This repository provides training on large language models (LLMs) for genomics, including lecture notes and lab classes covering pretraining, finetuning, zeroshot learning prediction of mutation effect, synthetic DNA sequence generation, and DNA sequence optimization.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

ManipVQA is a framework that enhances Multimodal Large Language Models (MLLMs) with manipulation-centric knowledge through a Visual Question-Answering (VQA) format. It addresses the deficiency of conventional MLLMs in understanding affordances and physical concepts crucial for manipulation tasks. By infusing robotics-specific knowledge, including tool detection, affordance recognition, and physical concept comprehension, ManipVQA improves the performance of robots in manipulation tasks. The framework involves fine-tuning MLLMs with a curated dataset of interactive objects, enabling robots to understand and execute natural language instructions more effectively.

A public repository collecting links to state-of-the-art training sets, QA, benchmarks and other evaluations for various ML and LLM applications in materials science and chemistry. It includes datasets related to chemistry, materials, multimodal data, and knowledge graphs in the field. The repository aims to provide resources for training and evaluating machine learning models in the materials science and chemistry domains.

LLM Hallucination Index - RAG Special is a comprehensive evaluation of large language models (LLMs) focusing on context length and open vs. closed-source attributes. The index explores the impact of context length on model performance and tests the assumption that closed-source LLMs outperform open-source ones. It also investigates the effectiveness of prompting techniques like Chain-of-Note across different context lengths. The evaluation includes 22 models from various brands, analyzing major trends and declaring overall winners based on short, medium, and long context insights. Methodologies involve rigorous testing with different context lengths and prompting techniques to assess models' abilities in handling extensive texts and detecting hallucinations.

LLM-RGB is a repository containing a collection of detailed test cases designed to evaluate the reasoning and generation capabilities of Language Learning Models (LLMs) in complex scenarios. The benchmark assesses LLMs' performance in understanding context, complying with instructions, and handling challenges like long context lengths, multi-step reasoning, and specific response formats. Each test case evaluates an LLM's output based on context length difficulty, reasoning depth difficulty, and instruction compliance difficulty, with a final score calculated for each test case. The repository provides a score table, evaluation details, and quick start guide for running evaluations using promptfoo testing tools.

SharpNEAT is a complete implementation of NEAT written in C# and targeting .NET 9. It provides an implementation of an Evolutionary Algorithm (EA) with the specific goal of evolving a population of neural networks towards solving some goal problem task. The framework facilitates research into evolutionary computation and specifically evolution of neural networks, allowing for modular experimentation with genetic coding and evolutionary algorithms.

Parsee AI is a high-level open source data extraction and structuring framework specialized for the extraction of data from a financial domain, but can be used for other use-cases as well. It aims to make the structuring of data from unstructured sources like PDFs, HTML files, and images as easy as possible. Parsee can be used locally in Python environments or through a hosted version for cloud-based jobs. It supports the extraction of tables, numbers, and other data elements, with the ability to create custom extraction templates and run jobs using different models.

AITom is an open-source platform for AI-driven cellular electron cryo-tomography analysis. It is developed to process large amounts of Cryo-ET data, reconstruct, detect, classify, recover, and spatially model different cellular components using state-of-the-art machine learning approaches. The platform aims to automate cellular structure discovery and provide new insights into molecular biology and medical applications.

LLM-Geo is an AI-powered geographic information system (GIS) that leverages Large Language Models (LLMs) for automatic spatial data collection, analysis, and visualization. By adopting LLM as the reasoning core, it addresses spatial problems with self-generating, self-organizing, self-verifying, self-executing, and self-growing capabilities. The tool aims to make spatial analysis easier, faster, and more accessible by reducing manual operation time and delivering accurate results through case studies. It uses GPT-4 API in a Python environment and advocates for further research and development in autonomous GIS.

Long-Context-Attention (YunChang) is a unified sequence parallel approach that combines the strengths of DeepSpeed-Ulysses-Attention and Ring-Attention to provide a versatile and high-performance solution for long context LLM model training and inference. It addresses the limitations of both methods by offering no limitation on the number of heads, compatibility with advanced parallel strategies, and enhanced performance benchmarks. The tool is verified in Megatron-LM and offers best practices for 4D parallelism, making it suitable for various attention mechanisms and parallel computing advancements.

This repository contains the source code and datasets for Graph Chain-of-Thought: Augmenting Large Language Models by Reasoning on Graphs accepted to ACL 2024. It proposes a framework called Graph Chain-of-thought (Graph-CoT) to enable Language Models to traverse graphs step-by-step for reasoning, interaction, and execution. The motivation is to alleviate hallucination issues in Language Models by augmenting them with structured knowledge sources represented as graphs.

DNAnalyzer is a nonprofit organization dedicated to revolutionizing DNA analysis through AI-powered tools. It aims to democratize access to DNA analysis for a deeper understanding of human health and disease. The tool provides innovative AI-powered analysis and interpretive tools to empower geneticists, physicians, and researchers to gain deep insights into DNA sequences, revolutionizing how we understand human health and disease.

The IBM Analog Hardware Acceleration Kit is an open-source Python toolkit for exploring and using the capabilities of in-memory computing devices in the context of artificial intelligence. It consists of two main components: Pytorch integration and Analog devices simulator. The Pytorch integration provides a series of primitives and features that allow using the toolkit within PyTorch, including analog neural network modules, analog training using torch training workflow, and analog inference using torch inference workflow. The Analog devices simulator is a high-performant (CUDA-capable) C++ simulator that allows for simulating a wide range of analog devices and crossbar configurations by using abstract functional models of material characteristics with adjustable parameters. Along with the two main components, the toolkit includes other functionalities such as a library of device presets, a module for executing high-level use cases, a utility to automatically convert a downloaded model to its equivalent Analog model, and integration with the AIHW Composer platform. The toolkit is currently in beta and under active development, and users are advised to be mindful of potential issues and keep an eye for improvements, new features, and bug fixes in upcoming versions.

LongRoPE is a method to extend the context window of large language models (LLMs) beyond 2 million tokens. It identifies and exploits non-uniformities in positional embeddings to enable 8x context extension without fine-tuning. The method utilizes a progressive extension strategy with 256k fine-tuning to reach a 2048k context. It adjusts embeddings for shorter contexts to maintain performance within the original window size. LongRoPE has been shown to be effective in maintaining performance across various tasks from 4k to 2048k context lengths.

AIKA (Artificial Intelligence for Knowledge Acquisition) is a new type of artificial neural network designed to mimic the behavior of a biological brain more closely and bridge the gap to classical AI. The network conceptually separates activations from neurons, creating two separate graphs to represent acquired knowledge and inferred information. It uses different types of neurons and synapses to propagate activation values, binding signals, causal relations, and training gradients. The network structure allows for flexible topology and supports the gradual population of neurons and synapses during training.

This repository provides training on large language models (LLMs) for genomics, including lecture notes and lab classes covering pretraining, finetuning, zeroshot learning prediction of mutation effect, synthetic DNA sequence generation, and DNA sequence optimization.

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.