AIMC Topic: Data Mining

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Using Large Language Models to Automate Data Extraction From Surgical Pathology Reports: Retrospective Cohort Study.

JMIR formative research Apr 7, 2025
BACKGROUND: Popularized by ChatGPT, large language models (LLMs) are poised to transform the scalability of clinical natural language processing (NLP) downstream tasks such as medical question answering (MQA) and automated data extraction from clinic...
Information Storage and Retrieval Large Language Models Pathology, Surgical Natural Language Processing Data Mining Retrospective Studies Thyroid Neoplasms Humans
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ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties.

Nature communications Apr 6, 2025
The UniProt database is a valuable resource for biocatalyst discovery, yet predicting enzymatic functions remains challenging, especially for low-similarity sequences. Identifying superior enzymes with enhanced catalytic properties is even harder. To...
Biocatalysis Oxidoreductases Hydrogen-Ion Concentration Data Mining Deep Learning Databases, Protein
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101 Machine Learning Algorithms for Mining Esophageal Squamous Cell Carcinoma Neoantigen Prognostic Models in Single-Cell Data.

International journal of molecular sciences Apr 4, 2025
Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignant tumors in the digestive tract, characterized by a high recurrence rate and inadequate immunotherapy options. We analyzed mutation data of ESCC from public databases and...
Humans Machine Learning Mutation Esophageal Neoplasms Esophageal Squamous Cell Carcinoma Data Mining Tumor Microenvironment Algorithms Single-Cell Analysis Prognosis Antigens, Neoplasm
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TransformDDI: The Transformer-Based Joint Multi-Task Model for End-to-End Drug-Drug Interaction Extraction.

IEEE journal of biomedical and health informatics Apr 4, 2025
Drug-Drug Interactions (DDI) identification is a part of the drug safety process, that focuses at avoiding potential adverse drug effects that can lead to patient health risks. With the exponential growth in published literature, it becomes increasin...
Humans Natural Language Processing Drug Interactions Drug-Related Side Effects and Adverse Reactions Machine Learning Algorithms Data Mining
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Aceso-DSAL: Discovering Clinical Evidences From Medical Literature Based on Distant Supervision and Active Learning.

IEEE journal of biomedical and health informatics Apr 4, 2025
Automatic extraction of valuable, structured evidence from the exponentially growing clinical trial literature can help physicians practice evidence-based medicine quickly and accurately. However, current research on evidence extraction has been limi...
Natural Language Processing Supervised Machine Learning Evidence-Based Medicine Data Mining Algorithms Humans Databases, Factual
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Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq.

Plant, cell & environment Mar 31, 2025
Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor st...
Transcription Factors Oryza Data Mining RNA-Seq Gene Regulatory Networks Gene Expression Regulation, Plant Droughts Chromatin Immunoprecipitation Sequencing Plant Proteins Stress, Physiological Neural Networks, Computer
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The interpretable machine learning model for depression associated with heavy metals via EMR mining method.

Scientific reports Mar 28, 2025
Limited research exists on the association between depression and heavy metal exposure. This study aims to develop an interpretable and efficient machine learning (ML) model with robust performance to identify depression linked to heavy metal exposur...
Nutrition Surveys Data Mining Metals, Heavy Middle Aged Depression Adult Male Machine Learning Algorithms Female Humans
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Large Language Model Applications for Health Information Extraction in Oncology: Scoping Review.

JMIR cancer Mar 28, 2025
BACKGROUND: Natural language processing systems for data extraction from unstructured clinical text require expert-driven input for labeled annotations and model training. The natural language processing competency of large language models (LLM) can ...
Data Mining Neoplasms Humans Medical Oncology Natural Language Processing Electronic Health Records
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Learning the rules of peptide self-assembly through data mining with large language models.

Science advances Mar 26, 2025
Peptides are ubiquitous and important biomolecules that self-assemble into diverse structures. Although extensive research has explored the effects of chemical composition and exterior conditions on self-assembly, a systematic study consolidating the...
Data Mining Machine Learning Peptides Humans Algorithms Databases, Protein
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An automated classification pipeline for tables in pharmacokinetic literature.

Scientific reports Mar 24, 2025
Pharmacokinetic (PK) models are essential for optimising drug candidate selection and dosing regimens in drug development. Preclinical and population PK models benefit from integrating prior knowledge from existing compounds. While tables in scientif...
Humans Data Mining Pharmacokinetics
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