This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

This repository implements speculative sampling for large language model (LLM) decoding, utilizing two models - a target model and an approximation model. The approximation model generates token guesses, corrected by the target model, resulting in improved efficiency. It includes implementations of Google's and Deepmind's versions of speculative sampling, supporting models like llama-7B and llama-1B. The tool is designed for fast inference from transformers via speculative decoding.

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.

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.

This repository provides a Python implementation of a method that leverages pre-trained large language models to construct and utilize world models for model-based task planning. It includes scripts to generate domain models using natural language descriptions, correct domain models based on feedback, and support plan generation for tasks in different domains. The code has been refactored for better readability and includes tools for validating PDDL syntax and handling corrective feedback.

Inspect AI is a framework developed by the UK AI Safety Institute for evaluating large language models. It offers various built-in components for prompt engineering, tool usage, multi-turn dialog, and model graded evaluations. Users can extend Inspect by adding new elicitation and scoring techniques through additional Python packages. The tool aims to provide a comprehensive solution for assessing the performance and safety of language models.

OpenSSA is an open-source framework for creating efficient, domain-specific AI agents. It enables the development of Small Specialist Agents (SSAs) that solve complex problems in specific domains. SSAs tackle multi-step problems that require planning and reasoning beyond traditional language models. They apply OODA for deliberative reasoning (OODAR) and iterative, hierarchical task planning (HTP). This "System-2 Intelligence" breaks down complex tasks into manageable steps. SSAs make informed decisions based on domain-specific knowledge. With OpenSSA, users can create agents that process, generate, and reason about information, making them more effective and efficient in solving real-world challenges.

SUQL (Structured and Unstructured Query Language) is a tool that augments SQL with free text primitives for building chatbots that can interact with relational data sources containing both structured and unstructured information. It seamlessly integrates retrieval models, large language models (LLMs), and traditional SQL to provide a clean interface for hybrid data access. SUQL supports optimizations to minimize expensive LLM calls, scalability to large databases with PostgreSQL, and general SQL operations like JOINs and GROUP BYs.

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.

Marlin is a highly optimized FP16xINT4 matmul kernel designed for large language model (LLM) inference, offering close to ideal speedups up to batchsizes of 16-32 tokens. It is suitable for larger-scale serving, speculative decoding, and advanced multi-inference schemes like CoT-Majority. Marlin achieves optimal performance by utilizing various techniques and optimizations to fully leverage GPU resources, ensuring efficient computation and memory management.

pyLLMSearch is an advanced RAG system that offers a convenient question-answering system with a simple YAML-based configuration. It enables interaction with multiple collections of local documents, with improvements in document parsing, hybrid search, chat history, deep linking, re-ranking, customizable embeddings, and more. The package is designed to work with custom Large Language Models (LLMs) from OpenAI or installed locally. It supports various document formats, incremental embedding updates, dense and sparse embeddings, multiple embedding models, 'Retrieve and Re-rank' strategy, HyDE (Hypothetical Document Embeddings), multi-querying, chat history, and interaction with embedded documents using different models. It also offers simple CLI and web interfaces, deep linking, offline response saving, and an experimental API.

AudioSeal is a method for speech localized watermarking, designed with state-of-the-art robustness and detector speed. It jointly trains a generator to embed a watermark in audio and a detector to detect watermarked fragments in longer audios, even in the presence of editing. The tool achieves top-notch detection performance at the sample level, generates minimal alteration of signal quality, and is robust to various audio editing types. With a fast, single-pass detector, AudioSeal surpasses existing models in speed, making it ideal for large-scale and real-time applications.

The AiTLAS toolbox (Artificial Intelligence Toolbox for Earth Observation) includes state-of-the-art machine learning methods for exploratory and predictive analysis of satellite imagery as well as a repository of AI-ready Earth Observation (EO) datasets. It can be easily applied for a variety of Earth Observation tasks, such as land use and cover classification, crop type prediction, localization of specific objects (semantic segmentation), etc. The main goal of AiTLAS is to facilitate better usability and adoption of novel AI methods (and models) by EO experts, while offering easy access and standardized format of EO datasets to AI experts which allows benchmarking of various existing and novel AI methods tailored for EO data.

LLM-Viewer is a tool for visualizing Language and Learning Models (LLMs) and analyzing performance on different hardware platforms. It enables network-wise analysis, considering factors such as peak memory consumption and total inference time cost. With LLM-Viewer, users can gain valuable insights into LLM inference and performance optimization. The tool can be used in a web browser or as a command line interface (CLI) for easy configuration and visualization. The ongoing project aims to enhance features like showing tensor shapes, expanding hardware platform compatibility, and supporting more LLMs with manual model graph configuration.

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.

JAX AI Stack is a suite of libraries built around the JAX Python package for array-oriented computation and program transformation. It provides a growing ecosystem of packages for specialized numerical computing across various domains, encouraging modularity and innovation in domain-specific libraries. The stack includes core packages like JAX, flax for building neural networks, ml_dtypes for NumPy dtype extensions, optax for gradient processing and optimization, and orbax for checkpointing and persistence utilities. Optional packages like grain data loader and tensorflow are also available for installation.

This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

The 'llm-past-tense' repository contains code related to the research paper 'Does Refusal Training in LLMs Generalize to the Past Tense?' by Maksym Andriushchenko and Nicolas Flammarion. It explores the generalization of refusal training in large language models (LLMs) to the past tense. The code includes experiments and examples for running different models and requests related to the study. Users can cite the work if found useful in their research, and the codebase is released under the MIT License.

This repository contains assets related to AI/ML workloads on Google Kubernetes Engine (GKE). Run optimized AI/ML workloads with Google Kubernetes Engine (GKE) platform orchestration capabilities. A robust AI/ML platform considers the following layers: Infrastructure orchestration that support GPUs and TPUs for training and serving workloads at scale Flexible integration with distributed computing and data processing frameworks Support for multiple teams on the same infrastructure to maximize utilization of resources

Ray is a unified framework for scaling AI and Python applications. It consists of a core distributed runtime and a set of AI libraries for simplifying ML compute, including Data, Train, Tune, RLlib, and Serve. Ray runs on any machine, cluster, cloud provider, and Kubernetes, and features a growing ecosystem of community integrations. With Ray, you can seamlessly scale the same code from a laptop to a cluster, making it easy to meet the compute-intensive demands of modern ML workloads.

Labelbox is a data-centric AI platform for enterprises to develop, optimize, and use AI to solve problems and power new products and services. Enterprises use Labelbox to curate data, generate high-quality human feedback data for computer vision and LLMs, evaluate model performance, and automate tasks by combining AI and human-centric workflows. The academic & research community uses Labelbox for cutting-edge AI research.

Deep Java Library (DJL) is an open-source, high-level, engine-agnostic Java framework for deep learning. It is designed to be easy to get started with and simple to use for Java developers. DJL provides a native Java development experience and allows users to integrate machine learning and deep learning models with their Java applications. The framework is deep learning engine agnostic, enabling users to switch engines at any point for optimal performance. DJL's ergonomic API interface guides users with best practices to accomplish deep learning tasks, such as running inference and training neural networks.

Mojo is a new programming language that bridges the gap between research and production by combining Python syntax and ecosystem with systems programming and metaprogramming features. Mojo is still young, but it is designed to become a superset of Python over time.

TT-NN is a python & C++ Neural Network OP library. It provides a low-level programming model, TT-Metalium, enabling kernel development for Tenstorrent hardware.

The Open MatSci ML Toolkit is a flexible framework for machine learning in materials science. It provides a unified interface to a variety of materials science datasets, as well as a set of tools for data preprocessing, model training, and evaluation. The toolkit is designed to be easy to use for both beginners and experienced researchers, and it can be used to train models for a wide range of tasks, including property prediction, materials discovery, and materials design.

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.

AlphaFold3 is an implementation of the Alpha Fold 3 model in PyTorch for accurate structure prediction of biomolecular interactions. It includes modules for genetic diffusion and full model examples for forward pass computations. The tool allows users to generate random pair and single representations, operate on atomic coordinates, and perform structure predictions based on input tensors. The implementation also provides functionalities for training and evaluating the model.

This repository contains the code for the paper Fine-Tuned Language Models Generate Stable Inorganic Materials as Text. It demonstrates how finetuned LLMs can be used to generate stable materials, match or exceed the performance of domain specific models, mutate existing materials, and sample crystal structures conditioned on text descriptions. The method is distinct from CrystaLLM, which trains language models from scratch on CIF-formatted crystals.

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.

MD-Agent is a LLM-agent based toolset for Molecular Dynamics. It uses Langchain and a collection of tools to set up and execute molecular dynamics simulations, particularly in OpenMM. The tool assists in environment setup, installation, and usage by providing detailed steps. It also requires API keys for certain functionalities, such as OpenAI and paper-qa for literature searches. Contributions to the project are welcome, with a detailed Contributor's Guide available for interested individuals.

AIMNet2 Calculator is a package that integrates the AIMNet2 neural network potential into simulation workflows, providing fast and reliable energy, force, and property calculations for molecules with diverse elements. It excels at modeling various systems, offers flexible interfaces for popular simulation packages, and supports long-range interactions using DSF or Ewald summation Coulomb models. The tool is designed for accurate and versatile molecular simulations, suitable for large molecules and periodic calculations.

ADMET-AI is a platform for ADMET prediction using Chemprop-RDKit models trained on ADMET datasets from the Therapeutics Data Commons. It offers command line, Python API, and web server interfaces for making ADMET predictions on new molecules. The platform can be easily installed using pip and supports GPU acceleration. It also provides options for processing TDC data, plotting results, and hosting a web server. ADMET-AI is a machine learning platform for evaluating large-scale chemical libraries.