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    57 repositories

    • CRADLE-VAE

      Public
      Python
      •1•9•0•0•Updated Jan 19, 2025Jan 19, 2025

    • ETHIC

      Public
      ETHIC: Evaluating Large Language Models on Long-Context Tasks with High Information Coverage
      benchmarkevaluationlong-context
      Python
      •0•14•0•0•Updated Jan 17, 2025Jan 17, 2025

    • Monet

      Public
      Monet: Mixture of Monosemantic Experts for Transformers
      sparse-autoencodersinterpretabilitymixture-of-expertslarge-language-models
      Python
      •
      Apache License 2.0
      •1•45•0•0•Updated Jan 16, 2025Jan 16, 2025

    • TPP_MOL_DPO

      Public
      Python
      •0•2•0•0•Updated Jan 12, 2025Jan 12, 2025

    • BADGER

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 10, 2025Jan 10, 2025

    • RAG2

      Public
      [Under Review] Rationale-Guided Retrieval Augmented Generation for Medical Question Answering
      Python
      •0•11•0•0•Updated Jan 4, 2025Jan 4, 2025

    • EquiCPI

      Public
      Python
      •0•1•0•0•Updated Jan 2, 2025Jan 2, 2025

    • ChroKnowledge

      Public
      Python
      •0•12•0•0•Updated Nov 28, 2024Nov 28, 2024

    • ParaCLIP

      Public
      Fine-tuning CLIP Text Encoders with Two-step Paraphrasing (EACL 2024, Findings)
      Python
      •
      Other
      •0•5•0•0•Updated Nov 23, 2024Nov 23, 2024

    • cookingsense

      Public
      CookingSense: A Culinary Knowledgebase with Multidisciplinary Assertions (LREC-COLING 2024)
      Python
      •0•17•0•0•Updated Oct 9, 2024Oct 9, 2024

    • CompAct

      Public
      [EMNLP 2024] CompAct: Compressing Retrieved Documents Actively for Question Answering
      compressionquestion-answering
      Python
      •0•20•0•0•Updated Sep 20, 2024Sep 20, 2024

    • ANGEL

      Public
      Learning from Negative samples for Biomedical Generative Entity Linking
      Python
      •
      GNU General Public License v3.0
      •0•17•0•0•Updated Sep 11, 2024Sep 11, 2024

    • bc7-chem-id

      Public
      DMIS at BioCreative VII NLMChem Track
      nernormalizationbionlp
      Python
      •1•5•0•0•Updated Sep 11, 2024Sep 11, 2024

    • OLAPH

      Public
      OLAPH: Improving Factuality in Biomedical Long-form Question Answering
      question-answeringhallucinationbiomedical-researchfactuality
      Python
      •4•38•1•0•Updated Sep 10, 2024Sep 10, 2024

    • KAZU-NER-module

      Public
      EMNLP 2022: Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework
      Python
      •1•10•1•0•Updated Aug 29, 2024Aug 29, 2024

    • KitchenScale

      Public
      KitchenScale: Learning Food Numeracy from Recipes through Context-Aware Ingredient Quantity Prediction
      Python
      •0•7•0•0•Updated Aug 15, 2024Aug 15, 2024

    • MulinforCPI

      Public
      MulinforCPI: enhancing precision of compound-protein interaction prediction through novel perspectives on multi-level information integration
      Python
      •3•10•0•0•Updated Jun 20, 2024Jun 20, 2024

    • LAPIS

      Public
      Python
      •0•2•0•1•Updated May 20, 2024May 20, 2024

    • self-biorag

      Public
      ISMB'24 "Self-BioRAG: Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language Models"
      Python
      •5•45•2•0•Updated Apr 4, 2024Apr 4, 2024

    • BERN2

      Public
      BERN2: an advanced neural biomedical namedentity recognition and normalization tool
      biomedical-text-mining
      Python
      •
      BSD 2-Clause "Simplified" License
      •42•177•15•0•Updated Mar 28, 2024Mar 28, 2024

    • MolPLA

      Public
      Python
      •1•6•0•0•Updated Mar 13, 2024Mar 13, 2024

    • ReSimNet

      Public
      Implementation of ReSimNet for drug response similarity prediction
      Jupyter Notebook
      •
      Apache License 2.0
      •16•39•1•0•Updated Dec 20, 2023Dec 20, 2023

    • PerceiverCPI

      Public
      Bioinformatics'2022 PerceiverCPI: A nested cross-attention network for compound-protein interaction prediction
      Python
      •
      MIT License
      •6•36•0•0•Updated Nov 9, 2023Nov 9, 2023

    • TouR

      Public
      Findings of ACL'2023: Optimizing Test-Time Query Representations for Dense Retrieval
      Python
      •
      Apache License 2.0
      •2•29•0•0•Updated Oct 24, 2023Oct 24, 2023

    • moable

      Public
      Predicting mechanism of action of novelcompounds using compound structure andtranscriptomic signature co-embedding
      pytorch
      Python
      •1•14•3•0•Updated Oct 17, 2023Oct 17, 2023

    • biobert

      Public
      Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining
      Python
      •
      Other
      •458•2k•54•3•Updated Aug 13, 2023Aug 13, 2023

    • BioSyn

      Public
      ACL'2020: Biomedical Entity Representations with Synonym Marginalization
      Python
      •
      MIT License
      •28•161•3•0•Updated Jul 7, 2023Jul 7, 2023

    • SeqTagQA

      Public
      Sequence Tagging for Biomedical Extractive Question Answering (Bioinformatics'2020)
      bioasqquestion-answering
      Python
      •3•11•2•0•Updated Jul 3, 2023Jul 3, 2023

    • nesa

      Public
      NESA: Neural Event Scheduling Assistant
      neural-networkcalendarschedulingeventpytorch
      Python
      •
      Apache License 2.0
      •12•28•0•0•Updated Jul 1, 2023Jul 1, 2023

    • biobert-pytorch

      Public
      PyTorch Implementation of BioBERT
      Java
      •
      Other
      •109•317•26•4•Updated Jun 24, 2023Jun 24, 2023