The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to infectious and neglected disease research. It offers an open-source, low-code solution that provides seamless access to AI/ML models for drug discovery. Models housed in the hub come from two sources: published models from literature (with due third-party acknowledgment) and custom models developed by the Ersilia team or contributors.

Discover the journey of building a generative AI application using LangChain.js and Azure. This demo explores the development process from idea to production, using a RAG-based approach for a Q&A system based on YouTube video transcripts. The application allows to ask text-based questions about a YouTube video and uses the transcript of the video to generate responses. The code comes in two versions: local prototype using FAISS and Ollama with LLaMa3 model for completion and all-minilm-l6-v2 for embeddings, and Azure cloud version using Azure AI Search and GPT-4 Turbo model for completion and text-embedding-3-large for embeddings. Either version can be run as an API using the Azure Functions runtime.

NVIDIA BioNeMo Framework is a collection of programming tools, libraries, and models for computational drug discovery. It accelerates building and adapting biomolecular AI models by providing domain-specific, optimized models and tooling for GPU-based computational resources. The framework offers comprehensive documentation and support for both community and enterprise users.

The Codebase Context Specification (CCS) project aims to standardize embedding contextual information within codebases to enhance understanding for both AI and human developers. It introduces a convention similar to `.env` and `.editorconfig` files but focused on documenting code for both AI and humans. By providing structured contextual metadata, collaborative documentation guidelines, and standardized context files, developers can improve code comprehension, collaboration, and development efficiency. The project includes a linter for validating context files and provides guidelines for using the specification with AI assistants. Tooling recommendations suggest creating memory systems, IDE plugins, AI model integrations, and agents for context creation and utilization. Future directions include integration with existing documentation systems, dynamic context generation, and support for explicit context overriding.

AI Exploits is a repository that showcases practical attacks against AI/Machine Learning infrastructure, aiming to raise awareness about vulnerabilities in the AI/ML ecosystem. It contains exploits and scanning templates for responsibly disclosed vulnerabilities affecting machine learning tools, including Metasploit modules, Nuclei templates, and CSRF templates. Users can use the provided Docker image to easily run the modules and templates. The repository also provides guidelines for using Metasploit modules, Nuclei templates, and CSRF templates to exploit vulnerabilities in machine learning tools.

Gemma is a family of open-weights Large Language Model (LLM) by Google DeepMind, based on Gemini research and technology. This repository contains an inference implementation and examples, based on the Flax and JAX frameworks. Gemma can run on CPU, GPU, and TPU, with model checkpoints available for download. It provides tutorials, reference implementations, and Colab notebooks for tasks like sampling and fine-tuning. Users can contribute to Gemma through bug reports and pull requests. The code is licensed under the Apache License, Version 2.0.

Pathway is a Python data processing framework for analytics and AI pipelines over data streams. It's the ideal solution for real-time processing use cases like streaming ETL or RAG pipelines for unstructured data. Pathway comes with an **easy-to-use Python API** , allowing you to seamlessly integrate your favorite Python ML libraries. Pathway code is versatile and robust: **you can use it in both development and production environments, handling both batch and streaming data effectively**. The same code can be used for local development, CI/CD tests, running batch jobs, handling stream replays, and processing data streams. Pathway is powered by a **scalable Rust engine** based on Differential Dataflow and performs incremental computation. Your Pathway code, despite being written in Python, is run by the Rust engine, enabling multithreading, multiprocessing, and distributed computations. All the pipeline is kept in memory and can be easily deployed with **Docker and Kubernetes**. You can install Pathway with pip: `pip install -U pathway` For any questions, you will find the community and team behind the project on Discord.

Council is an open-source platform designed for the rapid development and deployment of customized generative AI applications using teams of agents. It extends the LLM tool ecosystem by providing advanced control flow and scalable oversight for AI agents. Users can create sophisticated agents with predictable behavior by leveraging Council's powerful approach to control flow using Controllers, Filters, Evaluators, and Budgets. The framework allows for automated routing between agents, comparing, evaluating, and selecting the best results for a task. Council aims to facilitate packaging and deploying agents at scale on multiple platforms while enabling enterprise-grade monitoring and quality control.

The Microsoft Health Intelligence Machine Learning Toolbox is a repository that provides low-level and high-level building blocks for Machine Learning / AI researchers and practitioners. It simplifies and streamlines work on deep learning models for healthcare and life sciences by offering tested components such as data loaders, pre-processing tools, deep learning models, and cloud integration utilities. The repository includes two Python packages, 'hi-ml-azure' for helper functions in AzureML, 'hi-ml' for ML components, and 'hi-ml-cpath' for models and workflows related to histopathology images.

This repository provides a fullstack example of building a Retrieval Augmented Generation (RAG) app with Cloudflare. It utilizes Cloudflare Workers, Pages, D1, KV, R2, AI Gateway, and Workers AI. The app features streaming interactions to the UI, hybrid RAG with Full-Text Search and Vector Search, switchable providers using AI Gateway, per-IP rate limiting with Cloudflare's KV, OCR within Cloudflare Worker, and Smart Placement for workload optimization. The development setup requires Node, pnpm, and wrangler CLI, along with setting up necessary primitives and API keys. Deployment involves setting up secrets and deploying the app to Cloudflare Pages. The project implements a Hybrid Search RAG approach combining Full Text Search against D1 and Hybrid Search with embeddings against Vectorize to enhance context for the LLM.

LangSim is a tool developed to address the challenge of using simulation tools in computational chemistry and materials science, which typically require cryptic input files or programming experience. The tool provides a Large Language Model (LLM) extension with agents to couple the LLM to scientific simulation codes and calculate physical properties from a natural language interface. It aims to simplify the process of interacting with simulation tools by enabling users to query the large language model directly from a Python environment or a web-based interface.

MARS5 is a novel English speech model (TTS) developed by CAMB.AI, featuring a two-stage AR-NAR pipeline with a unique NAR component. The model can generate speech for various scenarios like sports commentary and anime with just 5 seconds of audio and a text snippet. It allows steering prosody using punctuation and capitalization in the transcript. Speaker identity is specified using an audio reference file, enabling 'deep clone' for improved quality. The model can be used via torch.hub or HuggingFace, supporting both shallow and deep cloning for inference. Checkpoints are provided for AR and NAR models, with hardware requirements of 750M+450M params on GPU. Contributions to improve model stability, performance, and reference audio selection are welcome.

The LlamaEdge project makes it easy to run LLM inference apps and create OpenAI-compatible API services for the Llama2 series of LLMs locally. It provides a Rust+Wasm stack for fast, portable, and secure LLM inference on heterogeneous edge devices. The project includes source code for text generation, chatbot, and API server applications, supporting all LLMs based on the llama2 framework in the GGUF format. LlamaEdge is committed to continuously testing and validating new open-source models and offers a list of supported models with download links and startup commands. It is cross-platform, supporting various OSes, CPUs, and GPUs, and provides troubleshooting tips for common errors.

The Atomic Agents framework is a modular and extensible tool designed for creating powerful applications. It leverages Pydantic for data validation and serialization. The framework follows the principles of Atomic Design, providing small and single-purpose components that can be combined. It integrates with Instructor for AI agent architecture and supports various APIs like Cohere, Anthropic, and Gemini. The tool includes documentation, examples, and testing features to ensure smooth development and usage.

CoLLM is a novel method that integrates collaborative information into Large Language Models (LLMs) for recommendation. It converts recommendation data into language prompts, encodes them with both textual and collaborative information, and uses a two-step tuning method to train the model. The method incorporates user/item ID fields in prompts and employs a conventional collaborative model to generate user/item representations. CoLLM is built upon MiniGPT-4 and utilizes pretrained Vicuna weights for training.

Kafka-ML is a framework designed to manage the pipeline of Tensorflow/Keras and PyTorch machine learning models on Kubernetes. It enables the design, training, and inference of ML models with datasets fed through Apache Kafka, connecting them directly to data streams like those from IoT devices. The Web UI allows easy definition of ML models without external libraries, catering to both experts and non-experts in ML/AI.

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to infectious and neglected disease research. It offers an open-source, low-code solution that provides seamless access to AI/ML models for drug discovery. Models housed in the hub come from two sources: published models from literature (with due third-party acknowledgment) and custom models developed by the Ersilia team or contributors.

NoLabs is an open-source biolab that provides easy access to state-of-the-art models for bio research. It supports various tasks, including drug discovery, protein analysis, and small molecule design. NoLabs aims to accelerate bio research by making inference models accessible to everyone.

OpenCRISPR is a set of free and open gene editing systems designed by Profluent Bio. The OpenCRISPR-1 protein maintains the prototypical architecture of a Type II Cas9 nuclease but is hundreds of mutations away from SpCas9 or any other known natural CRISPR-associated protein. You can view OpenCRISPR-1 as a drop-in replacement for many protocols that need a cas9-like protein with an NGG PAM and you can even use it with canonical SpCas9 gRNAs. OpenCRISPR-1 can be fused in a deactivated or nickase format for next generation gene editing techniques like base, prime, or epigenome editing.

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to infectious and neglected disease research. It offers an open-source, low-code solution that provides seamless access to AI/ML models for drug discovery. Models housed in the hub come from two sources: published models from literature (with due third-party acknowledgment) and custom models developed by the Ersilia team or contributors.

OntoGPT is a Python package for extracting structured information from text using large language models, instruction prompts, and ontology-based grounding. It provides a command line interface and a minimal web app for easy usage. The tool has been evaluated on test data and is used in related projects like TALISMAN for gene set analysis. OntoGPT enables users to extract information from text by specifying relevant terms and provides the extracted objects as output.

BIA `bob` is a Jupyter-based assistant for interacting with data using large language models to generate Python code. It can utilize OpenAI's chatGPT, Google's Gemini, Helmholtz' blablador, and Ollama. Users need respective accounts to access these services. Bob can assist in code generation, bug fixing, code documentation, GPU-acceleration, and offers a no-code custom Jupyter Kernel. It provides example notebooks for various tasks like bio-image analysis, model selection, and bug fixing. Installation is recommended via conda/mamba environment. Custom endpoints like blablador and ollama can be used. Google Cloud AI API integration is also supported. The tool is extensible for Python libraries to enhance Bob's functionality.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

Polaris establishes a novel, industry‑certified standard to foster the development of impactful methods in AI-based drug discovery. This library is a Python client to interact with the Polaris Hub. It allows you to download Polaris datasets and benchmarks, evaluate a custom method against a Polaris benchmark, and create and upload new datasets and benchmarks.

The 'awesome-AI4MolConformation-MD' repository focuses on protein conformations and molecular dynamics using generative artificial intelligence and deep learning. It provides resources, reviews, datasets, packages, and tools related to AI-driven molecular dynamics simulations. The repository covers a wide range of topics such as neural networks potentials, force fields, AI engines/frameworks, trajectory analysis, visualization tools, and various AI-based models for protein conformational sampling. It serves as a comprehensive guide for researchers and practitioners interested in leveraging AI for studying molecular structures and dynamics.