evanseitz / squid-nnLinks
surrogate quantitative interpretability for deepnets
☆24Updated 5 months ago
Alternatives and similar repositories for squid-nn
Users that are interested in squid-nn are comparing it to the libraries listed below
Sorting:
- Large language modeling applied to T-cell receptor (TCR) sequences.☆59Updated 3 years ago
- Interpretation by Deep Generative Masking for Biological Sequences☆37Updated 4 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆43Updated 7 months ago
- a framework for predicting global protein-protein interaction networks from dynamic mass spec data☆24Updated last year
- Computational Optimization of DNA Activity (CODA)☆67Updated 10 months ago
- Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity☆75Updated 2 years ago
- Scripts and datasets to reproduce the experiment of the paper "Exploring non-coding RNA functions with deep learning tools"☆16Updated 4 years ago
- ERGO-II, an updated version of ERGO including more features for TCR-peptide binding prediction☆34Updated 3 years ago
- ☆19Updated last year
- HLA-II ligand predictor.☆46Updated 2 years ago
- ☆86Updated 2 years ago
- Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2…☆30Updated 6 months ago
- RiboNN: predicting translation efficiencies from mRNA sequences☆50Updated 3 weeks ago
- The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)☆37Updated 2 years ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Updated last year
- Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.☆57Updated 6 years ago
- ☆42Updated last week
- STAPLER (Shared TCR And Peptide Language bidirectional Encoder Representations from transformers) is a language model that uses a joint T…☆28Updated 9 months ago
- Functional Embedding of Gene Signatures☆48Updated last year
- TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…☆26Updated 3 years ago
- BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity☆60Updated last month
- 📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential☆24Updated 4 months ago
- ☆22Updated 3 years ago
- Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor☆50Updated last year
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆39Updated 10 months ago
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆35Updated 6 months ago
- ☆15Updated 4 months ago
- Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…☆67Updated 3 years ago
- Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors☆43Updated last year
- NetTCR-2.0. Sequence-based prediction of peptide-TCR binding☆35Updated 3 years ago