fteufel

fteufel's Stars

• prescient-design/holo-bench

  Benchmark for Biophysical Sequence Optimization Algorithms

  Language:Python101

• Genentech/gReLU

  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

  Language:Python15914

• zi-w/Ensemble-Bayesian-Optimization

  Code repository for Ensemble Bayesian Optimization

  Language:Python4611

• leojklarner/gauche

  A Library for Gaussian Processes in Chemistry

  Language:Jupyter Notebook18718

• EiffL/SpectralFlow

  Tensorflow implementation of stochastic spectral-sums estimators

  Language:Jupyter Notebook5

• generatebio/chroma

  A generative model for programmable protein design

  Language:Python63877

• eric-mitchell/direct-preference-optimization

  Reference implementation for DPO (Direct Preference Optimization)

  Language:Python1.9k147

• HazyResearch/hyena-dna

  Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

  Language:Assembly54777

• AIRI-Institute/GENA_LM

  GENA-LM is a transformer masked language model trained on human DNA sequence.

  Language:Jupyter Notebook15413

• jvkersch/tmtools

  Python bindings for the TM-align algorithm and code for protein structure comparison developed by Zhang et al.

  Language:Python245

• frederikkemarin/BEND

  Benchmarking DNA Language Models on Biologically Meaningful Tasks

  Language:Python8211

• samsinai/FLEXS

  Fitness landscape exploration sandbox for biological sequence design.

  Language:Jupyter Notebook14722

• Significant-Gravitas/AutoGPT

  AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

  Language:Python165k43.8k

• graph-part/graph-part

  GraphPart, a data partitioning method for ML on biological sequences

  Language:Jupyter Notebook204

• soedinglab/MMseqs2

  MMseqs2: ultra fast and sensitive search and clustering suite

  Language:C1.3k185

• allegro/allRank

  allRank is a framework for training learning-to-rank neural models based on PyTorch.

  Language:Python831114

• alexviiia/RandProt

  Generate high-order Markov random protein sequences

  Language:Perl2

• BioGenies/peptide-prediction-list

  Collects software dedicated to predicting specific properties of peptides

  Language:Shell488

• nalepae/pandarallel

  A simple and efficient tool to parallelize Pandas operations on all available CPUs

  Language:Python3.6k209

• lucidrains/performer-pytorch

  An implementation of Performer, a linear attention-based transformer, in Pytorch

  Language:Python1.1k143

• KevinMusgrave/pytorch-metric-learning

  The easiest way to use deep metric learning in your application. Modular, flexible, and extensible. Written in PyTorch.

  Language:Python5.9k657

• atarashansky/SCTransformPy

  A python port of the R package SCTransform:

  Language:Jupyter Notebook185

• sugarme/gotch

  Go binding for Pytorch C++ API (libtorch)

  Language:Go54144

• webermarcolivier/statannot

  add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot

  Language:Jupyter Notebook39074

• microsoft/fastformers

  FastFormers - highly efficient transformer models for NLU

  Language:Python69653

• yangkky/Machine-learning-for-proteins

  Listing of papers about machine learning for proteins.

  1.5k196

• mikkelbrusen/embeddings-in-ppt

  Evaluation of Pre-trained Amino Acid Embeddings in Protein Prediction Tasks done in PyTorch

  Language:Jupyter Notebook31

• claying/OTK

  A Pytorch implementation of the optimal transport kernel embedding

  Language:Python11013

• huggingface/awesome-papers

  Papers & presentation materials from Hugging Face's internal science day

  2k117

• idiap/fast-transformers

  Pytorch library for fast transformer implementations

  Language:Python1.6k172