Search Results for "pipeline"

AlphaFold 3, developed by Google DeepMind, is an advanced deep learning system for predicting biomolecular structures and interactions with exceptional accuracy. This repository provides the complete inference pipeline for running AlphaFold 3, though access to the model parameters is restricted and must be obtained directly from Google under specific terms of use. The system is designed for scientific research applications in structural biology, biochemistry, and bioinformatics, enabling accurate modeling of proteins, ligands, and covalent modifications. ...

LLM Applications is a practical reference repository that demonstrates how to build production-grade applications powered by large language models. The project focuses particularly on Retrieval-Augmented Generation architectures, which combine language models with external knowledge sources to improve accuracy and reliability. It provides step-by-step guidance for constructing systems that ingest documents, split them into chunks, generate embeddings, index them in vector databases, and...

SimSiam is a PyTorch implementation of “Exploring Simple Siamese Representation Learning” by Xinlei Chen and Kaiming He. The project introduces a minimalist approach to self-supervised learning that avoids negative pairs, momentum encoders, or large memory banks—key complexities of prior contrastive methods. SimSiam learns image representations by maximizing similarity between two augmented views of the same image through a Siamese neural network with a stop-gradient operation, preventing...

Unsupervised Machine Translation is a research repository that implements both phrase-based SMT and neural MT approaches for translation without parallel corpora. The neural component supports multiple architectures—seq2seq, biLSTM with attention, and Transformer—and allows extensive parameter sharing across languages to improve data efficiency. Training relies on denoising auto-encoding and back-translation, with on-the-fly, multithreaded generation of synthetic parallel data to continually...

...Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. We have developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements. ...

Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. ...