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@Helix-Research-Lab

Helix Research Lab

Helix Research Lab under Professor Russ Altman at Stanford University

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  1. PGxPOP PGxPOP Public

    PGxPOP

    Python 16 2

  2. Pool_PaRTI 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 9 2

  3. COLLAPSE COLLAPSE Public

    Forked from awfderry/COLLAPSE

    Representation learning for protein functional site analysis

    Python 1

  4. opioid-social-media-platforms opioid-social-media-platforms Public

    Forked from kristycarp/opioid-social-media-platforms

    Assessing social media platforms for utility in monitoring the opioid epidemic.

    R

  5. gpt3-lexicon gpt3-lexicon Public

    Forked from kristycarp/gpt3-lexicon

    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

  6. ml-structure-bias ml-structure-bias Public

    Forked from awfderry/ml-structure-bias

    Code for "Training data composition affects performance of protein structure analysis algorithms", published at the Pacific Symposium on Biocomputing 2022

    Jupyter Notebook

Repositories

Showing 10 of 18 repositories
  • 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.

    Helix-Research-Lab/Pool_PaRTI’s past year of commit activity
    Jupyter Notebook 9 Apache-2.0 2 0 0 Updated May 19, 2025
  • opioid-social-media-platforms Public Forked from kristycarp/opioid-social-media-platforms

    Assessing social media platforms for utility in monitoring the opioid epidemic.

    Helix-Research-Lab/opioid-social-media-platforms’s past year of commit activity
    R 0 MIT 1 0 0 Updated Jul 1, 2024
  • PARSE Public Forked from awfderry/PARSE

    Protein Annotation by Residue-Specific Enrichment: a site-based statistical method for interpretable protein function annotation

    Helix-Research-Lab/PARSE’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Apr 14, 2024
  • kgemb-sens Public Forked from dnsosa/kgemb-sens

    A package for setting up and running experiments on the sensitivity of knowledge graph (KG) embedding methods to sparsity and inconsistency.

    Helix-Research-Lab/kgemb-sens’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Mar 22, 2024
  • Helix-Research-Lab/collapse-motifs’s past year of commit activity
    Jupyter Notebook 0 MIT 3 0 0 Updated Feb 24, 2024
  • COLLAPSE Public Forked from awfderry/COLLAPSE

    Representation learning for protein functional site analysis

    Helix-Research-Lab/COLLAPSE’s past year of commit activity
    Python 1 MIT 2 0 0 Updated Aug 11, 2023
  • lit_contextizer Public Forked from dnsosa/lit_contextizer

    A package for augmenting extracted protein-protein relations with cell type and tissue context extracted from biomedical text.

    Helix-Research-Lab/lit_contextizer’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Aug 2, 2023
  • pan_omics_psych Public Forked from mguo123/pan_omics_psych

    Processing Scripts for RNA, ATAC, HiChIP data associated with the Guo et al. paper "Compendium of functional regulatory variants in human neuropsychiatric disease."

    Helix-Research-Lab/pan_omics_psych’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Jun 30, 2023
  • gpt3-lexicon Public Forked from kristycarp/gpt3-lexicon

    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)

    Helix-Research-Lab/gpt3-lexicon’s past year of commit activity
    Python 0 2 0 0 Updated Feb 20, 2023
  • PGxPOP Public

    PGxPOP

    Helix-Research-Lab/PGxPOP’s past year of commit activity
    Python 16 MPL-2.0 2 7 2 Updated Jan 25, 2023

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