turns blue when shaken and fades to colorless upon standing. This bluing/de-bluing cycle may be repeated and may be compared to blood colors in animal's respiratory cycle. Inspired by the blue bottle experiment, the colorful chemical bottle experiment kit was commercially developed in 2006. The kit is a versatile pedagogical tool, not only for physical chemistry but also for analytical, biological and organic chemistry. It also helps teaching concepts in scientific method and laboratory safety. This manuscript contains four parts, brief review on literature relating to the blue bottle experiment, description of the colorful chemical bottle experiment kit, pedagogical discussion of the experiments and preliminary evaluation from students.

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains underexplored. Here, we introduce RxnBench, a multi-tiered benchmark designed to rigorously evaluate MLLMs on chemical reaction understanding from scientific PDFs. RxnBench comprises two tasks: Single-Figure QA (SF-QA), which tests fine-grained visual perception and mechanistic reasoning using 1,525 questions derived from 305 curated reaction schemes, and Full-Document QA (FD-QA), which challenges models to synthesize information from 108 articles, requiring cross-modal integration of text, schemes, and tables. Our evaluation of MLLMs reveals a critical capability gap: while models excel at extracting explicit text, they struggle with deep chemical logic and precise structural recognition. Notably, models with inference-time reasoning significantly outperform standard architectures, yet none achieve 50\% accuracy on FD-QA. These findings underscore the urgent need for domain-specific visual encoders and stronger reasoning engines to advance autonomous AI chemists.

Automatic extraction of chemical structures from scientific literature plays a crucial role in accelerating research across fields ranging from drug discovery to materials science. Patent documents, in particular, contain molecular information in visual form, which is often inaccessible through traditional text-based searches. In this work, we introduce SubGrapher, a method for the visual fingerprinting of chemical structure images. Unlike conventional Optical Chemical Structure Recognition (OCSR) models that attempt to reconstruct full molecular graphs, SubGrapher focuses on extracting molecular fingerprints directly from chemical structure images. Using learning-based instance segmentation, SubGrapher identifies functional groups and carbon backbones, constructing a substructure-based fingerprint that enables chemical structure retrieval. Our approach is evaluated against state-of-the-art OCSR and fingerprinting methods, demonstrating superior retrieval performance and robustness across diverse molecular depictions. The dataset, models, and code are publicly available.

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS~70 disk and report the first chemical inventory of the system. With a spatial resolution of 0.4''-0.5'' (sim50 au), 12 species are detected, including CO isotopologues and formaldehyde, small hydrocarbons, HCN and HCO+ isotopologues, and S-bearing molecules. SO and CH3OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub-)mm continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the non detections. Excitation temperature is obtained for H2CO. Deuteration and nitrogen fractionation profiles from the hydro-cyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon to oxygen ratio C/O>1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep learning framework that unifies molecule detection, reaction diagram parsing, and optical chemical structure recognition (OCSR) into a single pipeline for automating the extraction of chemical data directly from page-level documents. Recognizing the lack of a standard page-level benchmark and evaluation metric, we also present a testset of 550 pages annotated with molecule bounding boxes, reaction labels, and MOLfiles, along with a novel evaluation metric. Experimental results demonstrate that MolMole outperforms existing toolkits on both our benchmark and public datasets. The benchmark testset will be publicly available, and the MolMole toolkit will be accessible soon through an interactive demo on the LG AI Research website. For commercial inquiries, please contact us at mailto:contact_ddu@lgresearch.ai{contact\_ddu@lgresearch.ai}.

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups.

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning, which involves pre-training Transformers on SMILES sequences -- textual descriptors of molecules. Despite its success in molecular property prediction, current practices often lead to overfitting and limited scalability due to early convergence. In this paper, we introduce a novel chemical language representation learning framework, called MolTRES, to address these issues. MolTRES incorporates generator-discriminator training, allowing the model to learn from more challenging examples that require structural understanding. In addition, we enrich molecular representations by transferring knowledge from scientific literature by integrating external materials embedding. Experimental results show that our model outperforms existing state-of-the-art models on popular molecular property prediction tasks.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

The automatic extraction of materials and related properties from the scientific literature is gaining attention in data-driven materials science (Materials Informatics). In this paper, we discuss Grobid-superconductors, our solution for automatically extracting superconductor material names and respective properties from text. Built as a Grobid module, it combines machine learning and heuristic approaches in a multi-step architecture that supports input data as raw text or PDF documents. Using Grobid-superconductors, we built SuperCon2, a database of 40324 materials and properties records from 37700 papers. The material (or sample) information is represented by name, chemical formula, and material class, and is characterized by shape, doping, substitution variables for components, and substrate as adjoined information. The properties include the Tc superconducting critical temperature and, when available, applied pressure with the Tc measurement method.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

Fundamental experimental measurements of quantities such as ignition delay times, laminar flame speeds, and species profiles (among others) serve important roles in understanding fuel chemistry and validating chemical kinetic models. However, despite both the importance and abundance of such information in the literature, the community lacks a widely adopted standard format for this data. This impedes both sharing and wide use by the community. Here we introduce a new chemical kinetics experimental data format, ChemKED, and the related Python-based package for validating and working with ChemKED-formatted files called PyKED. We also review past and related efforts, and motivate the need for a new solution. ChemKED currently supports the representation of autoignition delay time measurements from shock tubes and rapid compression machines. ChemKED-formatted files contain all of the information needed to simulate experimental data points, including the uncertainty of the data. ChemKED is based on the YAML data serialization language, and is intended as a human- and machine-readable standard for easy creation and automated use. Development of ChemKED and PyKED occurs openly on GitHub under the BSD 3-clause license, and contributions from the community are welcome. Plans for future development include support for experimental data from laminar flame, jet stirred reactor, and speciation measurements.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

Since the advent of various pre-trained large language models, extracting structured knowledge from scientific text has experienced a revolutionary change compared with traditional machine learning or natural language processing techniques. Despite these advances, accessible automated tools that allow users to construct, validate, and visualise datasets from scientific literature extraction remain scarce. We therefore developed ComProScanner, an autonomous multi-agent platform that facilitates the extraction, validation, classification, and visualisation of machine-readable chemical compositions and properties, integrated with synthesis data from journal articles for comprehensive database creation. We evaluated our framework using 100 journal articles against 10 different LLMs, including both open-source and proprietary models, to extract highly complex compositions associated with ceramic piezoelectric materials and corresponding piezoelectric strain coefficients (d33), motivated by the lack of a large dataset for such materials. DeepSeek-V3-0324 outperformed all models with a significant overall accuracy of 0.82. This framework provides a simple, user-friendly, readily-usable package for extracting highly complex experimental data buried in the literature to build machine learning or deep learning datasets.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

This technical report introduces Uni-Parser, an industrial-grade document parsing engine tailored for scientific literature and patents, delivering high throughput, robust accuracy, and cost efficiency. Unlike pipeline-based document parsing methods, Uni-Parser employs a modular, loosely coupled multi-expert architecture that preserves fine-grained cross-modal alignments across text, equations, tables, figures, and chemical structures, while remaining easily extensible to emerging modalities. The system incorporates adaptive GPU load balancing, distributed inference, dynamic module orchestration, and configurable modes that support either holistic or modality-specific parsing. Optimized for large-scale cloud deployment, Uni-Parser achieves a processing rate of up to 20 PDF pages per second on 8 x NVIDIA RTX 4090D GPUs, enabling cost-efficient inference across billions of pages. This level of scalability facilitates a broad spectrum of downstream applications, ranging from literature retrieval and summarization to the extraction of chemical structures, reaction schemes, and bioactivity data, as well as the curation of large-scale corpora for training next-generation large language models and AI4Science models.

The advent of artificial intelligence (AI) has enabled a comprehensive exploration of materials for various applications. However, AI models often prioritize frequently encountered materials in the scientific literature, limiting the selection of suitable candidates based on inherent physical and chemical properties. To address this imbalance, we have generated a dataset of 1,494,017 natural language-material paragraphs based on combined OQMD, Materials Project, JARVIS, COD and AFLOW2 databases, which are dominated by ab initio calculations and tend to be much more evenly distributed on the periodic table. The generated text narratives were then polled and scored by both human experts and ChatGPT-4, based on three rubrics: technical accuracy, language and structure, and relevance and depth of content, showing similar scores but with human-scored depth of content being the most lagging. The merger of multi-modality data sources and large language model (LLM) holds immense potential for AI frameworks to help the exploration and discovery of solid-state materials for specific applications.

Recent advancements in multimodal large language models (MLLMs) and video agent systems have significantly improved general video understanding. However, when applied to scientific video understanding and educating, a domain that demands external professional knowledge integration and rigorous step-wise reasoning, existing approaches often struggle. To bridge this gap, we propose SciEducator, the first iterative self-evolving multi-agent system for scientific video comprehension and education. Rooted in the classical Deming Cycle from management science, our design reformulates its Plan-Do-Study-Act philosophy into a self-evolving reasoning and feedback mechanism, which facilitates the interpretation of intricate scientific activities in videos. Moreover, SciEducator can produce multimodal educational content tailored to specific scientific processes, including textual instructions, visual guides, audio narrations, and interactive references. To support evaluation, we construct SciVBench, a benchmark consisting of 500 expert-verified and literature-grounded science QA pairs across five categories, covering physical, chemical, and everyday phenomena. Extensive experiments demonstrate that SciEducator substantially outperforms leading closed-source MLLMs (e.g., Gemini, GPT-4o) and state-of-the-art video agents on the benchmark, establishing a new paradigm for the community.

The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge. To support advancements in chemistry-focused natural language processing (NLP), we present ChemRxivQuest, a curated dataset of 970 high-quality question-answer (QA) pairs derived from 155 ChemRxiv preprints across 17 subfields of chemistry. Each QA pair is explicitly linked to its source text segment to ensure traceability and contextual accuracy. ChemRxivQuest was constructed using an automated pipeline that combines optical character recognition (OCR), GPT-4o-based QA generation, and a fuzzy matching technique for answer verification. The dataset emphasizes conceptual, mechanistic, applied, and experimental questions, enabling applications in retrieval-based QA systems, search engine development, and fine-tuning of domain-adapted large language models. We analyze the dataset's structure, coverage, and limitations, and outline future directions for expansion and expert validation. ChemRxivQuest provides a foundational resource for chemistry NLP research, education, and tool development.

Literature research, vital for scientific work, faces the challenge of the surging torrent of information in the vast ocean of literature exceeding researchers' processing capabilities. To address this issue, we present an automated review generation method based on Large Language Models (LLMs), aimed at overcoming efficiency bottlenecks in literature processing and reducing cognitive load. Our statistically validated evaluation framework demonstrates that the generated reviews match or exceed manual quality, offering broad applicability across research fields due to minimal domain knowledge requirements. In a case study on propane dehydrogenation (PDH) catalysts, our method swiftly analyzed 343 articles, averaging seconds per article per LLM account, producing comprehensive reviews spanning 35 topics. Extended analysis of 1041 articles provided deep insights into catalysts' composition, structure, and performance. Recognizing LLMs' hallucinations, we implemented a multi-layered quality control strategy, effectively mitigating risks and ensuring reliability, as quantitatively demonstrated through manual verification. Expert verification confirms the accuracy and citation integrity of generated reviews, demonstrating LLM hallucination risks reduced to below 0.5\% with over 95\% confidence. Released Windows application enables one-click review generation, aiding researchers in tracking advancements and recommending literature. This approach showcases LLMs' role in enhancing scientific research productivity and sets the stage for further exploration.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

Chemical patent documents describe a broad range of applications holding key reaction and compound information, such as chemical structure, reaction formulas, and molecular properties. These informational entities should be first identified in text passages to be utilized in downstream tasks. Text mining provides means to extract relevant information from chemical patents through information extraction techniques. As part of the Information Extraction task of the Cheminformatics Elsevier Melbourne University challenge, in this work we study the effectiveness of contextualized language models to extract reaction information in chemical patents. We assess transformer architectures trained on a generic and specialised corpora to propose a new ensemble model. Our best model, based on a majority ensemble approach, achieves an exact F1-score of 92.30% and a relaxed F1-score of 96.24%. The results show that ensemble of contextualized language models can provide an effective method to extract information from chemical patents.

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g., mixed-initiative visual analytics papers may not use the same terminology as papers on model-steering, yet the two topics are relevant to one another). In this paper, we introduce a system, VitaLITy, intended to complement existing practices. In particular, VitaLITy promotes serendipitous discovery of relevant literature using transformer language models, allowing users to find semantically similar papers in a word embedding space given (1) a list of input paper(s) or (2) a working abstract. VitaLITy visualizes this document-level embedding space in an interactive 2-D scatterplot using dimension reduction. VitaLITy also summarizes meta information about the document corpus or search query, including keywords and co-authors, and allows users to save and export papers for use in a literature review. We present qualitative findings from an evaluation of VitaLITy, suggesting it can be a promising complementary technique for conducting academic literature reviews. Furthermore, we contribute data from 38 popular data visualization publication venues in VitaLITy, and we provide scrapers for the open-source community to continue to grow the list of supported venues.

The ever-increasing number of materials science articles makes it hard to infer chemistry-structure-property relations from published literature. We used natural language processing (NLP) methods to automatically extract material property data from the abstracts of polymer literature. As a component of our pipeline, we trained MaterialsBERT, a language model, using 2.4 million materials science abstracts, which outperforms other baseline models in three out of five named entity recognition datasets when used as the encoder for text. Using this pipeline, we obtained ~300,000 material property records from ~130,000 abstracts in 60 hours. The extracted data was analyzed for a diverse range of applications such as fuel cells, supercapacitors, and polymer solar cells to recover non-trivial insights. The data extracted through our pipeline is made available through a web platform at https://polymerscholar.org which can be used to locate material property data recorded in abstracts conveniently. This work demonstrates the feasibility of an automatic pipeline that starts from published literature and ends with a complete set of extracted material property information.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

Academic literature reviews have traditionally relied on techniques such as keyword searches and accumulation of relevant back-references, using databases like Google Scholar or IEEEXplore. However, both the precision and accuracy of these search techniques is limited by the presence or absence of specific keywords, making literature review akin to searching for needles in a haystack. We present vitaLITy 2, a solution that uses a Large Language Model or LLM-based approach to identify semantically relevant literature in a textual embedding space. We include a corpus of 66,692 papers from 1970-2023 which are searchable through text embeddings created by three language models. vitaLITy 2 contributes a novel Retrieval Augmented Generation (RAG) architecture and can be interacted with through an LLM with augmented prompts, including summarization of a collection of papers. vitaLITy 2 also provides a chat interface that allow users to perform complex queries without learning any new programming language. This also enables users to take advantage of the knowledge captured in the LLM from its enormous training corpus. Finally, we demonstrate the applicability of vitaLITy 2 through two usage scenarios. vitaLITy 2 is available as open-source software at https://vitality-vis.github.io.

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

In scientific research and its application, scientific literature analysis is crucial as it allows researchers to build on the work of others. However, the fast growth of scientific knowledge has led to a massive increase in scholarly articles, making in-depth literature analysis increasingly challenging and time-consuming. The emergence of Large Language Models (LLMs) has offered a new way to address this challenge. Known for their strong abilities in summarizing texts, LLMs are seen as a potential tool to improve the analysis of scientific literature. However, existing LLMs have their own limits. Scientific literature often includes a wide range of multimodal elements, such as molecular structure, tables, and charts, which are hard for text-focused LLMs to understand and analyze. This issue points to the urgent need for new solutions that can fully understand and analyze multimodal content in scientific literature. To answer this demand, we present Uni-SMART (Universal Science Multimodal Analysis and Research Transformer), an innovative model designed for in-depth understanding of multimodal scientific literature. Through rigorous quantitative evaluation across several domains, Uni-SMART demonstrates superior performance over leading text-focused LLMs. Furthermore, our exploration extends to practical applications, including patent infringement detection and nuanced analysis of charts. These applications not only highlight Uni-SMART's adaptability but also its potential to revolutionize how we interact with scientific literature.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, igniting a surge of interest in leveraging these technologies in the field of scientific literature analysis. Existing benchmarks, however, inadequately evaluate the proficiency of LLMs in scientific literature analysis, especially in scenarios involving complex comprehension and multimodal data. In response, we introduced SciAssess, a benchmark tailored for the in-depth analysis of scientific literature, crafted to provide a thorough assessment of LLMs' efficacy. SciAssess focuses on evaluating LLMs' abilities in memorization, comprehension, and analysis within the context of scientific literature analysis. It includes representative tasks from diverse scientific fields, such as general chemistry, organic materials, and alloy materials. And rigorous quality control measures ensure its reliability in terms of correctness, anonymization, and copyright compliance. SciAssess evaluates leading LLMs, including GPT-4, GPT-3.5, and Gemini, identifying their strengths and aspects for improvement and supporting the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are made available at https://sci-assess.github.io, offering a valuable tool for advancing LLM capabilities in scientific literature analysis.

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its promise, the application of RAG in the chemistry domain remains underexplored, primarily due to the lack of high-quality, domain-specific corpora and well-curated evaluation benchmarks. In this work, we introduce ChemRAG-Bench, a comprehensive benchmark designed to systematically assess the effectiveness of RAG across a diverse set of chemistry-related tasks. The accompanying chemistry corpus integrates heterogeneous knowledge sources, including scientific literature, the PubChem database, PubMed abstracts, textbooks, and Wikipedia entries. In addition, we present ChemRAG-Toolkit, a modular and extensible RAG toolkit that supports five retrieval algorithms and eight LLMs. Using ChemRAG-Toolkit, we demonstrate that RAG yields a substantial performance gain -- achieving an average relative improvement of 17.4% over direct inference methods. We further conduct in-depth analyses on retriever architectures, corpus selection, and the number of retrieved passages, culminating in practical recommendations to guide future research and deployment of RAG systems in the chemistry domain. The code and data is available at https://chemrag.github.io.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Scientific literature review generation aims to extract and organize important information from an abundant collection of reference papers and produces corresponding reviews while lacking a clear and logical hierarchy. We observe that a high-quality catalogue-guided generation process can effectively alleviate this problem. Therefore, we present an atomic and challenging task named Hierarchical Catalogue Generation for Literature Review as the first step for review generation, which aims to produce a hierarchical catalogue of a review paper given various references. We construct a novel English Hierarchical Catalogues of Literature Reviews Dataset with 7.6k literature review catalogues and 389k reference papers. To accurately assess the model performance, we design two evaluation metrics for informativeness and similarity to ground truth from semantics and structure.Our extensive analyses verify the high quality of our dataset and the effectiveness of our evaluation metrics. We further benchmark diverse experiments on state-of-the-art summarization models like BART and large language models like ChatGPT to evaluate their capabilities. We further discuss potential directions for this task to motivate future research.

Scientific literature is typically dense, requiring significant background knowledge and deep comprehension for effective engagement. We introduce SciDQA, a new dataset for reading comprehension that challenges LLMs for a deep understanding of scientific articles, consisting of 2,937 QA pairs. Unlike other scientific QA datasets, SciDQA sources questions from peer reviews by domain experts and answers by paper authors, ensuring a thorough examination of the literature. We enhance the dataset's quality through a process that carefully filters out lower quality questions, decontextualizes the content, tracks the source document across different versions, and incorporates a bibliography for multi-document question-answering. Questions in SciDQA necessitate reasoning across figures, tables, equations, appendices, and supplementary materials, and require multi-document reasoning. We evaluate several open-source and proprietary LLMs across various configurations to explore their capabilities in generating relevant and factual responses. Our comprehensive evaluation, based on metrics for surface-level similarity and LLM judgements, highlights notable performance discrepancies. SciDQA represents a rigorously curated, naturally derived scientific QA dataset, designed to facilitate research on complex scientific text understanding.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

The exponential growth of knowledge and the increasing complexity of interdisciplinary research pose significant challenges for researchers, including information overload and difficulties in exploring novel ideas. The advancements in large language models (LLMs), such as GPT-4, have shown great potential in enhancing idea proposals, but how to effectively utilize large models for reasonable idea proposal has not been thoroughly explored. This paper proposes a scientific paper idea proposer (SciPIP). Based on a user-provided research background, SciPIP retrieves helpful papers from a literature database while leveraging the capabilities of LLMs to generate more novel and feasible ideas. To this end, 1) we construct a literature retrieval database, extracting lots of papers' multi-dimension information for fast access. Then, a literature retrieval method based on semantics, entity, and citation co-occurrences is proposed to search relevant literature from multiple aspects based on the user-provided background. 2) After literature retrieval, we introduce dual-path idea proposal strategies, where one path infers solutions from the retrieved literature and the other path generates original ideas through model brainstorming. We then combine the two to achieve a good balance between feasibility and originality. Through extensive experiments on the natural language processing (NLP) field, we demonstrate that SciPIP can retrieve citations similar to those of existing top conference papers and generate many ideas consistent with them. Additionally, we evaluate the originality of other ideas generated by SciPIP using large language models, further validating the effectiveness of our proposed method. The code and the database are released at https://github.com/cheerss/SciPIP.

Scientific text is a promising source of data in materials science, with ongoing research into utilising textual data for materials discovery. In this study, we developed and tested a novel approach to extract material-property relationships from scientific publications using the Question Answering (QA) method. QA performance was evaluated for information extraction of perovskite bandgaps based on a human query. We observed considerable variation in results with five different large language models fine-tuned for the QA task. Best extraction accuracy was achieved with the QA MatBERT and F1-scores improved on the current state-of-the-art. This work demonstrates the QA workflow and paves the way towards further applications. The simplicity, versatility and accuracy of the QA approach all point to its considerable potential for text-driven discoveries in materials research.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

In this technical report, we propose ChemVLM, the first open-source multimodal large language model dedicated to the fields of chemistry, designed to address the incompatibility between chemical image understanding and text analysis. Built upon the VIT-MLP-LLM architecture, we leverage ChemLLM-20B as the foundational large model, endowing our model with robust capabilities in understanding and utilizing chemical text knowledge. Additionally, we employ InternVIT-6B as a powerful image encoder. We have curated high-quality data from the chemical domain, including molecules, reaction formulas, and chemistry examination data, and compiled these into a bilingual multimodal question-answering dataset. We test the performance of our model on multiple open-source benchmarks and three custom evaluation sets. Experimental results demonstrate that our model achieves excellent performance, securing state-of-the-art results in five out of six involved tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

This paper presents the development and application of a Large Language Model Retrieval-Augmented Generation (LLM-RAG) system tailored for nanotechnology research. The system leverages the capabilities of a sophisticated language model to serve as an intelligent research assistant, enhancing the efficiency and comprehensiveness of literature reviews in the nanotechnology domain. Central to this LLM-RAG system is its advanced query backend retrieval mechanism, which integrates data from multiple reputable sources. The system retrieves relevant literature by utilizing Google Scholar's advanced search, and scraping open-access papers from Elsevier, Springer Nature, and ACS Publications. This multifaceted approach ensures a broad and diverse collection of up-to-date scholarly articles and papers. The proposed system demonstrates significant potential in aiding researchers by providing a streamlined, accurate, and exhaustive literature retrieval process, thereby accelerating research advancements in nanotechnology. The effectiveness of the LLM-RAG system is validated through rigorous testing, illustrating its capability to significantly reduce the time and effort required for comprehensive literature reviews, while maintaining high accuracy, query relevance and outperforming standard, publicly available LLMS.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

Traditionally, theory and practice of Cognitive Control are linked via literature reviews by human domain experts. This approach, however, is inadequate to track the ever-growing literature. It may also be biased, and yield redundancies and confusion. Here we present an alternative approach. We performed automated text analyses on a large body of scientific texts to create a joint representation of tasks and constructs. More specifically, 385,705 scientific abstracts were first mapped into an embedding space using a transformers-based language model. Document embeddings were then used to identify a task-construct graph embedding that grounds constructs on tasks and supports nuanced meaning of the constructs by taking advantage of constrained random walks in the graph. This joint task-construct graph embedding, can be queried to generate task batteries targeting specific constructs, may reveal knowledge gaps in the literature, and inspire new tasks and novel hypotheses.

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

We explore the ability of GPT-4 to perform ad-hoc schema based information extraction from scientific literature. We assess specifically whether it can, with a basic prompting approach, replicate two existing material science datasets, given the manuscripts from which they were originally manually extracted. We employ materials scientists to perform a detailed manual error analysis to assess where the model struggles to faithfully extract the desired information, and draw on their insights to suggest research directions to address this broadly important task.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

Effective scientific communication depends on accurate citations that validate sources and guide readers to supporting evidence. Yet academic literature faces mounting challenges: semantic citation errors that misrepresent sources, AI-generated hallucinated references, and traditional citation formats that point to entire papers without indicating which sections substantiate specific claims. We introduce SemanticCite, an AI-powered system that verifies citation accuracy through full-text source analysis while providing rich contextual information via detailed reasoning and relevant text snippets. Our approach combines multiple retrieval methods with a four-class classification system (Supported, Partially Supported, Unsupported, Uncertain) that captures nuanced claim-source relationships and enables appropriate remedial actions for different error types. Our experiments show that fine-tuned lightweight language models achieve performance comparable to large commercial systems with significantly lower computational requirements, making large-scale citation verification practically feasible. The system provides transparent, evidence-based explanations that support user understanding and trust. We contribute a comprehensive dataset of over 1,000 citations with detailed alignments, functional classifications, semantic annotations, and bibliometric metadata across eight disciplines, alongside fine-tuned models and the complete verification framework as open-source software. SemanticCite addresses critical challenges in research integrity through scalable citation verification, streamlined peer review, and quality control for AI-generated content, providing an open-source foundation for maintaining citation accuracy at scale.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Scientific progress depends on researchers' ability to synthesize the growing body of literature. Can large language models (LMs) assist scientists in this task? We introduce OpenScholar, a specialized retrieval-augmented LM that answers scientific queries by identifying relevant passages from 45 million open-access papers and synthesizing citation-backed responses. To evaluate OpenScholar, we develop ScholarQABench, the first large-scale multi-domain benchmark for literature search, comprising 2,967 expert-written queries and 208 long-form answers across computer science, physics, neuroscience, and biomedicine. On ScholarQABench, OpenScholar-8B outperforms GPT-4o by 5% and PaperQA2 by 7% in correctness, despite being a smaller, open model. While GPT4o hallucinates citations 78 to 90% of the time, OpenScholar achieves citation accuracy on par with human experts. OpenScholar's datastore, retriever, and self-feedback inference loop also improves off-the-shelf LMs: for instance, OpenScholar-GPT4o improves GPT-4o's correctness by 12%. In human evaluations, experts preferred OpenScholar-8B and OpenScholar-GPT4o responses over expert-written ones 51% and 70% of the time, respectively, compared to GPT4o's 32%. We open-source all of our code, models, datastore, data and a public demo.

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce Scito2M, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. Using Scito2M, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years).

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

The rapid expansion of scientific literature in computer science presents challenges in tracking research trends and extracting key insights. Existing datasets provide metadata but lack structured summaries that capture core contributions and methodologies. We introduce CS-PaperSum, a large-scale dataset of 91,919 papers from 31 top-tier computer science conferences, enriched with AI-generated structured summaries using ChatGPT. To assess summary quality, we conduct embedding alignment analysis and keyword overlap analysis, demonstrating strong preservation of key concepts. We further present a case study on AI research trends, highlighting shifts in methodologies and interdisciplinary crossovers, including the rise of self-supervised learning, retrieval-augmented generation, and multimodal AI. Our dataset enables automated literature analysis, research trend forecasting, and AI-driven scientific discovery, providing a valuable resource for researchers, policymakers, and scientific information retrieval systems.

Thousands of new scientific papers are published each month. Such information overload complicates researcher efforts to stay current with the state-of-the-art as well as to verify and correctly attribute claims. We pose the following research question: Given a text excerpt referencing a paper, could an LM act as a research assistant to correctly identify the referenced paper? We advance efforts to answer this question by building a benchmark that evaluates the abilities of LMs in citation attribution. Our benchmark, CiteME, consists of text excerpts from recent machine learning papers, each referencing a single other paper. CiteME use reveals a large gap between frontier LMs and human performance, with LMs achieving only 4.2-18.5% accuracy and humans 69.7%. We close this gap by introducing CiteAgent, an autonomous system built on the GPT-4o LM that can also search and read papers, which achieves an accuracy of 35.3\% on CiteME. Overall, CiteME serves as a challenging testbed for open-ended claim attribution, driving the research community towards a future where any claim made by an LM can be automatically verified and discarded if found to be incorrect.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Large Language Models (LLMs) generalize well across language tasks, but suffer from hallucinations and uninterpretability, making it difficult to assess their accuracy without ground-truth. Retrieval-Augmented Generation (RAG) models have been proposed to reduce hallucinations and provide provenance for how an answer was generated. Applying such models to the scientific literature may enable large-scale, systematic processing of scientific knowledge. We present PaperQA, a RAG agent for answering questions over the scientific literature. PaperQA is an agent that performs information retrieval across full-text scientific articles, assesses the relevance of sources and passages, and uses RAG to provide answers. Viewing this agent as a question answering model, we find it exceeds performance of existing LLMs and LLM agents on current science QA benchmarks. To push the field closer to how humans perform research on scientific literature, we also introduce LitQA, a more complex benchmark that requires retrieval and synthesis of information from full-text scientific papers across the literature. Finally, we demonstrate PaperQA's matches expert human researchers on LitQA.

Accurately identifying the synthesis conditions of metal-organic frameworks (MOFs) is essential for guiding experimental design, yet remains challenging because relevant information in the literature is often scattered, inconsistent, and difficult to interpret. We present MOFh6, a large language model driven system that reads raw articles or crystal codes and converts them into standardized synthesis tables. It links related descriptions across paragraphs, unifies ligand abbreviations with full names, and outputs structured parameters ready for use. MOFh6 achieved 99% extraction accuracy, resolved 94.1% of abbreviation cases across five major publishers, and maintained a precision of 0.93 +/- 0.01. Processing a full text takes 9.6 s, locating synthesis descriptions 36 s, with 100 papers processed for USD 4.24. By replacing static database lookups with real-time extraction, MOFh6 reshapes MOF synthesis research, accelerating the conversion of literature knowledge into practical synthesis protocols and enabling scalable, data-driven materials discovery.

The exponential growth of scientific literature has made it increasingly difficult for researchers to keep up with the literature. In an attempt to alleviate this problem, we propose CASPER, a sparse retrieval model for scientific search that utilizes tokens and keyphrases as representation units (i.e. dimensions in the sparse embedding space), enabling it to represent queries and documents with research concepts and match them at both granular and conceptual levels. To overcome the lack of suitable training data, we propose mining training data by leveraging scholarly references (i.e. signals that capture how research concepts of papers are expressed in different settings), including titles, citation contexts, author-assigned keyphrases, and co-citations. CASPER outperforms strong dense and sparse retrieval baselines on eight scientific retrieval benchmarks. Moreover, we demonstrate that through simple post-processing, CASPER can be effectively used for the keyphrase generation tasks, achieving competitive performance with the established CopyRNN while producing more diverse keyphrases and being nearly four times faster.

Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific knowledge effectively, thus improving their performance in a wide range of tasks. Due to the power of LLMs, they require extremely expensive computational resources, intense amounts of data, and training time. Therefore, in recent years, researchers have proposed various methodologies to make scientific LLMs more affordable. The most well-known approaches align in two directions. It can be either focusing on the size of the models or enhancing the quality of data. To date, a comprehensive review of these two families of methods has not yet been undertaken. In this paper, we (I) summarize the current advances in the emerging abilities of LLMs into more accessible AI solutions for science, and (II) investigate the challenges and opportunities of developing affordable solutions for scientific domains using LLMs.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

When conducting literature reviews, scientists often create literature review tables - tables whose rows are publications and whose columns constitute a schema, a set of aspects used to compare and contrast the papers. Can we automatically generate these tables using language models (LMs)? In this work, we introduce a framework that leverages LMs to perform this task by decomposing it into separate schema and value generation steps. To enable experimentation, we address two main challenges: First, we overcome a lack of high-quality datasets to benchmark table generation by curating and releasing arxivDIGESTables, a new dataset of 2,228 literature review tables extracted from ArXiv papers that synthesize a total of 7,542 research papers. Second, to support scalable evaluation of model generations against human-authored reference tables, we develop DecontextEval, an automatic evaluation method that aligns elements of tables with the same underlying aspects despite differing surface forms. Given these tools, we evaluate LMs' abilities to reconstruct reference tables, finding this task benefits from additional context to ground the generation (e.g. table captions, in-text references). Finally, through a human evaluation study we find that even when LMs fail to fully reconstruct a reference table, their generated novel aspects can still be useful.

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

Scientific paper retrieval is essential for supporting literature discovery and research. While dense retrieval methods demonstrate effectiveness in general-purpose tasks, they often fail to capture fine-grained scientific concepts that are essential for accurate understanding of scientific queries. Recent studies also use large language models (LLMs) for query understanding; however, these methods often lack grounding in corpus-specific knowledge and may generate unreliable or unfaithful content. To overcome these limitations, we propose SemRank, an effective and efficient paper retrieval framework that combines LLM-guided query understanding with a concept-based semantic index. Each paper is indexed using multi-granular scientific concepts, including general research topics and detailed key phrases. At query time, an LLM identifies core concepts derived from the corpus to explicitly capture the query's information need. These identified concepts enable precise semantic matching, significantly enhancing retrieval accuracy. Experiments show that SemRank consistently improves the performance of various base retrievers, surpasses strong existing LLM-based baselines, and remains highly efficient.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

This paper focuses on text detoxification, i.e., automatically converting toxic text into non-toxic text. This task contributes to safer and more respectful online communication and can be considered a Text Style Transfer (TST) task, where the text style changes while its content is preserved. We present three approaches: knowledge transfer from a similar task, multi-task learning approach, combining sequence-to-sequence modeling with various toxicity classification tasks, and delete and reconstruct approach. To support our research, we utilize a dataset provided by Dementieva et al.(2021), which contains multiple versions of detoxified texts corresponding to toxic texts. In our experiments, we selected the best variants through expert human annotators, creating a dataset where each toxic sentence is paired with a single, appropriate detoxified version. Additionally, we introduced a small Hindi parallel dataset, aligning with a part of the English dataset, suitable for evaluation purposes. Our results demonstrate that our approach effectively balances text detoxication while preserving the actual content and maintaining fluency.

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future deliberations. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, providing a foundation for advancements in data assimilation and utilization.

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.

Scientific literature understanding tasks have gained significant attention due to their potential to accelerate scientific discovery. Pre-trained language models (LMs) have shown effectiveness in these tasks, especially when tuned via contrastive learning. However, jointly utilizing pre-training data across multiple heterogeneous tasks (e.g., extreme classification, citation prediction, and literature search) remains largely unexplored. To bridge this gap, we propose a multi-task contrastive learning framework, SciMult, with a focus on facilitating common knowledge sharing across different scientific literature understanding tasks while preventing task-specific skills from interfering with each other. To be specific, we explore two techniques -- task-aware specialization and instruction tuning. The former adopts a Mixture-of-Experts Transformer architecture with task-aware sub-layers; the latter prepends task-specific instructions to the input text so as to produce task-aware outputs. Extensive experiments on a comprehensive collection of benchmark datasets verify the effectiveness of our task-aware specialization strategy in various tasks, where we outperform state-of-the-art scientific LMs.

This research presents and compares multiple approaches to automate the generation of literature reviews using several Natural Language Processing (NLP) techniques and retrieval-augmented generation (RAG) with a Large Language Model (LLM). The ever-increasing number of research articles provides a huge challenge for manual literature review. It has resulted in an increased demand for automation. Developing a system capable of automatically generating the literature reviews from only the PDF files as input is the primary objective of this research work. The effectiveness of several Natural Language Processing (NLP) strategies, such as the frequency-based method (spaCy), the transformer model (Simple T5), and retrieval-augmented generation (RAG) with Large Language Model (GPT-3.5-turbo), is evaluated to meet the primary objective. The SciTLDR dataset is chosen for this research experiment and three distinct techniques are utilized to implement three different systems for auto-generating the literature reviews. The ROUGE scores are used for the evaluation of all three systems. Based on the evaluation, the Large Language Model GPT-3.5-turbo achieved the highest ROUGE-1 score, 0.364. The transformer model comes in second place and spaCy is at the last position. Finally, a graphical user interface is created for the best system based on the large language model.

In this paper we address the challenge of extracting scientific references from patents. We approach the problem as a sequence labelling task and investigate the merits of BERT models to the extraction of these long sequences. References in patents to scientific literature are relevant to study the connection between science and industry. Most prior work only uses the front-page citations for this analysis, which are provided in the metadata of patent archives. In this paper we build on prior work using Conditional Random Fields (CRF) and Flair for reference extraction. We improve the quality of the training data and train three BERT-based models on the labelled data (BERT, bioBERT, sciBERT). We find that the improved training data leads to a large improvement in the quality of the trained models. In addition, the BERT models beat CRF and Flair, with recall scores around 97% obtained with cross validation. With the best model we label a large collection of 33 thousand patents, extract the citations, and match them to publications in the Web of Science database. We extract 50% more references than with the old training data and methods: 735 thousand references in total. With these patent-publication links, follow-up research will further analyze which types of scientific work lead to inventions.

Large Language Models provide significant new opportunities for the generation of high-quality written works. However, their employment in the research community is inhibited by their tendency to hallucinate invalid sources and lack of direct access to a knowledge base of relevant scientific articles. In this work, we present Citegeist: An application pipeline using dynamic Retrieval Augmented Generation (RAG) on the arXiv Corpus to generate a related work section and other citation-backed outputs. For this purpose, we employ a mixture of embedding-based similarity matching, summarization, and multi-stage filtering. To adapt to the continuous growth of the document base, we also present an optimized way of incorporating new and modified papers. To enable easy utilization in the scientific community, we release both, a website (https://citegeist.org), as well as an implementation harness that works with several different LLM implementations.

Researchers struggle to efficiently locate and manage relevant literature within the exponentially growing body of scientific publications. We present WisPaper, an intelligent academic retrieval and literature management platform that addresses this challenge through three integrated capabilities: (1) Scholar Search, featuring both quick keyword-based and deep agentic search modes for efficient paper discovery; (2) Library, a customizable knowledge base for systematic literature organization; and (3) AI Feeds, an intelligent recommendation system that automatically delivers relevant new publications based on user interests. Unlike existing academic tools, WisPaper provides a closed-loop workflow that seamlessly connects literature discovery, management, and continuous tracking of research frontiers. Our multilingual and multidisciplinary system significantly reduces the time researchers from diverse backgrounds spend on paper screening and management, enabling them to focus on their core research activities. The platform is publicly accessible and serves researchers across academia and industry.

Paywalls, licenses and copyright rules often restrict the broad dissemination and reuse of scientific knowledge. We take the position that it is both legally and technically feasible to extract the scientific knowledge in scholarly texts. Current methods, like text embeddings, fail to reliably preserve factual content, and simple paraphrasing may not be legally sound. We urge the community to adopt a new idea: convert scholarly documents into Knowledge Units using LLMs. These units use structured data capturing entities, attributes and relationships without stylistic content. We provide evidence that Knowledge Units: (1) form a legally defensible framework for sharing knowledge from copyrighted research texts, based on legal analyses of German copyright law and U.S. Fair Use doctrine, and (2) preserve most (~95%) factual knowledge from original text, measured by MCQ performance on facts from the original copyrighted text across four research domains. Freeing scientific knowledge from copyright promises transformative benefits for scientific research and education by allowing language models to reuse important facts from copyrighted text. To support this, we share open-source tools for converting research documents into Knowledge Units. Overall, our work posits the feasibility of democratizing access to scientific knowledge while respecting copyright.

This paper presents a hybrid framework for literature reviews that augments traditional bibliometric methods with large language models (LLMs). By fine-tuning open-source LLMs, our approach enables scalable extraction of qualitative insights from large volumes of research content, enhancing both the breadth and depth of knowledge synthesis. To improve annotation efficiency and consistency, we introduce an error-focused validation process in which LLMs generate initial labels and human reviewers correct misclassifications. Applying this framework to over 20000 scientific articles about human migration, we demonstrate that a domain-adapted LLM can serve as a "specialist" model - capable of accurately selecting relevant studies, detecting emerging trends, and identifying critical research gaps. Notably, the LLM-assisted review reveals a growing scholarly interest in climate-induced migration. However, existing literature disproportionately centers on a narrow set of environmental hazards (e.g., floods, droughts, sea-level rise, and land degradation), while overlooking others that more directly affect human health and well-being, such as air and water pollution or infectious diseases. This imbalance highlights the need for more comprehensive research that goes beyond physical environmental changes to examine their ecological and societal consequences, particularly in shaping migration as an adaptive response. Overall, our proposed framework demonstrates the potential of fine-tuned LLMs to conduct more efficient, consistent, and insightful literature reviews across disciplines, ultimately accelerating knowledge synthesis and scientific discovery.

Humanities scholars commonly provide evidence for claims that they make about a work of literature (e.g., a novel) in the form of quotations from the work. We collect a large-scale dataset (RELiC) of 78K literary quotations and surrounding critical analysis and use it to formulate the novel task of literary evidence retrieval, in which models are given an excerpt of literary analysis surrounding a masked quotation and asked to retrieve the quoted passage from the set of all passages in the work. Solving this retrieval task requires a deep understanding of complex literary and linguistic phenomena, which proves challenging to methods that overwhelmingly rely on lexical and semantic similarity matching. We implement a RoBERTa-based dense passage retriever for this task that outperforms existing pretrained information retrieval baselines; however, experiments and analysis by human domain experts indicate that there is substantial room for improvement over our dense retriever.

Scientific knowledge is predominantly stored in books and scientific journals, often in the form of PDFs. However, the PDF format leads to a loss of semantic information, particularly for mathematical expressions. We propose Nougat (Neural Optical Understanding for Academic Documents), a Visual Transformer model that performs an Optical Character Recognition (OCR) task for processing scientific documents into a markup language, and demonstrate the effectiveness of our model on a new dataset of scientific documents. The proposed approach offers a promising solution to enhance the accessibility of scientific knowledge in the digital age, by bridging the gap between human-readable documents and machine-readable text. We release the models and code to accelerate future work on scientific text recognition.

Language models are known to hallucinate incorrect information, and it is unclear if they are sufficiently accurate and reliable for use in scientific research. We developed a rigorous human-AI comparison methodology to evaluate language model agents on real-world literature search tasks covering information retrieval, summarization, and contradiction detection tasks. We show that PaperQA2, a frontier language model agent optimized for improved factuality, matches or exceeds subject matter expert performance on three realistic literature research tasks without any restrictions on humans (i.e., full access to internet, search tools, and time). PaperQA2 writes cited, Wikipedia-style summaries of scientific topics that are significantly more accurate than existing, human-written Wikipedia articles. We also introduce a hard benchmark for scientific literature research called LitQA2 that guided design of PaperQA2, leading to it exceeding human performance. Finally, we apply PaperQA2 to identify contradictions within the scientific literature, an important scientific task that is challenging for humans. PaperQA2 identifies 2.34 +/- 1.99 contradictions per paper in a random subset of biology papers, of which 70% are validated by human experts. These results demonstrate that language model agents are now capable of exceeding domain experts across meaningful tasks on scientific literature.

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".

In this paper, we present a novel approach to knowledge extraction and retrieval using Natural Language Processing (NLP) techniques for material science. Our goal is to automatically mine structured knowledge from millions of research articles in the field of polycrystalline materials and make it easily accessible to the broader community. The proposed method leverages NLP techniques such as entity recognition and document classification to extract relevant information and build an extensive knowledge base, from a collection of 9.5 Million publications. The resulting knowledge base is integrated into a search engine, which enables users to search for information about specific materials, properties, and experiments with greater precision than traditional search engines like Google. We hope our results can enable material scientists quickly locate desired experimental procedures, compare their differences, and even inspire them to design new experiments. Our website will be available at Github https://github.com/Xianjun-Yang/PcMSP.git soon.

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, in this paper, we propose ChemMLLM, a unified chemical multimodal large language model for molecule understanding and generation. Also, we design five multimodal tasks across text, molecular SMILES strings, and image, and curate the datasets. We benchmark ChemMLLM against a range of general leading MLLMs and Chemical LLMs on these tasks. Experimental results show that ChemMLLM achieves superior performance across all evaluated tasks. For example, in molecule image optimization task, ChemMLLM outperforms the best baseline (GPT-4o) by 118.9\% (4.27 vs 1.95 property improvement). The code is publicly available at https://github.com/bbsbz/ChemMLLM.git.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Predicting highly-cited papers is a long-standing challenge due to the complex interactions of research content, scholarly communities, and temporal dynamics. Recent advances in large language models (LLMs) raise the question of whether early-stage textual information can provide useful signals of long-term scientific impact. Focusing on statistical publications, we propose a flexible, text-centered framework that leverages LLMs and structured prompt design to predict highly cited papers. Specifically, we utilize information available at the time of publication, including titles, abstracts, keywords, and limited bibliographic metadata. Using a large corpus of statistical papers, we evaluate predictive performance across multiple publication periods and alternative definitions of highly cited papers. The proposed approach achieves stable and competitive performance relative to existing methods and demonstrates strong generalization over time. Textual analysis further reveals that papers predicted as highly cited concentrate on recurring topics such as causal inference and deep learning. To facilitate practical use of the proposed approach, we further develop a WeChat mini program, Stat Highly Cited Papers, which provides an accessible interface for early-stage citation impact assessment. Overall, our results provide empirical evidence that LLMs can capture meaningful early signals of long-term citation impact, while also highlighting their limitations as tools for research impact assessment.

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

By consolidating scattered knowledge, the literature review provides a comprehensive understanding of the investigated topic. However, reading, conducting, or peer-reviewing review papers generally demands a significant investment of time and effort from researchers. To improve efficiency, this paper aims to provide a thorough review of reviews in the PAMI field from diverse perspectives. First, this paper proposes several article-level, field-normalized, and large language model-empowered bibliometric indicators to evaluate reviews. To facilitate this, a meta-data database dubbed RiPAMI, and a topic dataset are constructed. Second, based on these indicators, the study presents comparative analyses of representative reviews, unveiling the characteristics of publications across various fields, periods, and journals. The newly emerging AI-generated literature reviews are also appraised, and the observed differences suggest that most AI-generated reviews still lag behind human-authored reviews in multiple aspects. Third, we briefly provide a subjective evaluation of representative PAMI reviews and introduce a paper structure-based typology of literature reviews. This typology may improve the clarity and effectiveness for scholars in reading and writing reviews, while also serving as a guide for AI systems in generating well-organized reviews. Finally, this work offers insights into the current challenges of literature reviews and envisions future directions for their development.

Academic writing requires both coherent text generation and precise citation of relevant literature. Although recent Retrieval-Augmented Generation (RAG) systems have significantly improved factual accuracy in general-purpose text generation, their capacity to adequately support professional academic writing remains limited. In this work, we introduce ScholarCopilot, a unified framework designed to enhance existing large language models for generating professional academic articles with accurate and contextually relevant citations. ScholarCopilot dynamically determines when to retrieve scholarly references by generating a retrieval token [RET], and then utilizes its representation to look up relevant citations from a database. The retrieved references are fed into the model to augment the generation process. We jointly optimize both the generation and citation tasks within a single framework to increase efficiency. Trained on 500K papers from arXiv, our model achieves a top-1 retrieval accuracy of 40.1% on our evaluation dataset, outperforming baselines such as E5-Mistral-7B-Instruct (15.0%) and BM25 (9.8%). On a dataset of 1,000 academic writing samples, ScholarCopilot scores 16.2/25 in generation quality (measured across relevance, coherence, academic rigor, completeness, and innovation), surpassing models with 10x more parameters such as Qwen-2.5-72B-Instruct (15.8/25). Human studies also confirm ScholarCopilot's superior performance in citation recall, writing efficiency, and overall user experience, confirming the effectiveness of our approach.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.