Target identification for tractography studies requires solid anatomical knowledge validated by an extensive literature review across species for each seed structure to be studied. Manual literature review to identify targets for a given seed region is tedious and potentially subjective. Therefore, complementary approaches would be useful. We propose to use text-mining models to automatically suggest potential targets from the neuroscientific literature, full-text articles and abstracts, so that they can be used for anatomical connection studies and more specifically for tractography. We applied text-mining models to three structures: two well-studied structures, since validated deep brain stimulation targets, the internal globus pallidus and the subthalamic nucleus and, the nucleus accumbens, an exploratory target for treating psychiatric disorders. We performed a systematic review of the literature to document the projections of the three selected structures and compared it with the targets proposed by text-mining models, both in rat and primate (including human). We ran probabilistic tractography on the nucleus accumbens and compared the output with the results of the text-mining models and literature review. Overall, text-mining the literature could find three times as many targets as two man-weeks of curation could. The overall efficiency of the text-mining against literature review in our study was 98% recall (at 36% precision), meaning that over all the targets for the three selected seeds, only one target has been missed by text-mining. We demonstrate that connectivity for a structure of interest can be extracted from a very large amount of publications and abstracts. We believe this tool will be useful in helping the neuroscience community to facilitate connectivity studies of particular brain regions. The text mining tools used for the study are part of the HBP Neuroinformatics Platform, publicly available at http://connectivity-brainer.rhcloud.com
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.
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external environmental stimuli on the self-assembly behaviour of these systems. However, there is yet to be a systematic study that gathers this rich literature data and collectively examines these experimental factors to provide a global picture of the fundamental rules that govern protein self-assembly behavior. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining facilitated by a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the collected data, ML models are trained and evaluated, demonstrating excellent accuracy (>80\%) and efficiency in peptide assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. We find that this workflow can substantially improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly. In doing so, novel structures can be accessed for a range of applications including sensing, catalysis and biomaterials.
Growing evidence suggests that social determinants of health (SDoH), a set of nonmedical factors, affect individuals' risks of developing Alzheimer's disease (AD) and related dementias. Nevertheless, the etiological mechanisms underlying such relationships remain largely unclear, mainly due to difficulties in collecting relevant information. This study presents a novel, automated framework that leverages recent advancements of large language model (LLM) and natural language processing techniques to mine SDoH knowledge from extensive literature and integrate it with AD-related biological entities extracted from the general-purpose knowledge graph PrimeKG. Utilizing graph neural networks, we performed link prediction tasks to evaluate the resultant SDoH-augmented knowledge graph. Our framework shows promise for enhancing knowledge discovery in AD and can be generalized to other SDoH-related research areas, offering a new tool for exploring the impact of social determinants on health outcomes. Our code is available at: https://github.com/hwq0726/SDoHenPKG
Objective: To develop a corpus annotated for diet-microbiome associations from the biomedical literature and train natural language processing (NLP) models to identify these associations, thereby improving the understanding of their role in health and disease, and supporting personalized nutrition strategies. Materials and Methods: We constructed 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 fine-tuned and evaluated state-of-the-art NLP models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. In addition, we benchmarked two generative large language models (GPT-4o-mini and GPT-4o) on a subset of the dataset in zero- and one-shot settings. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 publications (including 30 full-text Results sections). Fine-tuned NLP models performed reasonably well for named entity recognition (0.800 F1 score), while end-to-end relation extraction performance was modest (0.445 F1). The use of Results section annotations improved relation extraction. The impact of trigger detection was mixed. Generative models showed lower accuracy compared to fine-tuned models. Discussion: To our knowledge, DiMB-RE is the largest and most diverse corpus focusing on diet-microbiome interactions. NLP models fine-tuned on DiMB-RE exhibit lower performance compared to similar corpora, highlighting the complexity of information extraction in this domain. Misclassified entities, missed triggers, and cross-sentence relations are the major sources of relation extraction errors. Conclusions: DiMB-RE can serve as a benchmark corpus for biomedical literature mining. DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.
Assessing different material properties to predict specific attributes, such as band gap, resistivity, young modulus, work function, and refractive index, is a fundamental requirement for materials science-based applications. However, the process is time-consuming and often requires extensive literature reviews and numerous experiments. Our study addresses these challenges by leveraging machine learning to analyze material properties with greater precision and efficiency. By automating the data extraction process and using the extracted information to train machine learning models, our developed model, SciQu, optimizes material properties. As a proof of concept, we predicted the refractive index of materials using data extracted from numerous research articles with SciQu, considering input descriptors such as space group, volume, and bandgap with Root Mean Square Error (RMSE) 0.068 and R2 0.94. Thus, SciQu not only predicts the properties of materials but also plays a key role in self-driving laboratories by optimizing the synthesis parameters to achieve precise shape, size, and phase of the materials subjected to the input parameters.
A comprehensive view of factors associated with AD/ADRD will significantly aid in studies to develop new treatments for AD/ADRD and identify high-risk populations and patients for prevention efforts. In our study, we summarized the risk factors for AD/ADRD by reviewing existing meta-analyses and review articles on risk and preventive factors for AD/ADRD. In total, we extracted 477 risk factors in 10 categories from 537 studies. We constructed an interactive knowledge map to disseminate our study results. Most of the risk factors are accessible from structured Electronic Health Records (EHRs), and clinical narratives show promise as information sources. However, evaluating genomic risk factors using RWD remains a challenge, as genetic testing for AD/ADRD is still not a common practice and is poorly documented in both structured and unstructured EHRs. Considering the constantly evolving research on AD/ADRD risk factors, literature mining via NLP methods offers a solution to automatically update our knowledge map.
In an era marked by a rapid increase in scientific publications, researchers grapple with the challenge of keeping pace with field-specific advances. We present the `AHAM' methodology and a metric that guides the domain-specific \textbf{adapt}ation of the BERTopic topic modeling framework to improve scientific text analysis. By utilizing the LLaMa2 generative language model, we generate topic definitions via one-shot learning by crafting prompts with the \textbf{help} of domain experts to guide the LLM for literature mining by \textbf{asking} it to model the topic names. For inter-topic similarity evaluation, we leverage metrics from language generation and translation processes to assess lexical and semantic similarity of the generated topics. Our system aims to reduce both the ratio of outlier topics to the total number of topics and the similarity between topic definitions. The methodology has been assessed on a newly gathered corpus of scientific papers on literature-based discovery. Through rigorous evaluation by domain experts, AHAM has been validated as effective in uncovering intriguing and novel insights within broad research areas. We explore the impact of domain adaptation of sentence-transformers for the task of topic \textbf{model}ing using two datasets, each specialized to specific scientific domains within arXiv and medarxiv. We evaluate the impact of data size, the niche of adaptation, and the importance of domain adaptation. Our results suggest a strong interaction between domain adaptation and topic modeling precision in terms of outliers and topic definitions.
Causality and eXplainable Artificial Intelligence (XAI) have developed as separate fields in computer science, even though the underlying concepts of causation and explanation share common ancient roots. This is further enforced by the lack of review works jointly covering these two fields. In this paper, we investigate the literature to try to understand how and to what extent causality and XAI are intertwined. More precisely, we seek to uncover what kinds of relationships exist between the two concepts and how one can benefit from them, for instance, in building trust in AI systems. As a result, three main perspectives are identified. In the first one, the lack of causality is seen as one of the major limitations of current AI and XAI approaches, and the "optimal" form of explanations is investigated. The second is a pragmatic perspective and considers XAI as a tool to foster scientific exploration for causal inquiry, via the identification of pursue-worthy experimental manipulations. Finally, the third perspective supports the idea that causality is propaedeutic to XAI in three possible manners: exploiting concepts borrowed from causality to support or improve XAI, utilizing counterfactuals for explainability, and considering accessing a causal model as explaining itself. To complement our analysis, we also provide relevant software solutions used to automate causal tasks. We believe our work provides a unified view of the two fields of causality and XAI by highlighting potential domain bridges and uncovering possible limitations.
The biomedical field relies heavily on concept linking in various areas such as literature mining, graph alignment, information retrieval, question-answering, data, and knowledge integration. Although large language models (LLMs) have made significant strides in many natural language processing tasks, their effectiveness in biomedical concept mapping is yet to be fully explored. This research investigates a method that exploits the in-context learning (ICL) capabilities of large models for biomedical concept linking. The proposed approach adopts a two-stage retrieve-and-rank framework. Initially, biomedical concepts are embedded using language models, and then embedding similarity is utilized to retrieve the top candidates. These candidates' contextual information is subsequently incorporated into the prompt and processed by a large language model to re-rank the concepts. This approach achieved an accuracy of 90.% in BC5CDR disease entity normalization and 94.7% in chemical entity normalization, exhibiting a competitive performance relative to supervised learning methods. Further, it showed a significant improvement, with an over 20-point absolute increase in F1 score on an oncology matching dataset. Extensive qualitative assessments were conducted, and the benefits and potential shortcomings of using large language models within the biomedical domain were discussed. were discussed.
Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformers (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks. We evaluated the performance of PPI identification of multiple GPT and BERT models using three manually curated gold-standard corpora: Learning Language in Logic (LLL) with 164 PPIs in 77 sentences, Human Protein Reference Database with 163 PPIs in 145 sentences, and Interaction Extraction Performance Assessment with 335 PPIs in 486 sentences. BERT-based models achieved the best overall performance, with BioBERT achieving the highest recall (91.95%) and F1-score (86.84%) and PubMedBERT achieving the highest precision (85.25%). Interestingly, despite not being explicitly trained for biomedical texts, GPT-4 achieved commendable performance, comparable to the top-performing BERT models. It achieved a precision of 88.37%, a recall of 85.14%, and an F1-score of 86.49% on the LLL dataset. These results suggest that GPT models can effectively detect PPIs from text data, offering promising avenues for application in biomedical literature mining. Further research could explore how these models might be fine-tuned for even more specialized tasks within the biomedical domain.
The novel coronavirus disease (COVID-19) began in Wuhan, China, in late 2019 and to date has infected over 148M people worldwide, resulting in 3.12M deaths. On March 10, 2020, the World Health Organisation (WHO) declared it as a global pandemic. Many academicians and researchers started to publish papers describing the latest discoveries on covid-19. The large influx of publications made it hard for other researchers to go through a large amount of data and find the appropriate one that helps their research. So, the proposed model attempts to extract relavent titles from the large corpus of research publications which makes the job easy for the researchers. Allen Institute for AI released the CORD-19 dataset, which consists of 2,00,000 journal articles related to coronavirus-related research publications from PubMed's PMC, WHO (World Health Organization), bioRxiv, and medRxiv pre-prints. Along with this document corpus, they have also provided a topics dataset named topics-rnd3 consisting of a list of topics. Each topic has three types of representations like query, question, and narrative. These Datasets are made open for research, and also they released a TREC-COVID competition on Kaggle. Using these topics like queries, our goal is to find out the relevant documents in the CORD-19 dataset. In this research, relevant documents should be recognized for the posed topics in topics-rnd3 data set. The proposed model uses Natural Language Processing(NLP) techniques like Bag-of-Words, Average Word-2-Vec, Average BERT Base model and Tf-Idf weighted Word2Vec model to fabricate vectors for query, question, narrative, and combinations of them. Similarly, fabricate vectors for titles in the CORD-19 dataset. After fabricating vectors, cosine similarity is used for finding similarities between every two vectors. Cosine similarity helps us to find relevant documents for the given topic.
Genome-wide association studies (GWAS) have successfully identified a large number of genetic variants associated with traits and diseases. However, it still remains challenging to fully understand functional mechanisms underlying many associated variants. This is especially the case when we are interested in variants shared across multiple phenotypes. To address this challenge, we propose graph-GPA 2.0 (GGPA 2.0), a novel statistical framework to integrate GWAS datasets for multiple phenotypes and incorporate functional annotations within a unified framework. We conducted simulation studies to evaluate GGPA 2.0. The results indicate that incorporating functional annotation data using GGPA 2.0 does not only improve detection of disease-associated variants, but also allows to identify more accurate relationships among diseases. We analyzed five autoimmune diseases and five psychiatric disorders with the functional annotations derived from GenoSkyline and GenoSkyline-Plus and the prior disease graph generated by biomedical literature mining. For autoimmune diseases, GGPA 2.0 identified enrichment for blood, especially B cells and regulatory T cells across multiple diseases. Psychiatric disorders were enriched for brain, especially prefrontal cortex and inferior temporal lobe for bipolar disorder (BIP) and schizophrenia (SCZ), respectively. Finally, GGPA 2.0 successfully identified the pleiotropy between BIP and SCZ. These results demonstrate that GGPA 2.0 can be a powerful tool to identify associated variants associated with each phenotype or those shared across multiple phenotypes, while also promoting understanding of functional mechanisms underlying the associated variants.
To date, there are no effective treatments for most neurodegenerative diseases. However, certain foods may be associated with these diseases and bring an opportunity to prevent or delay neurodegenerative progression. Our objective is to construct a knowledge graph for neurodegenerative diseases using literature mining to study their relations with diet. We collected biomedical annotations (Disease, Chemical, Gene, Species, SNP&Mutation) in the abstracts from 4,300 publications relevant to both neurodegenerative diseases and diet using PubTator, an NIH-supported tool that can extract biomedical concepts from literature. A knowledge graph was created from these annotations. Graph embeddings were then trained with the node2vec algorithm to support potential concept clustering and similar concept identification. We found several food-related species and chemicals that might come from diet and have an impact on neurodegenerative diseases.
The Covid-19 pandemic has caused a spur in the medical research literature. With new research advances in understanding the virus, there is a need for robust text mining tools which can process, extract and present answers from the literature in a concise and consumable way. With a DialoGPT based multi-turn conversation generation module, and BM-25 \& neural embeddings based ensemble information retrieval module, in this paper we present a conversational system, which can retrieve and answer coronavirus-related queries from the rich medical literature, and present it in a conversational setting with the user. We further perform experiments to compare neural embedding-based document retrieval and the traditional BM25 retrieval algorithm and report the results.
Breastfeeding benefits both infants and mothers. Nutrients in mother's milk help protect infants from multiple diseases including infections, cancers, diabetes, gastrointestinal and respiratory diseases. We performed literature mining on 31,496 mother's-milk-related abstracts from PubMed and the results suggest the need for individualized mother's milk fortification and proper maternal supplementations (e.g. probiotics, vitamin D), because mother's milk compositions (e.g. fatty acids) vary according to maternal diet and responses to infection in mothers and/or infants. We review at details the variability observed in mother's milk compositions and its possible health effects in infants. We also review the effects of storage practices on mother's milk nutrients, recommended durations for mother's milk intake and the associated health benefits.
Drug repositioning, that is finding new uses for existing drugs to treat more patients. Cumulative studies demonstrate that the mature miRNAs as well as their precursors can be targeted by small molecular drugs. At the same time, human diseases result from the disordered interplay of tissue- and cell lineage-specific processes. However, few computational researches predict drug-disease potential relationships based on miRNA data and tissue specificity. Therefore, based on miRNA data and the tissue specificity of diseases, we propose a new method named as miTS to predict the potential treatments for diseases. Firstly, based on miRNAs data, target genes and information of FDA approved drugs, we evaluate the relationships between miRNAs and drugs in the tissue-specific PPI network. Then, we construct a tripartite network: drug-miRNA-disease Finally, we obtain the potential drug-disease associations based on the tripartite network. In this paper, we take breast cancer as case study and focus on the top-30 predicted drugs. 25 of them (83.3%) are found having known connections with breast cancer in CTD benchmark and the other 5 drugs are potential drugs for breast cancer. We further evaluate the 5 newly predicted drugs from clinical records, literature mining, KEGG pathways enrichment analysis and overlapping genes between enriched pathways. For each of the 5 new drugs, strongly supported evidences can be found in three or more aspects. In particular, Regorafenib has 15 overlapping KEGG pathways with breast cancer and their p-values are all very small. In addition, whether in the literature curation or clinical validation, Regorafenib has a strong correlation with breast cancer. All the facts show that Regorafenib is likely to be a truly effective drug, worthy of our further study. It further follows that our method miTS is effective and practical for predicting new drug indications.
The knowledge contained in academic literature is interesting to mine. Inspired by the idea of molecular markers tracing in the field of biochemistry, three named entities, namely, methods, datasets and metrics are used as AI markers for AI literature. These entities can be used to trace the research process described in the bodies of papers, which opens up new perspectives for seeking and mining more valuable academic information. Firstly, the entity extraction model is used in this study to extract AI markers from large-scale AI literature. Secondly, original papers are traced for AI markers. Statistical and propagation analysis are performed based on tracing results. Finally, the co-occurrences of AI markers are used to achieve clustering. The evolution within method clusters and the influencing relationships amongst different research scene clusters are explored. The above-mentioned mining based on AI markers yields many meaningful discoveries. For example, the propagation of effective methods on the datasets is rapidly increasing with the development of time; effective methods proposed by China in recent years have increasing influence on other countries, whilst France is the opposite. Saliency detection, a classic computer vision research scene, is the least likely to be affected by other research scenes.
The abundance of literature related to the widespread COVID-19 pandemic is beyond manual inspection of a single expert. Development of systems, capable of automatically processing tens of thousands of scientific publications with the aim to enrich existing empirical evidence with literature-based associations is challenging and relevant. We propose a system for contextualization of empirical expression data by approximating relations between entities, for which representations were learned from one of the largest COVID-19-related literature corpora. In order to exploit a larger scientific context by transfer learning, we propose a novel embedding generation technique that leverages SciBERT language model pretrained on a large multi-domain corpus of scientific publications and fine-tuned for domain adaptation on the CORD-19 dataset. The conducted manual evaluation by the medical expert and the quantitative evaluation based on therapy targets identified in the related work suggest that the proposed method can be successfully employed for COVID-19 therapy target discovery and that it outperforms the baseline FastText method by a large margin.
We are presenting COVID-19Base, a knowledgebase highlighting the biomedical entities related to COVID-19 disease based on literature mining. To develop COVID-19Base, we mine the information from publicly available scientific literature and related public resources. We considered seven topic-specific dictionaries, including human genes, human miRNAs, human lncRNAs, diseases, Protein Databank, drugs, and drug side effects, are integrated to mine all scientific evidence related to COVID-19. We have employed an automated literature mining and labeling system through a novel approach to measure the effectiveness of drugs against diseases based on natural language processing, sentiment analysis, and deep learning. To the best of our knowledge, this is the first knowledgebase dedicated to COVID-19, which integrates such large variety of related biomedical entities through literature mining. Proper investigation of the mined biomedical entities along with the identified interactions among those, reported in COVID-19Base, would help the research community to discover possible ways for the therapeutic treatment of COVID-19.