Daily Papers

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

Data-driven materials discovery requires large-scale experimental datasets, yet most of the information remains trapped in unstructured literature. Existing extraction efforts often focus on a limited set of features and have not addressed the integrated composition-processing-microstructure-property relationships essential for understanding materials behavior, thereby posing challenges for building comprehensive databases. To address this gap, we propose a multi-stage information extraction pipeline powered by large language models, which captures 47 features spanning composition, processing, microstructure, and properties exclusively from experimentally reported materials. The pipeline integrates iterative extraction with source tracking to enhance both accuracy and reliability. Evaluations at the feature level (independent attributes) and tuple level (interdependent features) yielded F1 scores around 0.96. Compared with single-pass extraction without source tracking, our approach improved F1 scores of microstructure category by 10.0% (feature level) and 13.7% (tuple level), and reduced missed materials from 49 to 13 out of 396 materials in 100 articles on precipitate-containing multi-principal element alloys (miss rate reduced from 12.4% to 3.3%). The pipeline enables scalable and efficient literature mining, producing databases with high precision, minimal omissions, and zero false positives. These datasets provide trustworthy inputs for machine learning and materials informatics, while the modular design generalizes to diverse material classes, enabling comprehensive materials information extraction.

The convergence of artificial intelligence and materials science presents a transformative opportunity, but achieving true acceleration in discovery requires moving beyond task-isolated, fine-tuned models toward agentic systems that plan, act, and learn across the full discovery loop. This survey advances a unique pipeline-centric view that spans from corpus curation and pretraining, through domain adaptation and instruction tuning, to goal-conditioned agents interfacing with simulation and experimental platforms. Unlike prior reviews, we treat the entire process as an end-to-end system to be optimized for tangible discovery outcomes rather than proxy benchmarks. This perspective allows us to trace how upstream design choices-such as data curation and training objectives-can be aligned with downstream experimental success through effective credit assignment. To bridge communities and establish a shared frame of reference, we first present an integrated lens that aligns terminology, evaluation, and workflow stages across AI and materials science. We then analyze the field through two focused lenses: From the AI perspective, the survey details LLM strengths in pattern recognition, predictive analytics, and natural language processing for literature mining, materials characterization, and property prediction; from the materials science perspective, it highlights applications in materials design, process optimization, and the acceleration of computational workflows via integration with external tools (e.g., DFT, robotic labs). Finally, we contrast passive, reactive approaches with agentic design, cataloging current contributions while motivating systems that pursue long-horizon goals with autonomy, memory, and tool use. This survey charts a practical roadmap towards autonomous, safety-aware LLM agents aimed at discovering novel and useful materials.

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}.

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.

The whole slide image (WSI) classification is often formulated as a multiple instance learning (MIL) problem. Since the positive tissue is only a small fraction of the gigapixel WSI, existing MIL methods intuitively focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting hard-to-classify instances. Some literature has revealed that hard examples are beneficial for modeling a discriminative boundary accurately. By applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which uses a Siamese structure (Teacher-Student) with a consistency constraint to explore the potential hard instances. With several instance masking strategies based on attention scores, MHIM-MIL employs a momentum teacher to implicitly mine hard instances for training the student model, which can be any attention-based MIL model. This counter-intuitive strategy essentially enables the student to learn a better discriminating boundary. Moreover, the student is used to update the teacher with an exponential moving average (EMA), which in turn identifies new hard instances for subsequent training iterations and stabilizes the optimization. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that MHIM-MIL outperforms other latest methods in terms of performance and training cost. The code is available at: https://github.com/DearCaat/MHIM-MIL.

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.

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.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Training with sparse annotations is known to reduce the performance of object detectors. Previous methods have focused on proxies for missing ground truth annotations in the form of pseudo-labels for unlabeled boxes. We observe that existing methods suffer at higher levels of sparsity in the data due to noisy pseudo-labels. To prevent this, we propose an end-to-end system that learns to separate the proposals into labeled and unlabeled regions using Pseudo-positive mining. While the labeled regions are processed as usual, self-supervised learning is used to process the unlabeled regions thereby preventing the negative effects of noisy pseudo-labels. This novel approach has multiple advantages such as improved robustness to higher sparsity when compared to existing methods. We conduct exhaustive experiments on five splits on the PASCAL-VOC and COCO datasets achieving state-of-the-art performance. We also unify various splits used across literature for this task and present a standardized benchmark. On average, we improve by 2.6, 3.9 and 9.6 mAP over previous state-of-the-art methods on three splits of increasing sparsity on COCO. Our project is publicly available at https://www.cs.umd.edu/~sakshams/SparseDet.

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

Traditional data sources on bushfire evacuation behaviour, such as quantitative surveys and manual observations have severe limitations. Mining social media data related to bushfire evacuations promises to close this gap by allowing the collection and processing of a large amount of behavioural data, which are low-cost, accurate, possibly including location information and rich contextual information. However, social media data have many limitations, such as being scattered, incomplete, informal, etc. Together, these limitations represent several challenges to their usefulness to better understand bushfire evacuation. To overcome these challenges and provide guidance on which and how social media data can be used, this scoping review of the literature reports on recent advances in relevant data mining techniques. In addition, future applications and open problems are discussed. We envision future applications such as evacuation model calibration and validation, emergency communication, personalised evacuation training, and resource allocation for evacuation preparedness. We identify open problems such as data quality, bias and representativeness, geolocation accuracy, contextual understanding, crisis-specific lexicon and semantics, and multimodal data interpretation.

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.

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

This data paper introduces MajinBook, an open catalogue designed to facilitate the use of shadow libraries--such as Library Genesis and Z-Library--for computational social science and cultural analytics. By linking metadata from these vast, crowd-sourced archives with structured bibliographic data from Goodreads, we create a high-precision corpus of over 539,000 references to English-language books spanning three centuries, enriched with first publication dates, genres, and popularity metrics like ratings and reviews. Our methodology prioritizes natively digital EPUB files to ensure machine-readable quality, while addressing biases in traditional corpora like HathiTrust, and includes secondary datasets for French, German, and Spanish. We evaluate the linkage strategy for accuracy, release all underlying data openly, and discuss the project's legal permissibility under EU and US frameworks for text and data mining in research.

An overwhelmingly large amount of knowledge in the materials domain is generated and stored as text published in peer-reviewed scientific literature. Recent developments in natural language processing, such as bidirectional encoder representations from transformers (BERT) models, provide promising tools to extract information from these texts. However, direct application of these models in the materials domain may yield suboptimal results as the models themselves may not be trained on notations and jargon that are specific to the domain. Here, we present a materials-aware language model, namely, MatSciBERT, which is trained on a large corpus of scientific literature published in the materials domain. We further evaluate the performance of MatSciBERT on three downstream tasks, namely, abstract classification, named entity recognition, and relation extraction, on different materials datasets. We show that MatSciBERT outperforms SciBERT, a language model trained on science corpus, on all the tasks. Further, we discuss some of the applications of MatSciBERT in the materials domain for extracting information, which can, in turn, contribute to materials discovery or optimization. Finally, to make the work accessible to the larger materials community, we make the pretrained and finetuned weights and the models of MatSciBERT freely accessible.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

We propose a semi-automatic staging area for efficiently building an accurate database of experimental physical properties of superconductors from literature, called SuperCon2, to enrich the existing manually-built superconductor database SuperCon. Here we report our curation interface (SuperCon2 Interface) and a workflow managing the state transitions of each examined record, to validate the dataset of superconductors from PDF documents collected using Grobid-superconductors in a previous work. This curation workflow allows both automatic and manual operations, the former contains ``anomaly detection'' that scans new data identifying outliers, and a ``training data collector'' mechanism that collects training data examples based on manual corrections. Such training data collection policy is effective in improving the machine-learning models with a reduced number of examples. For manual operations, the interface (SuperCon2 interface) is developed to increase efficiency during manual correction by providing a smart interface and an enhanced PDF document viewer. We show that our interface significantly improves the curation quality by boosting precision and recall as compared with the traditional ``manual correction''. Our semi-automatic approach would provide a solution for achieving a reliable database with text-data mining of scientific documents.

In this article, we conduct data mining to discover the countries, universities and companies, produced or collaborated the most research on Covid-19 since the pandemic started. We present some interesting findings, but despite analysing all available records on COVID-19 from the Web of Science Core Collection, we failed to reach any significant conclusions on how the world responded to the COVID-19 pandemic. Therefore, we increased our analysis to include all available data records on pandemics and epidemics from 1900 to 2020. We discover some interesting results on countries, universities and companies, that produced collaborated most the most in research on pandemic and epidemics. Then we compared the results with the analysing on COVID-19 data records. This has created some interesting findings that are explained and graphically visualised in the article.

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.

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.

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.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

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.

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.

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.

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.

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.

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.

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

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.

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.

With the widespread use of the internet, it has become increasingly crucial to extract specific information from vast amounts of academic articles efficiently. Data mining techniques are generally employed to solve this issue. However, data mining for academic articles is challenging since it requires automatically extracting specific patterns in complex and unstructured layout documents. Current data mining methods for academic articles employ rule-based(RB) or machine learning(ML) approaches. However, using rule-based methods incurs a high coding cost for complex typesetting articles. On the other hand, simply using machine learning methods requires annotation work for complex content types within the paper, which can be costly. Furthermore, only using machine learning can lead to cases where patterns easily recognized by rule-based methods are mistakenly extracted. To overcome these issues, from the perspective of analyzing the standard layout and typesetting used in the specified publication, we emphasize implementing specific methods for specific characteristics in academic articles. We have developed a novel Text Block Refinement Framework (TBRF), a machine learning and rule-based scheme hybrid. We used the well-known ACL proceeding articles as experimental data for the validation experiment. The experiment shows that our approach achieved over 95% classification accuracy and 90% detection accuracy for tables and figures.

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.

We present a new scientific document similarity model based on matching fine-grained aspects of texts. To train our model, we exploit a naturally-occurring source of supervision: sentences in the full-text of papers that cite multiple papers together (co-citations). Such co-citations not only reflect close paper relatedness, but also provide textual descriptions of how the co-cited papers are related. This novel form of textual supervision is used for learning to match aspects across papers. We develop multi-vector representations where vectors correspond to sentence-level aspects of documents, and present two methods for aspect matching: (1) A fast method that only matches single aspects, and (2) a method that makes sparse multiple matches with an Optimal Transport mechanism that computes an Earth Mover's Distance between aspects. Our approach improves performance on document similarity tasks in four datasets. Further, our fast single-match method achieves competitive results, paving the way for applying fine-grained similarity to large scientific corpora. Code, data, and models available at: https://github.com/allenai/aspire

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.

Text summarization research has undergone several significant transformations with the advent of deep neural networks, pre-trained language models (PLMs), and recent large language models (LLMs). This survey thus provides a comprehensive review of the research progress and evolution in text summarization through the lens of these paradigm shifts. It is organized into two main parts: (1) a detailed overview of datasets, evaluation metrics, and summarization methods before the LLM era, encompassing traditional statistical methods, deep learning approaches, and PLM fine-tuning techniques, and (2) the first detailed examination of recent advancements in benchmarking, modeling, and evaluating summarization in the LLM era. By synthesizing existing literature and presenting a cohesive overview, this survey also discusses research trends, open challenges, and proposes promising research directions in summarization, aiming to guide researchers through the evolving landscape of summarization research.

We show that large language models (LLMs) can be used to distinguish the writings of different authors. Specifically, an individual GPT-2 model, trained from scratch on the works of one author, will predict held-out text from that author more accurately than held-out text from other authors. We suggest that, in this way, a model trained on one author's works embodies the unique writing style of that author. We first demonstrate our approach on books written by eight different (known) authors. We also use this approach to confirm R. P. Thompson's authorship of the well-studied 15th book of the Oz series, originally attributed to F. L. Baum.

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.

We provide a literature review about Automatic Text Summarization (ATS) systems. We consider a citation-based approach. We start with some popular and well-known papers that we have in hand about each topic we want to cover and we have tracked the "backward citations" (papers that are cited by the set of papers we knew beforehand) and the "forward citations" (newer papers that cite the set of papers we knew beforehand). In order to organize the different methods, we present the diverse approaches to ATS guided by the mechanisms they use to generate a summary. Besides presenting the methods, we also present an extensive review of the datasets available for summarization tasks and the methods used to evaluate the quality of the summaries. Finally, we present an empirical exploration of these methods using the CNN Corpus dataset that provides golden summaries for extractive and abstractive methods.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

In recent years, there has been an exponential growth in the number of complex documents and texts that require a deeper understanding of machine learning methods to be able to accurately classify texts in many applications. Many machine learning approaches have achieved surpassing results in natural language processing. The success of these learning algorithms relies on their capacity to understand complex models and non-linear relationships within data. However, finding suitable structures, architectures, and techniques for text classification is a challenge for researchers. In this paper, a brief overview of text classification algorithms is discussed. This overview covers different text feature extractions, dimensionality reduction methods, existing algorithms and techniques, and evaluations methods. Finally, the limitations of each technique and their application in the real-world problem are discussed.

Learning semantically meaningful representations from scientific documents can facilitate academic literature search and improve performance of recommendation systems. Pre-trained language models have been shown to learn rich textual representations, yet they cannot provide powerful document-level representations for scientific articles. We propose MIReAD, a simple method that learns high-quality representations of scientific papers by fine-tuning transformer model to predict the target journal class based on the abstract. We train MIReAD on more than 500,000 PubMed and arXiv abstracts across over 2,000 journal classes. We show that MIReAD produces representations that can be used for similar papers retrieval, topic categorization and literature search. Our proposed approach outperforms six existing models for representation learning on scientific documents across four evaluation standards.

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.

Text retrieval is a long-standing research topic on information seeking, where a system is required to return relevant information resources to user's queries in natural language. From classic retrieval methods to learning-based ranking functions, the underlying retrieval models have been continually evolved with the ever-lasting technical innovation. To design effective retrieval models, a key point lies in how to learn the text representation and model the relevance matching. The recent success of pretrained language models (PLMs) sheds light on developing more capable text retrieval approaches by leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can effectively learn the representations of queries and texts in the latent representation space, and further construct the semantic matching function between the dense vectors for relevance modeling. Such a retrieval approach is referred to as dense retrieval, since it employs dense vectors (a.k.a., embeddings) to represent the texts. Considering the rapid progress on dense retrieval, in this survey, we systematically review the recent advances on PLM-based dense retrieval. Different from previous surveys on dense retrieval, we take a new perspective to organize the related work by four major aspects, including architecture, training, indexing and integration, and summarize the mainstream techniques for each aspect. We thoroughly survey the literature, and include 300+ related reference papers on dense retrieval. To support our survey, we create a website for providing useful resources, and release a code repertory and toolkit for implementing dense retrieval models. This survey aims to provide a comprehensive, practical reference focused on the major progress for dense text retrieval.

This work delved into the realm of automatic text generation, exploring a variety of techniques ranging from traditional deterministic approaches to more modern stochastic methods. Through analysis of greedy search, beam search, top-k sampling, top-p sampling, contrastive searching, and locally typical searching, this work has provided valuable insights into the strengths, weaknesses, and potential applications of each method. Each text-generating method is evaluated using several standard metrics and a comparative study has been made on the performance of the approaches. Finally, some future directions of research in the field of automatic text generation are also identified.

We consider the problem of translating high-level textual descriptions to formal representations in technical documentation as part of an effort to model the meaning of such documentation. We focus specifically on the problem of learning translational correspondences between text descriptions and grounded representations in the target documentation, such as formal representation of functions or code templates. Our approach exploits the parallel nature of such documentation, or the tight coupling between high-level text and the low-level representations we aim to learn. Data is collected by mining technical documents for such parallel text-representation pairs, which we use to train a simple semantic parsing model. We report new baseline results on sixteen novel datasets, including the standard library documentation for nine popular programming languages across seven natural languages, and a small collection of Unix utility manuals.

Text generation has become more accessible than ever, and the increasing interest in these systems, especially those using large language models, has spurred an increasing number of related publications. We provide a systematic literature review comprising 244 selected papers between 2017 and 2024. This review categorizes works in text generation into five main tasks: open-ended text generation, summarization, translation, paraphrasing, and question answering. For each task, we review their relevant characteristics, sub-tasks, and specific challenges (e.g., missing datasets for multi-document summarization, coherence in story generation, and complex reasoning for question answering). Additionally, we assess current approaches for evaluating text generation systems and ascertain problems with current metrics. Our investigation shows nine prominent challenges common to all tasks and sub-tasks in recent text generation publications: bias, reasoning, hallucinations, misuse, privacy, interpretability, transparency, datasets, and computing. We provide a detailed analysis of these challenges, their potential solutions, and which gaps still require further engagement from the community. This systematic literature review targets two main audiences: early career researchers in natural language processing looking for an overview of the field and promising research directions, as well as experienced researchers seeking a detailed view of tasks, evaluation methodologies, open challenges, and recent mitigation strategies.

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 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.

Text embedding models have been popular for information retrieval applications such as semantic search and Question-Answering systems based on Retrieval-Augmented Generation (RAG). Those models are typically Transformer models that are fine-tuned with contrastive learning objectives. Many papers introduced new embedding model architectures and training approaches, however, one of the key ingredients, the process of mining negative passages, remains poorly explored or described. One of the challenging aspects of fine-tuning embedding models is the selection of high quality hard-negative passages for contrastive learning. In this paper we propose a family of positive-aware mining methods that leverage the positive relevance score for more effective false negatives removal. We also provide a comprehensive ablation study on hard-negative mining methods over their configurations, exploring different teacher and base models. We demonstrate the efficacy of our proposed methods by introducing the NV-Retriever-v1 model, which scores 60.9 on MTEB Retrieval (BEIR) benchmark and 0.65 points higher than previous methods. The model placed 1st when it was published to MTEB Retrieval on July 07, 2024.

The successful analysis of argumentative techniques from user-generated text is central to many downstream tasks such as political and market analysis. Recent argument mining tools use state-of-the-art deep learning methods to extract and annotate argumentative techniques from various online text corpora, however each task is treated as separate and different bespoke models are fine-tuned for each dataset. We show that different argument mining tasks share common semantic and logical structure by implementing a multi-task approach to argument mining that achieves better performance than state-of-the-art methods for the same problems. Our model builds a shared representation of the input text that is common to all tasks and exploits similarities between tasks in order to further boost performance via parameter-sharing. Our results are important for argument mining as they show that different tasks share substantial similarities and suggest a holistic approach to the extraction of argumentative techniques from text.

We present the task of modeling information propagation in literature, in which we seek to identify pieces of information passing from character A to character B to character C, only given a description of their activity in text. We describe a new pipeline for measuring information propagation in this domain and publish a new dataset for speaker attribution, enabling the evaluation of an important component of this pipeline on a wider range of literary texts than previously studied. Using this pipeline, we analyze the dynamics of information propagation in over 5,000 works of fiction, finding that information flows through characters that fill structural holes connecting different communities, and that characters who are women are depicted as filling this role much more frequently than characters who are men.

Digital Humanities and Computational Literary Studies apply text mining methods to investigate literature. Such automated approaches enable quantitative studies on large corpora which would not be feasible by manual inspection alone. However, due to copyright restrictions, the availability of relevant digitized literary works is limited. Derived Text Formats (DTFs) have been proposed as a solution. Here, textual materials are transformed in such a way that copyright-critical features are removed, but that the use of certain analytical methods remains possible. Contextualized word embeddings produced by transformer-encoders (like BERT) are promising candidates for DTFs because they allow for state-of-the-art performance on various analytical tasks and, at first sight, do not disclose the original text. However, in this paper we demonstrate that under certain conditions the reconstruction of the original copyrighted text becomes feasible and its publication in the form of contextualized token representations is not safe. Our attempts to invert BERT suggest, that publishing the encoder as a black box together with the contextualized embeddings is critical, since it allows to generate data to train a decoder with a reconstruction accuracy sufficient to violate copyright laws.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

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 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.

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.

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.

Large Language Models (LLMs) have emerged as powerful tools in the field of Natural Language Processing (NLP) and have recently gained significant attention in the domain of Recommendation Systems (RS). These models, trained on massive amounts of data using self-supervised learning, have demonstrated remarkable success in learning universal representations and have the potential to enhance various aspects of recommendation systems by some effective transfer techniques such as fine-tuning and prompt tuning, and so on. The crucial aspect of harnessing the power of language models in enhancing recommendation quality is the utilization of their high-quality representations of textual features and their extensive coverage of external knowledge to establish correlations between items and users. To provide a comprehensive understanding of the existing LLM-based recommendation systems, this survey presents a taxonomy that categorizes these models into two major paradigms, respectively Discriminative LLM for Recommendation (DLLM4Rec) and Generative LLM for Recommendation (GLLM4Rec), with the latter being systematically sorted out for the first time. Furthermore, we systematically review and analyze existing LLM-based recommendation systems within each paradigm, providing insights into their methodologies, techniques, and performance. Additionally, we identify key challenges and several valuable findings to provide researchers and practitioners with inspiration. We have also created a GitHub repository to index relevant papers on LLMs for recommendation, https://github.com/WLiK/LLM4Rec.

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.

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.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

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.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

The advancement of natural language processing (NLP) in biology hinges on models' ability to interpret intricate biomedical literature. Traditional models often struggle with the complex and domain-specific language in this field. In this paper, we present BioMamba, a pre-trained model specifically designed for biomedical text mining. BioMamba builds upon the Mamba architecture and is pre-trained on an extensive corpus of biomedical literature. Our empirical studies demonstrate that BioMamba significantly outperforms models like BioBERT and general-domain Mamba across various biomedical tasks. For instance, BioMamba achieves a 100 times reduction in perplexity and a 4 times reduction in cross-entropy loss on the BioASQ test set. We provide an overview of the model architecture, pre-training process, and fine-tuning techniques. Additionally, we release the code and trained model to facilitate further research.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

Recognizing the flow of time in a story is a crucial aspect of understanding it. Prior work related to time has primarily focused on identifying temporal expressions or relative sequencing of events, but here we propose computationally annotating each line of a book with wall clock times, even in the absence of explicit time-descriptive phrases. To do so, we construct a data set of hourly time phrases from 52,183 fictional books. We then construct a time-of-day classification model that achieves an average error of 2.27 hours. Furthermore, we show that by analyzing a book in whole using dynamic programming of breakpoints, we can roughly partition a book into segments that each correspond to a particular time-of-day. This approach improves upon baselines by over two hours. Finally, we apply our model to a corpus of literature categorized by different periods in history, to show interesting trends of hourly activity throughout the past. Among several observations we find that the fraction of events taking place past 10 P.M jumps past 1880 - coincident with the advent of the electric light bulb and city lights.

As language models become capable of processing increasingly long and complex texts, there has been growing interest in their application within computational literary studies. However, evaluating the usefulness of these models for such tasks remains challenging due to the cost of fine-grained annotation for long-form texts and the data contamination concerns inherent in using public-domain literature. Current embedding similarity datasets are not suitable for evaluating literary-domain tasks because of a focus on coarse-grained similarity and primarily on very short text. We assemble and release FICSIM, a dataset of long-form, recently written fiction, including scores along 12 axes of similarity informed by author-produced metadata and validated by digital humanities scholars. We evaluate a suite of embedding models on this task, demonstrating a tendency across models to focus on surface-level features over semantic categories that would be useful for computational literary studies tasks. Throughout our data-collection process, we prioritize author agency and rely on continual, informed author consent.

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.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

The task of discovering topics in text corpora has been dominated by Latent Dirichlet Allocation and other Topic Models for over a decade. In order to apply these approaches to massive text corpora, the vocabulary needs to be reduced considerably and large computer clusters and/or GPUs are typically required. Moreover, the number of topics must be provided beforehand but this depends on the corpus characteristics and it is often difficult to estimate, especially for massive text corpora. Unfortunately, both topic quality and time complexity are sensitive to this choice. This paper describes an alternative approach to discover topics based on Min-Hashing, which can handle massive text corpora and large vocabularies using modest computer hardware and does not require to fix the number of topics in advance. The basic idea is to generate multiple random partitions of the corpus vocabulary to find sets of highly co-occurring words, which are then clustered to produce the final topics. In contrast to probabilistic topic models where topics are distributions over the complete vocabulary, the topics discovered by the proposed approach are sets of highly co-occurring words. Interestingly, these topics underlie various thematics with different levels of granularity. An extensive qualitative and quantitative evaluation using the 20 Newsgroups (18K), Reuters (800K), Spanish Wikipedia (1M), and English Wikipedia (5M) corpora shows that the proposed approach is able to consistently discover meaningful and coherent topics. Remarkably, the time complexity of the proposed approach is linear with respect to corpus and vocabulary size; a non-parallel implementation was able to discover topics from the entire English edition of Wikipedia with over 5 million documents and 1 million words in less than 7 hours.

In recent years, large language models (LLMs) have demonstrated significant potential in constructing passage retrieval datasets. However, existing methods still face limitations in expressing cross-doc query needs and controlling annotation quality. To address these issues, this paper proposes a bidirectional generation pipeline, which aims to generate 3-level hierarchical queries for both intra-doc and cross-doc scenarios and mine additional relevance labels on top of direct mapping annotation. The pipeline introduces two query generation methods: bottom-up from single-doc text and top-down from multi-doc titles. The bottom-up method uses LLMs to disassemble and generate structured queries at both sentence-level and passage-level simultaneously from intra-doc passages. The top-down approach incorporates three key financial elements--industry, topic, and time--to divide report titles into clusters and prompts LLMs to generate topic-level queries from each cluster. For relevance annotation, our pipeline not only relies on direct mapping annotation from the generation relationship but also implements an indirect positives mining method to enrich the relevant query-passage pairs. Using this pipeline, we constructed a Financial Passage Retrieval Generated dataset (FinCPRG) from almost 1.3k Chinese financial research reports, which includes hierarchical queries and rich relevance labels. Through evaluations of mined relevance labels, benchmarking and training experiments, we assessed the quality of FinCPRG and validated its effectiveness as a passage retrieval dataset for both training and benchmarking.

"An idea is nothing more nor less than a new combination of old elements" (Young, J.W.). The widespread adoption of Large Language Models (LLMs) and publicly available ChatGPT have marked a significant turning point in the integration of Artificial Intelligence (AI) into people's everyday lives. This study explores the capability of LLMs in generating novel research ideas based on information from research papers. We conduct a thorough examination of 4 LLMs in five domains (e.g., Chemistry, Computer, Economics, Medical, and Physics). We found that the future research ideas generated by Claude-2 and GPT-4 are more aligned with the author's perspective than GPT-3.5 and Gemini. We also found that Claude-2 generates more diverse future research ideas than GPT-4, GPT-3.5, and Gemini 1.0. We further performed a human evaluation of the novelty, relevancy, and feasibility of the generated future research ideas. This investigation offers insights into the evolving role of LLMs in idea generation, highlighting both its capability and limitations. Our work contributes to the ongoing efforts in evaluating and utilizing language models for generating future research ideas. We make our datasets and codes publicly available.

News headline generation is a crucial task in increasing productivity for both the readers and producers of news. This task can easily be aided by automated News headline-generation models. However, the presence of irrelevant headlines in scraped news articles results in sub-optimal performance of generation models. We propose that relevance-based headline classification can greatly aid the task of generating relevant headlines. Relevance-based headline classification involves categorizing news headlines based on their relevance to the corresponding news articles. While this task is well-established in English, it remains under-explored in low-resource languages like Telugu due to a lack of annotated data. To address this gap, we present TeClass, the first-ever human-annotated Telugu news headline classification dataset, containing 78,534 annotations across 26,178 article-headline pairs. We experiment with various baseline models and provide a comprehensive analysis of their results. We further demonstrate the impact of this work by fine-tuning various headline generation models using TeClass dataset. The headlines generated by the models fine-tuned on highly relevant article-headline pairs, showed about a 5 point increment in the ROUGE-L scores. To encourage future research, the annotated dataset as well as the annotation guidelines will be made publicly available.

Keyword extraction is the process of identifying the words or phrases that express the main concepts of text to the best of one's ability. Electronic infrastructure creates a considerable amount of text every day and at all times. This massive volume of documents makes it practically impossible for human resources to study and manage them. Nevertheless, the need for these documents to be accessed efficiently and effectively is evident in numerous purposes. A blog, news article, or technical note is considered a relatively long text since the reader aims to learn the subject based on keywords or topics. Our approach consists of a combination of two models: graph centrality features and textural features. The proposed method has been used to extract the best keyword among the candidate keywords with an optimal combination of graph centralities, such as degree, betweenness, eigenvector, closeness centrality and etc, and textural, such as Casing, Term position, Term frequency normalization, Term different sentence, Part Of Speech tagging. There have also been attempts to distinguish keywords from candidate phrases and consider them on separate keywords. For evaluating the proposed method, seven datasets were used: Semeval2010, SemEval2017, Inspec, fao30, Thesis100, pak2018, and Wikinews, with results reported as Precision, Recall, and F- measure. Our proposed method performed much better in terms of evaluation metrics in all reviewed datasets compared with available methods in literature. An approximate 16.9% increase was witnessed in F-score metric and this was much more for the Inspec in English datasets and WikiNews in forgone languages.

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.

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.

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

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.

The adoption of Deep Neural Networks (DNNs) has greatly benefited Natural Language Processing (NLP) during the past decade. However, the demands of long document analysis are quite different from those of shorter texts, while the ever increasing size of documents uploaded on-line renders automated understanding of lengthy texts a critical issue. Relevant applications include automated Web mining, legal document review, medical records analysis, financial reports analysis, contract management, environmental impact assessment, news aggregation, etc. Despite the relatively recent development of efficient algorithms for analyzing long documents, practical tools in this field are currently flourishing. This article serves as an entry point into this dynamic domain and aims to achieve two objectives. Firstly, it provides an overview of the relevant neural building blocks, serving as a concise tutorial for the field. Secondly, it offers a brief examination of the current state-of-the-art in long document NLP, with a primary focus on two key tasks: document classification and document summarization. Sentiment analysis for long texts is also covered, since it is typically treated as a particular case of document classification. Consequently, this article presents an introductory exploration of document-level analysis, addressing the primary challenges, concerns, and existing solutions. Finally, the article presents publicly available annotated datasets that can facilitate further research in this area.

The majority of available text summarization datasets include short-form source documents that lack long-range causal and temporal dependencies, and often contain strong layout and stylistic biases. While relevant, such datasets will offer limited challenges for future generations of text summarization systems. We address these issues by introducing BookSum, a collection of datasets for long-form narrative summarization. Our dataset covers source documents from the literature domain, such as novels, plays and stories, and includes highly abstractive, human written summaries on three levels of granularity of increasing difficulty: paragraph-, chapter-, and book-level. The domain and structure of our dataset poses a unique set of challenges for summarization systems, which include: processing very long documents, non-trivial causal and temporal dependencies, and rich discourse structures. To facilitate future work, we trained and evaluated multiple extractive and abstractive summarization models as baselines for our dataset.

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.

Co-occurrence networks are an important method in the field of natural language processing and text mining for discovering semantic relationships within texts. However, the traditional traversal algorithm for constructing co-occurrence networks has high time complexity and space complexity when dealing with large-scale text data. In this paper, we propose an optimized algorithm based on inverted indexing and breadth-first search to improve the efficiency of co-occurrence network construction and reduce memory consumption. Firstly, the traditional traversal algorithm is analyzed, and its performance issues in constructing co-occurrence networks are identified. Then, the detailed implementation process of the optimized algorithm is presented. Subsequently, the CSL large-scale Chinese scientific literature dataset is used for experimental validation, comparing the performance of the traditional traversal algorithm and the optimized algorithm in terms of running time and memory usage. Finally, using non-parametric test methods, the optimized algorithm is proven to have significantly better performance than the traditional traversal algorithm. The research in this paper provides an effective method for the rapid construction of co-occurrence networks, contributing to the further development of the Information Organization fields.

Documents are a core part of many businesses in many fields such as law, finance, and technology among others. Automatic understanding of documents such as invoices, contracts, and resumes is lucrative, opening up many new avenues of business. The fields of natural language processing and computer vision have seen tremendous progress through the development of deep learning such that these methods have started to become infused in contemporary document understanding systems. In this survey paper, we review different techniques for document understanding for documents written in English and consolidate methodologies present in literature to act as a jumping-off point for researchers exploring this area.

Oscar Wilde said, "The difference between literature and journalism is that journalism is unreadable, and literature is not read." Unfortunately, The digitally archived journalism of Oscar Wilde's 19th century often has no or poor quality Optical Character Recognition (OCR), reducing the accessibility of these archives and making them unreadable both figuratively and literally. This paper helps address the issue by performing OCR on "The Nineteenth Century Serials Edition" (NCSE), an 84k-page collection of 19th-century English newspapers and periodicals, using Pixtral 12B, a pre-trained image-to-text language model. The OCR capability of Pixtral was compared to 4 other OCR approaches, achieving a median character error rate of 1%, 5x lower than the next best model. The resulting NCSE v2.0 dataset features improved article identification, high-quality OCR, and text classified into four types and seventeen topics. The dataset contains 1.4 million entries, and 321 million words. Example use cases demonstrate analysis of topic similarity, readability, and event tracking. NCSE v2.0 is freely available to encourage historical and sociological research. As a result, 21st-century readers can now share Oscar Wilde's disappointment with 19th-century journalistic standards, reading the unreadable from the comfort of their own computers.

Automatic patent summarization approaches that help in the patent analysis and comprehension procedure are in high demand due to the colossal growth of innovations. The development of natural language processing (NLP), text mining, and deep learning has notably amplified the efficacy of text summarization models for abundant types of documents. Summarizing patent text remains a pertinent challenge due to the labyrinthine writing style of these documents, which includes technical and legal intricacies. Additionally, these patent document contents are considerably lengthier than archetypal documents, which complicates the process of extracting pertinent information for summarization. Embodying extractive and abstractive text summarization methodologies into a hybrid framework, this study proposes a system for efficiently creating abstractive summaries of patent records. The procedure involves leveraging the LexRank graph-based algorithm to retrieve the important sentences from input parent texts, then utilizing a Bidirectional Auto-Regressive Transformer (BART) model that has been fine-tuned using Low-Ranking Adaptation (LoRA) for producing text summaries. This is accompanied by methodical testing and evaluation strategies. Furthermore, the author employed certain meta-learning techniques to achieve Domain Generalization (DG) of the abstractive component across multiple patent fields.

Analyzing the pattern of semantic variation in long real-world texts such as books or transcripts is interesting from the stylistic, cognitive, and linguistic perspectives. It is also useful for applications such as text segmentation, document summarization, and detection of semantic novelty. The recent emergence of several vector-space methods for sentence embedding has made such analysis feasible. However, this raises the issue of how consistent and meaningful the semantic representations produced by various methods are in themselves. In this paper, we compare several recent sentence embedding methods via time-series of semantic similarity between successive sentences and matrices of pairwise sentence similarity for multiple books of literature. In contrast to previous work using target tasks and curated datasets to compare sentence embedding methods, our approach provides an evaluation of the methods 'in the wild'. We find that most of the sentence embedding methods considered do infer highly correlated patterns of semantic similarity in a given document, but show interesting differences.

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Extraction and synthesis of structured knowledge from extensive scientific literature are crucial for advancing and disseminating scientific progress. Although many existing systems facilitate literature review and digest, they struggle to process multimodal, varied, and inconsistent information within and across the literature into structured data. We introduce SciDaSynth, a novel interactive system powered by large language models (LLMs) that enables researchers to efficiently build structured knowledge bases from scientific literature at scale. The system automatically creates data tables to organize and summarize users' interested knowledge in literature via question-answering. Furthermore, it provides multi-level and multi-faceted exploration of the generated data tables, facilitating iterative validation, correction, and refinement. Our within-subjects study with researchers demonstrates the effectiveness and efficiency of SciDaSynth in constructing quality scientific knowledge bases. We further discuss the design implications for human-AI interaction tools for data extraction and structuring.

In this work we address the problem of argument search. The purpose of argument search is the distillation of pro and contra arguments for requested topics from large text corpora. In previous works, the usual approach is to use a standard search engine to extract text parts which are relevant to the given topic and subsequently use an argument recognition algorithm to select arguments from them. The main challenge in the argument recognition task, which is also known as argument mining, is that often sentences containing arguments are structurally similar to purely informative sentences without any stance about the topic. In fact, they only differ semantically. Most approaches use topic or search term information only for the first search step and therefore assume that arguments can be classified independently of a topic. We argue that topic information is crucial for argument mining, since the topic defines the semantic context of an argument. Precisely, we propose different models for the classification of arguments, which take information about a topic of an argument into account. Moreover, to enrich the context of a topic and to let models understand the context of the potential argument better, we integrate information from different external sources such as Knowledge Graphs or pre-trained NLP models. Our evaluation shows that considering topic information, especially in connection with external information, provides a significant performance boost for the argument mining task.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

A major factor in the recent success of large language models is the use of enormous and ever-growing text datasets for unsupervised pre-training. However, naively training a model on all available data may not be optimal (or feasible), as the quality of available text data can vary. Filtering out data can also decrease the carbon footprint and financial costs of training models by reducing the amount of training required. Data selection methods aim to determine which candidate data points to include in the training dataset and how to appropriately sample from the selected data points. The promise of improved data selection methods has caused the volume of research in the area to rapidly expand. However, because deep learning is mostly driven by empirical evidence and experimentation on large-scale data is expensive, few organizations have the resources for extensive data selection research. Consequently, knowledge of effective data selection practices has become concentrated within a few organizations, many of which do not openly share their findings and methodologies. To narrow this gap in knowledge, we present a comprehensive review of existing literature on data selection methods and related research areas, providing a taxonomy of existing approaches. By describing the current landscape of research, this work aims to accelerate progress in data selection by establishing an entry point for new and established researchers. Additionally, throughout this review we draw attention to noticeable holes in the literature and conclude the paper by proposing promising avenues for future research.

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.

We present in this work a new dataset of coreference annotations for works of literature in English, covering 29,103 mentions in 210,532 tokens from 100 works of fiction. This dataset differs from previous coreference datasets in containing documents whose average length (2,105.3 words) is four times longer than other benchmark datasets (463.7 for OntoNotes), and contains examples of difficult coreference problems common in literature. This dataset allows for an evaluation of cross-domain performance for the task of coreference resolution, and analysis into the characteristics of long-distance within-document coreference.

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.

Large language models have led to remarkable progress on many NLP tasks, and researchers are turning to ever-larger text corpora to train them. Some of the largest corpora available are made by scraping significant portions of the internet, and are frequently introduced with only minimal documentation. In this work we provide some of the first documentation for the Colossal Clean Crawled Corpus (C4; Raffel et al., 2020), a dataset created by applying a set of filters to a single snapshot of Common Crawl. We begin by investigating where the data came from, and find a significant amount of text from unexpected sources like patents and US military websites. Then we explore the content of the text itself, and find machine-generated text (e.g., from machine translation systems) and evaluation examples from other benchmark NLP datasets. To understand the impact of the filters applied to create this dataset, we evaluate the text that was removed, and show that blocklist filtering disproportionately removes text from and about minority individuals. Finally, we conclude with some recommendations for how to created and document web-scale datasets from a scrape of the internet.

Although large language models (LLMs) are impressive in solving various tasks, they can quickly be outdated after deployment. Maintaining their up-to-date status is a pressing concern in the current era. This paper provides a comprehensive review of recent advances in aligning LLMs with the ever-changing world knowledge without re-training from scratch. We categorize research works systemically and provide in-depth comparisons and discussion. We also discuss existing challenges and highlight future directions to facilitate research in this field. We release the paper list at https://github.com/hyintell/awesome-refreshing-llms

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.

Identifying, classifying, and analyzing arguments in legal discourse has been a prominent area of research since the inception of the argument mining field. However, there has been a major discrepancy between the way natural language processing (NLP) researchers model and annotate arguments in court decisions and the way legal experts understand and analyze legal argumentation. While computational approaches typically simplify arguments into generic premises and claims, arguments in legal research usually exhibit a rich typology that is important for gaining insights into the particular case and applications of law in general. We address this problem and make several substantial contributions to move the field forward. First, we design a new annotation scheme for legal arguments in proceedings of the European Court of Human Rights (ECHR) that is deeply rooted in the theory and practice of legal argumentation research. Second, we compile and annotate a large corpus of 373 court decisions (2.3M tokens and 15k annotated argument spans). Finally, we train an argument mining model that outperforms state-of-the-art models in the legal NLP domain and provide a thorough expert-based evaluation. All datasets and source codes are available under open lincenses at https://github.com/trusthlt/mining-legal-arguments.

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

Recently, large language models (LLMs) have shown promising abilities to generate novel research ideas in science, a direction which coincides with many foundational principles in computational creativity (CC). In light of these developments, we present an idea generation system named Spark that couples retrieval-augmented idea generation using LLMs with a reviewer model named Judge trained on 600K scientific reviews from OpenReview. Our work is both a system demonstration and intended to inspire other CC researchers to explore grounding the generation and evaluation of scientific ideas within foundational CC principles. To this end, we release the annotated dataset used to train Judge, inviting other researchers to explore the use of LLMs for idea generation and creative evaluations.

As an efficient approach to understand, generate, and process natural language texts, research in natural language processing (NLP) has exhibited a rapid spread and wide adoption in recent years. Given the increasing research work in this area, several NLP-related approaches have been surveyed in the research community. However, a comprehensive study that categorizes established topics, identifies trends, and outlines areas for future research remains absent. Contributing to closing this gap, we have systematically classified and analyzed research papers in the ACL Anthology. As a result, we present a structured overview of the research landscape, provide a taxonomy of fields of study in NLP, analyze recent developments in NLP, summarize our findings, and highlight directions for future work.

This systematic review explores the application of Large Language Models (LLMs) in Combinatorial Optimization (CO). We report our findings using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We conduct a literature search via Scopus and Google Scholar, examining over 2,000 publications. We assess publications against four inclusion and four exclusion criteria related to their language, research focus, publication year, and type. Eventually, we select 103 studies. We classify these studies into semantic categories and topics to provide a comprehensive overview of the field, including the tasks performed by LLMs, the architectures of LLMs, the existing datasets specifically designed for evaluating LLMs in CO, and the field of application. Finally, we identify future directions for leveraging LLMs in this field.

Identifying significant references within the complex interrelations of a citation knowledge graph is challenging, which encompasses connections through citations, authorship, keywords, and other relational attributes. The Paper Source Tracing (PST) task seeks to automate the identification of pivotal references for given scholarly articles utilizing advanced data mining techniques. In the KDD CUP 2024, we design a recommendation-based framework tailored for the PST task. This framework employs the Neural Collaborative Filtering (NCF) model to generate final predictions. To process the textual attributes of the papers and extract input features for the model, we utilize SciBERT, a pre-trained language model. According to the experimental results, our method achieved a score of 0.37814 on the Mean Average Precision (MAP) metric, outperforming baseline models and ranking 11th among all participating teams. The source code is publicly available at https://github.com/MyLove-XAB/KDDCupFinal.

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the BioASQ challenge, which involves biomedical semantic question-answering for Task 13b and biomedical question-answering for developing topics for the Synergy task. We deploy a selection of open-source large language models (LLMs) as retrieval-augmented generators to answer biomedical questions. Various models are used to process the questions. A majority voting system combines their output to determine the final answer for Yes/No questions, while for list and factoid type questions, the union of their answers in used. We evaluated 13 state-of-the-art open source LLMs, exploring all possible model combinations to contribute to the final answer, resulting in tailored LLM pipelines for each question type. Our findings provide valuable insight into which combinations of LLMs consistently produce superior results for specific question types. In the four rounds of the 2025 BioASQ challenge, our system achieved notable results: in the Synergy task, we secured 1st place for ideal answers and 2nd place for exact answers in round 2, as well as two shared 1st places for exact answers in round 3 and 4.

Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult to estimate their performance on datasets containing biomedical texts as the word distributions of general and biomedical corpora are quite different. Moreover, the medical domain has long-tail concepts and terminologies that are difficult to be learned via language models. For the Chinese biomedical text, it is more difficult due to its complex structure and the variety of phrase combinations. In this paper, we investigate how the recently introduced pre-trained language model BERT can be adapted for Chinese biomedical corpora and propose a novel conceptualized representation learning approach. We also release a new Chinese Biomedical Language Understanding Evaluation benchmark (ChineseBLUE). We examine the effectiveness of Chinese pre-trained models: BERT, BERT-wwm, RoBERTa, and our approach. Experimental results on the benchmark show that our approach could bring significant gain. We release the pre-trained model on GitHub: https://github.com/alibaba-research/ChineseBLUE.

Mining parallel document pairs poses a significant challenge because existing sentence embedding models often have limited context windows, preventing them from effectively capturing document-level information. Another overlooked issue is the lack of concrete evaluation benchmarks comprising high-quality parallel document pairs for assessing document-level mining approaches, particularly for Indic languages. In this study, we introduce Pralekha, a large-scale benchmark for document-level alignment evaluation. Pralekha includes over 2 million documents, with a 1:2 ratio of unaligned to aligned pairs, covering 11 Indic languages and English. Using Pralekha, we evaluate various document-level mining approaches across three dimensions: the embedding models, the granularity levels, and the alignment algorithm. To address the challenge of aligning documents using sentence and chunk-level alignments, we propose a novel scoring method, Document Alignment Coefficient (DAC). DAC demonstrates substantial improvements over baseline pooling approaches, particularly in noisy scenarios, achieving average gains of 20-30% in precision and 15-20% in F1 score. These results highlight DAC's effectiveness in parallel document mining for Indic languages.

With increasing usage of generative models for text generation and widespread use of machine generated texts in various domains, being able to distinguish between human written and machine generated texts is a significant challenge. While existing models and proprietary systems focus on identifying whether given text is entirely human written or entirely machine generated, only a few systems provide insights at sentence or paragraph level at likelihood of being machine generated at a non reliable accuracy level, working well only for a set of domains and generators. This paper introduces few reliable approaches for the novel task of identifying which part of a given text is machine generated at a word level while comparing results from different approaches and methods. We present a comparison with proprietary systems , performance of our model on unseen domains' and generators' texts. The findings reveal significant improvements in detection accuracy along with comparison on other aspects of detection capabilities. Finally we discuss potential avenues for improvement and implications of our work. The proposed model is also well suited for detecting which parts of a text are machine generated in outputs of Instruct variants of many LLMs.

Rapid progress in the capabilities of machine learning approaches in natural language processing has culminated in the rise of large language models over the last two years. Recent works have shown unprecedented adoption of these for academic writing, especially in some fields, but their pervasiveness in astronomy has not been studied sufficiently. To remedy this, we extract words that ChatGPT uses more often than humans when generating academic text and search a total of 1 million articles for them. This way, we assess the frequency of word occurrence in published works in astronomy tracked by the NASA Astrophysics Data System since 2000. We then perform a statistical analysis of the occurrences. We identify a list of words favoured by ChatGPT and find a statistically significant increase for these words against a control group in 2024, which matches the trend in other disciplines. These results suggest a widespread adoption of these models in the writing of astronomy papers. We encourage organisations, publishers, and researchers to work together to identify ethical and pragmatic guidelines to maximise the benefits of these systems while maintaining scientific rigour.

Word embedding pioneered by Mikolov et al. is a staple technique for word representations in natural language processing (NLP) research which has also found popularity in music information retrieval tasks. Depending on the type of text data for word embedding, however, vocabulary size and the degree of musical pertinence can significantly vary. In this work, we (1) train the distributed representation of words using combinations of both general text data and music-specific data and (2) evaluate the system in terms of how they associate listening contexts with musical compositions.

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.

Large Language Models (LLMs) have demonstrated remarkable capabilities in important tasks such as natural language understanding, language generation, and complex reasoning and have the potential to make a substantial impact on our society. Such capabilities, however, come with the considerable resources they demand, highlighting the strong need to develop effective techniques for addressing their efficiency challenges. In this survey, we provide a systematic and comprehensive review of efficient LLMs research. We organize the literature in a taxonomy consisting of three main categories, covering distinct yet interconnected efficient LLMs topics from model-centric, data-centric, and framework-centric perspective, respectively. We have also created a GitHub repository where we compile the papers featured in this survey at https://github.com/AIoT-MLSys-Lab/EfficientLLMs, and will actively maintain this repository and incorporate new research as it emerges. We hope our survey can serve as a valuable resource to help researchers and practitioners gain a systematic understanding of the research developments in efficient LLMs and inspire them to contribute to this important and exciting field.

Creating an abridged version of a text involves shortening it while maintaining its linguistic qualities. In this paper, we examine this task from an NLP perspective for the first time. We present a new resource, AbLit, which is derived from abridged versions of English literature books. The dataset captures passage-level alignments between the original and abridged texts. We characterize the linguistic relations of these alignments, and create automated models to predict these relations as well as to generate abridgements for new texts. Our findings establish abridgement as a challenging task, motivating future resources and research. The dataset is available at github.com/roemmele/AbLit.

We present PyThaiNLP, a free and open-source natural language processing (NLP) library for Thai language implemented in Python. It provides a wide range of software, models, and datasets for Thai language. We first provide a brief historical context of tools for Thai language prior to the development of PyThaiNLP. We then outline the functionalities it provided as well as datasets and pre-trained language models. We later summarize its development milestones and discuss our experience during its development. We conclude by demonstrating how industrial and research communities utilize PyThaiNLP in their work. The library is freely available at https://github.com/pythainlp/pythainlp.