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

PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z

Python script that downloads all pubmed abstracts corresponding to user-specified keyword searches, by performing automated NCBI E-utility queries

Large Language Model Text Generation Inference

Load Google's pre-trained Word2Vec model using gensim APIs

MOB typing for plasmid metagenomic fragments

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Biological foundation modeling from molecular to genome scale

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

CodonBert: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism.

Genomic language model predicts protein co-regulation and function

Repository for mRNA Paper and CodonBERT publication.

A CLI tool for clustering with the Leiden algorithm

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

🤗 PEFT: State-of-the-art Parameter-Efficient Fine-Tuning.

Model API for GALACTICA

CONJScan models - Models for detection of conjugative, decayed conjugative and mobilisable elements

LAVIS - A One-stop Library for Language-Vision Intelligence

PLSDB pipeline to collect bacterial plasmids from NCBI

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Ollama Python library

主要记录大语言大模型（LLMs） 算法（应用）工程师相关的知识及面试题

Phage virion protein classifier

K-Means clustering - constrained with minimum and maximum cluster size. Documentation: https://joshlk.github.io/k-means-constrained

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