josephvalencia
PhD student in computer science at Oregon State University. Building interpretable machine learning tools for RNA biology
Oregon State UniversityCorvallis, OR
josephvalencia's Stars
samsinai/FLEXS
Fitness landscape exploration sandbox for biological sequence design.
Genentech/gReLU
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
Edinburgh-Genome-Foundry/DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
evo-design/evo
Biological foundation modeling from molecular to genome scale
state-spaces/mamba
Mamba SSM architecture
hristo-vrigazov/mmap.ninja
Memory mapped numpy arrays of varying shapes
BartoszJarocki/cv
Print-friendly, minimalist CV page
arogozhnikov/einops
Flexible and powerful tensor operations for readable and reliable code (for pytorch, jax, TF and others)
Sanofi-Public/CodonBERT
Repository for mRNA Paper and CodonBERT publication.
yikunpku/RNA-MSM
Nucleic Acids Research 2024:RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.
ML4GLand/EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets
samuela/torch2jax
Run PyTorch in JAX. 🤝
brandontrabucco/design-bench
Benchmarks for Model-Based Optimization
autosome-ru/LegNet
accurate prediction of promoter activity and variant effects from massive parallel reporter assays
microsoft/LoRA
Code for loralib, an implementation of "LoRA: Low-Rank Adaptation of Large Language Models"
ZhangLabGT/LinRace
single cell lineage reconstruction using paired lineage barcode and gene expression data
VincentStimper/normalizing-flows
PyTorch implementation of normalizing flow models
biotite-dev/biotite
A comprehensive library for computational molecular biology
kazukiosawa/asdl
ASDL: Automatic Second-order Differentiation Library for PyTorch
deepchem/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
Biobix/DeepRibo
microsoft/MMdnn
MMdnn is a set of tools to help users inter-operate among different deep learning frameworks. E.g. model conversion and visualization. Convert models between Caffe, Keras, MXNet, Tensorflow, CNTK, PyTorch Onnx and CoreML.
pjsample/human_5utr_modeling
Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.
instadeepai/nucleotide-transformer
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
ml4bio/RNA-FM
RNA foundation model
AIRI-Institute/GENA_LM
GENA-LM is a transformer masked language model trained on human DNA sequence.
jerryji1993/DNABERT
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
trevismd/statannotations
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
jmschrei/tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
f-dangel/backpack
BackPACK - a backpropagation package built on top of PyTorch which efficiently computes quantities other than the gradient.