sacdallago

qlora

QLoRA: Efficient Finetuning of Quantized LLMs

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

NeMo-Guardrails

NeMo Guardrails is an open-source toolkit for easily adding programmable guardrails to LLM-based conversational systems.

RFdiffusion

Code for running RFdiffusion

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

ProteinMPNN

Code for the ProteinMPNN paper

safari

Convolutions for Sequence Modeling

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

chroma

A generative model for programmable protein design

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

DiffSBDD

A Euclidean diffusion model for structure-based drug design.

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

serratus

Ultra-deep search for novel viruses

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

chroma-pytorch

Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch

proteinfer

Deep networks for protein functional inference

pyrelational

pyrelational is a python active learning library for rapidly implementing active learning pipelines from data management, model development (and Bayesian approximation), to creating novel active learning strategies.

masif_seed

Masif seed paper repository

block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

genslm

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

design_tools

A compilation of deep learning methods for protein design

uniclust-pipeline

CUDASW4

CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search

Phylogeny-MSA-Transformer

Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s41467-022-34032-y)

pyFIFOtax

Simple Tax Reporting Tool for share transactions on foreign exchanges

3Dseq