XieResearchGroup / CODE-AELinks
Coherent Deconfounding Autoencoder (CODE-AE) can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them
☆21Updated last year
Alternatives and similar repositories for CODE-AE
Users that are interested in CODE-AE are comparing it to the libraries listed below
Sorting:
- Exploring the space of drug combinations to discover synergistic drugs using Active Learning☆24Updated last year
- Code for CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction☆29Updated 2 years ago
- Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)☆97Updated 3 years ago
- Code for paper "A deep learning framework for drug repurposing via emulating clinical trials on real world patient data" (Accepted to Nat…☆100Updated 3 years ago
- Madrigal: Multimodal AI predicts clinical outcomes of drug combinations from preclinical data☆38Updated 3 months ago
- Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks☆97Updated last month
- Processing SIDER 4.1: the side effect resource☆23Updated 9 years ago
- A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials☆21Updated 6 years ago
- Drug Response Prediction and Biomarker Discovery Using Multi-Modal Deep Learning☆14Updated last year
- SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks (Scientific Reports)☆64Updated 5 years ago
- Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors☆42Updated last year
- A Generative Adversarial Network Model Alternative to Animal Studies for Clinical Pathology Assessment☆13Updated last year
- Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network☆92Updated 2 years ago
- code for Gogleva et al manuscript☆46Updated 2 years ago
- Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)☆73Updated 2 years ago
- ☆19Updated 2 years ago
- Analysis notebooks and database interaction scripts for the nsides project☆19Updated last year
- Replication attempt for the Protein Folding Model described in https://www.biorxiv.org/content/10.1101/2021.08.02.454840v1☆37Updated 3 years ago
- Build system for the RTX-KG2pre biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)☆52Updated 2 weeks ago
- ☆33Updated 3 months ago
- benchmark dataset and Deep learning method (Hierarchical Interaction Network, HINT) for clinical trial approval probability prediction, p…☆138Updated 5 months ago
- Python package is for paper 'Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data…☆39Updated 9 years ago
- GeneDisco is a benchmark suite for evaluating active learning algorithms for experimental design in drug discovery.☆40Updated 2 years ago
- Starter repository for submissions to the CausalBench challenge for gene-gene graph inference from genetic perturbation experiments.☆32Updated 2 years ago
- BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments☆91Updated 4 months ago
- Code to reproduce results in Ravindra NG* & Sehanobish A* et al. 2020, "Disease State Prediction From Single-Cell Data Using Graph Attent…☆18Updated 5 years ago
- PyTorch implementation of bimodal neural networks for drug-cell (pharmarcogenomics) and drug-protein (proteochemometrics) interaction pre…☆54Updated 3 months ago
- ☆55Updated last year
- Python package that wraps around the ClinicalTrials.gov API☆56Updated last year
- Benchmark for LLM-based Agents in Computational Biology☆62Updated last month