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    21 repositories

    • HOTPocket

      Public
      Code and data accompanying "The Human Omnibus of Targetable Pockets" by Kristy A. Carpenter and Russ B. Altman
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 17, 2025Aug 17, 2025

    • PathwayQA

      Public
      Benchmark QA dataset generation from Reactome and Evaluation with 9 LLMs
      Python
      •0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • ESM_highAttention

      Public
      Python
      •0•0•0•0•Updated Jul 3, 2025Jul 3, 2025

    • Pool_PaRTI

      Public
      Pooling by PageRank Token Importance. This is a weighted average pooling method where the weights are derived from the internal attention matrices of the encoder.
      Jupyter Notebook
      •
      Apache License 2.0
      •3•11•0•0•Updated Jun 11, 2025Jun 11, 2025

    • opioid-social-media-platforms

      Public
      Assessing social media platforms for utility in monitoring the opioid epidemic.
      R
      •
      MIT License
      •1•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • PARSE

      Public
      Protein Annotation by Residue-Specific Enrichment: a site-based statistical method for interpretable protein function annotation
      Python
      •
      MIT License
      •3•0•0•0•Updated Apr 14, 2024Apr 14, 2024

    • kgemb-sens

      Public
      A package for setting up and running experiments on the sensitivity of knowledge graph (KG) embedding methods to sparsity and inconsistency.
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • collapse-motifs

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • COLLAPSE

      Public
      Representation learning for protein functional site analysis
      Python
      •
      MIT License
      •2•1•0•0•Updated Aug 11, 2023Aug 11, 2023

    • lit_contextizer

      Public
      A package for augmenting extracted protein-protein relations with cell type and tissue context extracted from biomedical text.
      Jupyter Notebook
      •1•0•0•0•Updated Aug 2, 2023Aug 2, 2023

    • pan_omics_psych

      Public
      Processing Scripts for RNA, ATAC, HiChIP data associated with the Guo et al. paper "Compendium of functional regulatory variants in human neuropsychiatric disease."
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • gpt3-lexicon

      Public
      Using GPT-3 to build colloquial lexicons of drug terms. A companion to "Using GPT-3 to Build a Lexicon of Drugs of Abuse Synonyms for Social Media Pharmacovigilance." (Carpenter and Altman, 2023)
      Python
      •2•0•0•0•Updated Feb 20, 2023Feb 20, 2023

    • PGxPOP

      Public
      PGxPOP
      Python
      •
      Mozilla Public License 2.0
      •2•17•7•2•Updated Jan 25, 2023Jan 25, 2023

    • covid_lit_contra_claims

      Public
      A package for detecting contradictory claims in COVID-19 research with domain adaptation of LLMs
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jan 10, 2023Jan 10, 2023

    • redmed

      Public
      Annotation tool for flagging/counting drug mentions in social media data
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 9, 2023Jan 9, 2023

    • ml-structure-bias

      Public
      Code for "Training data composition affects performance of protein structure analysis algorithms", published at the Pacific Symposium on Biocomputing 2022
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 1, 2021Oct 1, 2021

    • PGx-GWAS-Review

      Public
      1•0•0•0•Updated Jun 15, 2021Jun 15, 2021

    • CovidFastFax

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 7, 2021Jun 7, 2021

    • Hubble2D6

      Public
      Python
      •4•0•0•0•Updated Sep 13, 2020Sep 13, 2020

    • drug-lit-contradictory-claims

      Public
      Package for detecting contradictory claims from literature regarding drug treatment
      Jupyter Notebook
      •
      MIT License
      •6•0•0•0•Updated Jul 20, 2020Jul 20, 2020

    • GNBR_api

      Public
      Global Network Derived from Text API system
      Python
      •5•0•0•0•Updated May 30, 2018May 30, 2018