jalew188

llama_index

LlamaIndex is a data framework for your LLM applications

ruff

An extremely fast Python linter and code formatter, written in Rust.

CLIP

CLIP (Contrastive Language-Image Pretraining), Predict the most relevant text snippet given an image

llm.c

LLM training in simple, raw C/CUDA

mojo

The Mojo Programming Language

candle

Minimalist ML framework for Rust

pybind11

Seamless operability between C++11 and Python

arrow

Apache Arrow is the universal columnar format and multi-language toolbox for fast data interchange and in-memory analytics

cmake-examples

Useful CMake Examples

xmake

🔥 A cross-platform build utility based on Lua

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

torchinfo

View model summaries in PyTorch!

DataFrame

C++ DataFrame for statistical, Financial, and ML analysis -- in modern C++ using native types and contiguous memory storage

StableDiffusionReconstruction

Takagi and Nishimoto, CVPR 2023

UniRepLKNet

[CVPR'24] UniRepLKNet: A Universal Perception Large-Kernel ConvNet for Audio, Video, Point Cloud, Time-Series and Image Recognition

libdivsufsort

A lightweight suffix-sorting library

FragPipe

A cross-platform proteomics data analysis suite

proteinshake

Protein structure datasets for machine learning.

alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.

PureHDF

A pure .NET library that makes reading and writing of HDF5 files (groups, datasets, attributes, ...) very easy.

RawFileReader

scPROTEIN

PepNet

The state of the art Deep CNN neural network for de novo sequencing of tandem mass spectra

MSBooster

MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

glycresoft

An LC-MS/MS glycan and glycopeptide search engine

PepPre.jl

Promote peptide identification using accurate and comprehensive precursors. https://doi.org/10.1021/acs.jproteome.3c00293

pGlycoQuant

Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with minuscule missing value via a deep residual network and includes a quantitative bioinformatics analysis module. At present, pFind, pGlyco, Byonic and MSFragger software glycosylation identification results can be used for quantification by pGlycoQuant.

AEGIS

MHC-II presentation predictor

GraphGPT

Extrapolating knowledge graphs from unstructured text using GPT-3 🕵️‍♂️