surrogate quantitative interpretability for deepnets
☆27Aug 28, 2026Updated 2 months ago
Alternatives and similar repositories for squid-nn
Users that are interested in squid-nn are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Jan 22, 2025Updated last year
- A multi-task neural network for predicting perturbation responses to Alternative Polyadenylation usage levels☆11May 18, 2023Updated 3 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆46Jul 3, 2025Updated last year
- ☆12Oct 4, 2021Updated 5 years ago
- systematic explanation of attribution-based mechanisms for regulatory genomics☆17Sep 16, 2026Updated last month
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated 2 years ago
- Code used to analyze single cell RNA and ATAC sequencing in developing human brain☆37Jan 4, 2022Updated 4 years ago
- Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics☆25Jun 3, 2025Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆100Jun 10, 2026Updated 4 months ago
- FluxGAT introduces a graph neural network (GNN) model designed to predict gene essentiality by utilising graphical representations derive…☆11Mar 5, 2026Updated 7 months ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆68Dec 2, 2024Updated last year
- Supplementary files and notebooks to recreate figures.☆24Aug 4, 2026Updated 2 months ago
- ☆52Oct 19, 2026Updated last week
- ☆37Jan 27, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Evaluation framework for computationally inferred gene networks from single-cell data.☆20Oct 23, 2025Updated last year
- ☆19Oct 21, 2024Updated 2 years ago
- ☆30Sep 9, 2025Updated last year
- Dataloader for applying sequence models to personalized genomics☆31Updated this week
- ☆17Jul 13, 2024Updated 2 years ago
- ☆17Oct 22, 2026Updated last week
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆23Oct 4, 2026Updated 3 weeks ago
- deep learning-inspired explainable sequence model for transcription initiation☆109Mar 3, 2025Updated last year
- Cherimoya is a lightweight sequence-to-function (S2F) model that is small, fast, and easy to use. Now usable by agents.☆70Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- DOLPHIN: Advances Single-cell RNA-seq Analysis Beyond Gene-Level by Integrating Exon-Level Quantification and Junction Reads with Deep Ne…☆17Sep 7, 2026Updated last month
- ☆15Nov 5, 2025Updated 11 months ago
- Analyses of Ribo-seq rRNA fragments for Differential Ribosome Heterogeneity and Collision predictions☆17Oct 13, 2026Updated 2 weeks ago
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆41Jul 29, 2025Updated last year
- code to run sei and obtain sei and sequence class predictions☆119Dec 20, 2022Updated 3 years ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆32Feb 21, 2023Updated 3 years ago
- ☆14Nov 6, 2025Updated 11 months ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- ☆17Sep 8, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A lightweight reimplementation of some of the algorithms in the MEME suite in Python.☆39Sep 29, 2026Updated last month
- "Global Importance Analysis: A Method to Quantify Importance of Genomic Features in Deep Neural Networks" by Koo et al.☆15Jun 22, 2022Updated 4 years ago
- R and MATLAB scripts for MAGICAL☆11Jun 26, 2024Updated 2 years ago
- ☆57May 23, 2026Updated 5 months ago
- ☆24Apr 14, 2022Updated 4 years ago
- RNA-seq prediction with deep convolutional neural networks.☆268Sep 30, 2026Updated last month
- Single-cell biological network inference using a heterogeneous graph transformer☆78Feb 24, 2025Updated last year