Best AI tools for< Computational Scientist >

Artificial Intelligence: Foundations of Computational Agents, 3rd edition by David L. Poole and Alan K. Mackworth, Cambridge University Press 2023, is a book about the science of artificial intelligence (AI). It presents artificial intelligence as the study of the design of intelligent computational agents. The book is structured as a textbook, but it is accessible to a wide audience of professionals and researchers. In the last decades we have witnessed the emergence of artificial intelligence as a serious science and engineering discipline. This book provides an accessible synthesis of the field aimed at undergraduate and graduate students. It provides a coherent vision of the foundations of the field as it is today. It aims to provide that synthesis as an integrated science, in terms of a multi-dimensional design space that has been partially explored. As with any science worth its salt, artificial intelligence has a coherent, formal theory and a rambunctious experimental wing. The book balances theory and experiment, showing how to link them intimately together. It develops the science of AI together with its engineering applications.

Proscia is a leading provider of digital pathology solutions for the modern laboratory. Its flagship product, Concentriq, is an enterprise pathology platform that enables anatomic pathology laboratories to achieve 100% digitization and deliver faster, more precise results. Proscia also offers a range of AI applications that can be used to automate tasks, improve diagnostic accuracy, and accelerate research. The company's mission is to perfect cancer diagnosis with intelligent software that changes the way the world practices pathology.

AIOZ Network is an AI-powered platform that focuses on Web3, AI, storage, and streaming services. It offers decentralized AI computation, fast and reliable storage solutions, and seamless video streaming for dApps within the network. AIOZ aims to empower a fast, secure, and decentralized future by providing a one-click integration of dApps on the AIOZ blockchain, supporting popular smart contract languages, and utilizing spare computing resources from a global community of nodes.

CCDS (Center for Computational & Data Sciences) is a research center at Independent University Bangladesh dedicated to artificial intelligence, data sciences, and computational science. The center has various wings focusing on AI, computational biology, physics, data science, human-computer interaction, and industry partnerships. CCDS explores the use of computation to understand nature and society, uncover hidden stories in data, and tackle complex challenges. The center collaborates with institutions like CERN and the Dunlap Institute for Astronomy and Astrophysics.

XtalPi is a world-leading technology company driven by artificial intelligence (AI) and robotics to innovate in the fields of life sciences and new materials. Founded in 2015 at the Massachusetts Institute of Technology (MIT), the company is committed to realizing digital and intelligent innovation in the fields of life sciences and new materials. Based on cutting-edge technologies and capabilities such as quantum physics, artificial intelligence, cloud computing, and large-scale experimental robot clusters, the company provides innovative technologies, services, and products for global industries such as biomedicine, chemicals, new energy, and new materials.

Iambic Therapeutics is a cutting-edge AI-driven drug discovery platform that tackles the most challenging design problems in drug discovery, addressing unmet patient need. Its physics-based AI algorithms drive a high-throughput experimental platform, converting new molecular designs to new biological insights each week. Iambic's platform optimizes target product profiles, exploring multiple profiles in parallel to ensure that molecules are designed to solve the right problems in disease biology. It also optimizes drug candidates, deeply exploring chemical space to reveal novel mechanisms of action and deliver diverse high-quality leads.

Owkin is a full-stack AI biotech company that integrates the best of human and artificial intelligence to deliver better drugs and diagnostics at scale. By understanding complex biology through AI, Owkin identifies new treatments, de-risks and accelerates clinical trials, and builds diagnostic tools to reduce time to impact for patients.

Variational AI is a company that uses generative AI to discover novel drug-like small molecules with optimized properties for defined targets. Their platform, Enki™, is the first commercially accessible foundation model for small molecules. It is designed to make generating novel molecule structures easy, with no data required. Users simply define their target product profile (TPP) and Enki does the rest. Enki is an ensemble of generative algorithms trained on decades worth of experimental data with proven results. The company was founded in September 2019 and is based in Vancouver, BC, Canada.

Bay Area AI is a technical AI meetup group based in San Francisco, CA, consisting of startup engineers, research scientists, computational linguists, mathematicians, and philosophers. The group focuses on understanding the meaning of text, reasoning, and human intent through technology to build new businesses and enhance the human experience in the modern connected world. They work on building systems with Machine Learning on top of Data Pipelines, exploring open-source solutions, and modeling human behavior in industry for practical results.

NLTK (Natural Language Toolkit) is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning, wrappers for industrial-strength NLP libraries, and an active discussion forum. Thanks to a hands-on guide introducing programming fundamentals alongside topics in computational linguistics, plus comprehensive API documentation, NLTK is suitable for linguists, engineers, students, educators, researchers, and industry users alike.

Cerebras is an AI tool that offers products and services related to AI supercomputers, cloud system processors, and applications for various industries. It provides high-performance computing solutions, including large language models, and caters to sectors such as health, energy, government, scientific computing, and financial services. Cerebras specializes in AI model services, offering state-of-the-art models and training services for tasks like multi-lingual chatbots and DNA sequence prediction. The platform also features the Cerebras Model Zoo, an open-source repository of AI models for developers and researchers.

Wolfram is a comprehensive platform that unifies algorithms, data, notebooks, linguistics, and deployment to provide a powerful computation platform. It offers a range of products and services for various industries, including education, engineering, science, and technology. Wolfram is known for its revolutionary knowledge-based programming language, Wolfram Language, and its flagship product Wolfram|Alpha, a computational knowledge engine. The platform also includes Wolfram Cloud for cloud-based services, Wolfram Engine for software implementation, and Wolfram Data Framework for real-world data analysis.

NeuReality is an AI-centric solution designed to democratize AI adoption by providing purpose-built tools for deploying and scaling inference workflows. Their innovative AI-centric architecture combines hardware and software components to optimize performance and scalability. The platform offers a one-stop shop for AI inference, addressing barriers to AI adoption and streamlining computational processes. NeuReality's tools enable users to deploy, afford, use, and manage AI more efficiently, making AI easy and accessible for a wide range of applications.

Altair is a global leader in computational intelligence, offering software and cloud solutions in simulation, HPC, data analytics, and AI. The platform provides advanced technology for accelerating AI adoption, powering engineering processes, and enabling sustainability solutions across various industries. Altair's products and platforms cater to diverse sectors such as aerospace, automotive, healthcare, and more, with a focus on digital twin technology, generative AI, and cloud computing. The company also hosts events, webinars, and training programs to support users in leveraging their tools effectively.

Wolfram|Alpha is a computational knowledge engine that answers questions using data, algorithms, and artificial intelligence. It can perform calculations, generate graphs, and provide information on a wide range of topics, including mathematics, science, history, and culture. Wolfram|Alpha is used by students, researchers, and professionals around the world to solve problems, learn new things, and make informed decisions.

The Institute for Protein Design is a research institute at the University of Washington that uses computational design to create new proteins that solve modern challenges in medicine, technology, and sustainability. The institute's research focuses on developing new protein therapeutics, vaccines, drug delivery systems, biological devices, self-assembling nanomaterials, and bioactive peptides. The institute also has a strong commitment to responsible AI development and has developed a set of principles to guide its use of AI in research.

Altera is an applied research lab focused on building digital human beings with fundamental human qualities. Led by Dr. Robert Yang, the team consists of computational neuroscientists, physics olympiads, and engineers from prestigious institutions. Their mission is to create digital beings that enhance human-to-human interactions, offering empathy, fun, friendship, and productivity at an unprecedented scale. Leveraging a state-of-the-art Composite Architecture inspired by the brain, Altera aims to develop agents with empathy, memory, and social norms. Starting with products in games, Altera plans to expand into multi-agent simulations and physical embodiment of digital intelligence, aspiring to become the most consequential technology company in the world.

Allchemy is a resource-aware AI platform for drug discovery. It combines state-of-the-art computational synthesis with AI algorithms to predict molecular properties. Within minutes, Allchemy creates thousands of synthesizable lead candidates meeting user-defined profiles of drug-likeness, affinity towards specific proteins, toxicity, and a range of other physical-chemical measures. Allchemy encompasses the entire resource-to-drug design process and has been used in academic, corporate and classified environments worldwide to: Design synthesizable leads targeting specific proteins Evolve scaffolds similar to desired drugs Design “circular” drug syntheses from renewable materials Interface with and instruct automated synthesis platforms and optimize pilot-scale processes Operate “iterative synthesis” schemes Predict side reactions and create forensic “synthetic signatures” of hazardous/toxic molecules Design synthetic degradation and recovery cycles for various types of feedstocks and functional target molecules

Sacred is a tool to configure, organize, log and reproduce computational experiments. It is designed to introduce only minimal overhead, while encouraging modularity and configurability of experiments. The ability to conveniently make experiments configurable is at the heart of Sacred. If the parameters of an experiment are exposed in this way, it will help you to: keep track of all the parameters of your experiment easily run your experiment for different settings save configurations for individual runs in files or a database reproduce your results In Sacred we achieve this through the following main mechanisms: Config Scopes are functions with a @ex.config decorator, that turn all local variables into configuration entries. This helps to set up your configuration really easily. Those entries can then be used in captured functions via dependency injection. That way the system takes care of passing parameters around for you, which makes using your config values really easy. The command-line interface can be used to change the parameters, which makes it really easy to run your experiment with modified parameters. Observers log every information about your experiment and the configuration you used, and saves them for example to a Database. This helps to keep track of all your experiments. Automatic seeding helps controlling the randomness in your experiments, such that they stay reproducible.

Julius AI is an advanced AI data analyst tool that allows users to analyze data with computational AI, chat with files to get expert-level insights, create sleek data visualizations, perform modeling and predictive forecasting, solve math, physics, and chemistry problems, generate polished analyses and summaries, save time by automating data work, and unlock statistical modeling without complexity. It offers features like generating visualizations, asking data questions, effortless cleaning, instant data export, creating animations, and supercharging data analysis. Julius AI is loved by over 1,200,000 users worldwide and is designed to help knowledge workers make the most out of their data.

AiiDA (www.aiida.net) is a workflow manager for computational science with a strong focus on provenance, performance and extensibility. **Features** * **Workflows:** Write complex, auto-documenting workflows in python, linked to arbitrary executables on local and remote computers. The event-based workflow engine supports tens of thousands of processes per hour with full checkpointing. * **Data provenance:** Automatically track inputs, outputs & metadata of all calculations in a provenance graph for full reproducibility. Perform fast queries on graphs containing millions of nodes. * **HPC interface:** Move your calculations to a different computer by changing one line of code. AiiDA is compatible with schedulers like SLURM, PBS Pro, torque, SGE or LSF out of the box. * **Plugin interface:** Extend AiiDA with plugins for new simulation codes (input generation & parsing), data types, schedulers, transport modes and more. * **Open Science:** Export subsets of your provenance graph and share them with peers or make them available online for everyone on the Materials Cloud. * **Open source:** AiiDA is released under the MIT open source license

SciMLBenchmarks.jl holds webpages, pdfs, and notebooks showing the benchmarks for the SciML Scientific Machine Learning Software ecosystem, including: * Benchmarks of equation solver implementations * Speed and robustness comparisons of methods for parameter estimation / inverse problems * Training universal differential equations (and subsets like neural ODEs) * Training of physics-informed neural networks (PINNs) * Surrogate comparisons, including radial basis functions, neural operators (DeepONets, Fourier Neural Operators), and more The SciML Bench suite is made to be a comprehensive open source benchmark from the ground up, covering the methods of computational science and scientific computing all the way to AI for science.

This repository contains a student training series focusing on AI-driven science on supercomputers. It covers topics such as ALCF systems overview, AI on supercomputers, neural networks, LLMs, and parallel training techniques. The content is organized into subdirectories with prefixed indexes for easy navigation. The series aims to provide hands-on experience and knowledge in utilizing AI on supercomputers for scientific research.

2025-AI-College-Jobs is a repository containing a comprehensive list of AI/ML & Data Science jobs suitable for college students seeking internships or new graduate positions. The repository is regularly updated with positions posted within the last 120 days, featuring opportunities from various companies in the USA and internationally. The list includes positions in areas such as research scientist internships, quantitative research analyst roles, and other data science-related positions. The repository aims to provide a valuable resource for students looking to kickstart their careers in the field of artificial intelligence and machine learning.

The 'machine-learning-research' repository is a comprehensive collection of resources related to mathematics, machine learning, deep learning, artificial intelligence, data science, and various scientific fields. It includes materials such as courses, tutorials, books, podcasts, communities, online courses, papers, and dissertations. The repository covers topics ranging from fundamental math skills to advanced machine learning concepts, with a focus on applications in healthcare, genetics, computational biology, precision health, and AI in science. It serves as a valuable resource for individuals interested in learning and researching in the fields of machine learning and related disciplines.

The LLM course is divided into three parts: 1. 🧩 **LLM Fundamentals** covers essential knowledge about mathematics, Python, and neural networks. 2. 🧑‍🔬 **The LLM Scientist** focuses on building the best possible LLMs using the latest techniques. 3. 👷 **The LLM Engineer** focuses on creating LLM-based applications and deploying them. For an interactive version of this course, I created two **LLM assistants** that will answer questions and test your knowledge in a personalized way: * 🤗 **HuggingChat Assistant**: Free version using Mixtral-8x7B. * 🤖 **ChatGPT Assistant**: Requires a premium account. ## 📝 Notebooks A list of notebooks and articles related to large language models. ### Tools | Notebook | Description | Notebook | |----------|-------------|----------| | 🧐 LLM AutoEval | Automatically evaluate your LLMs using RunPod |  | | 🥱 LazyMergekit | Easily merge models using MergeKit in one click. |  | | 🦎 LazyAxolotl | Fine-tune models in the cloud using Axolotl in one click. |  | | ⚡ AutoQuant | Quantize LLMs in GGUF, GPTQ, EXL2, AWQ, and HQQ formats in one click. |  | | 🌳 Model Family Tree | Visualize the family tree of merged models. |  | | 🚀 ZeroSpace | Automatically create a Gradio chat interface using a free ZeroGPU. |  |

The Expected Parrot Domain-Specific Language (EDSL) package enables users to conduct computational social science and market research with AI. It facilitates designing surveys and experiments, simulating responses using large language models, and performing data labeling and other research tasks. EDSL includes built-in methods for analyzing, visualizing, and sharing research results. It is compatible with Python 3.9 - 3.11 and requires API keys for LLMs stored in a `.env` file.

Pipeline is a Python library designed for constructing computational flows for AI/ML models. It supports both development and production environments, offering capabilities for inference, training, and finetuning. The library serves as an interface to Mystic, enabling the execution of pipelines at scale and on enterprise GPUs. Users can also utilize this SDK with Pipeline Core on a private hosted cluster. The syntax for defining AI/ML pipelines is reminiscent of sessions in Tensorflow v1 and Flows in Prefect.

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.

EZKL is a library and command-line tool for doing inference for deep learning models and other computational graphs in a zk-snark (ZKML). It enables the following workflow: 1. Define a computational graph, for instance a neural network (but really any arbitrary set of operations), as you would normally in pytorch or tensorflow. 2. Export the final graph of operations as an .onnx file and some sample inputs to a .json file. 3. Point ezkl to the .onnx and .json files to generate a ZK-SNARK circuit with which you can prove statements such as: > "I ran this publicly available neural network on some private data and it produced this output" > "I ran my private neural network on some public data and it produced this output" > "I correctly ran this publicly available neural network on some public data and it produced this output" In the backend we use the collaboratively-developed Halo2 as a proof system. The generated proofs can then be verified with much less computational resources, including on-chain (with the Ethereum Virtual Machine), in a browser, or on a device.

PEFT (Parameter-Efficient Fine-Tuning) is a collection of state-of-the-art methods that enable efficient adaptation of large pretrained models to various downstream applications. By only fine-tuning a small number of extra model parameters instead of all the model's parameters, PEFT significantly decreases the computational and storage costs while achieving performance comparable to fully fine-tuned models.

This repository contains Jupyter-based tutorials for NLP, ML, AI in Python for classes in Computational Linguistics, Natural Language Processing (NLP), Machine Learning (ML), and Artificial Intelligence (AI) at Indiana University.

PyTensor is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. It provides the computational backend for `PyMC `__. PyTensor is a fork of `Aesara `__, which is a fork of `Theano `__. PyTensor maintains a static graph which can be modified in-place to allow for advanced optimizations. Contrary to PyTorch and TensorFlow, PyTensor maintains a static graph which can be modified in-place to allow for advanced optimizations.

HippoRAG is a novel retrieval augmented generation (RAG) framework inspired by the neurobiology of human long-term memory that enables Large Language Models (LLMs) to continuously integrate knowledge across external documents. It provides RAG systems with capabilities that usually require a costly and high-latency iterative LLM pipeline for only a fraction of the computational cost. The tool facilitates setting up retrieval corpus, indexing, and retrieval processes for LLMs, offering flexibility in choosing different online LLM APIs or offline LLM deployments through LangChain integration. Users can run retrieval on pre-defined queries or integrate directly with the HippoRAG API. The tool also supports reproducibility of experiments and provides data, baselines, and hyperparameter tuning scripts for research purposes.

Pai-Megatron-Patch is a deep learning training toolkit built for developers to train and predict LLMs & VLMs by using Megatron framework easily. With the continuous development of LLMs, the model structure and scale are rapidly evolving. Although these models can be conveniently manufactured using Transformers or DeepSpeed training framework, the training efficiency is comparably low. This phenomenon becomes even severer when the model scale exceeds 10 billion. The primary objective of Pai-Megatron-Patch is to effectively utilize the computational power of GPUs for LLM. This tool allows convenient training of commonly used LLM with all the accelerating techniques provided by Megatron-LM.

The Beta Machine Learning Toolkit is a package containing various algorithms and utilities for implementing machine learning workflows in multiple languages, including Julia, Python, and R. It offers a range of supervised and unsupervised models, data transformers, and assessment tools. The models are implemented entirely in Julia and are not wrappers for third-party models. Users can easily contribute new models or request implementations. The focus is on user-friendliness rather than computational efficiency, making it suitable for educational and research purposes.

Superlinked is a compute framework for information retrieval and feature engineering systems, focusing on converting complex data into vector embeddings for RAG, Search, RecSys, and Analytics stack integration. It enables custom model performance in machine learning with pre-trained model convenience. The tool allows users to build multimodal vectors, define weights at query time, and avoid postprocessing & rerank requirements. Users can explore the computational model through simple scripts and python notebooks, with a future release planned for production usage with built-in data infra and vector database integrations.

AI-resources is a repository containing links to various resources for learning Artificial Intelligence. It includes video lectures, courses, tutorials, and open-source libraries related to deep learning, reinforcement learning, machine learning, and more. The repository categorizes resources for beginners, average users, and advanced users/researchers, providing a comprehensive collection of materials to enhance knowledge and skills in AI.

ReproModel is an open-source toolbox designed to boost AI research efficiency by enabling researchers to reproduce, compare, train, and test AI models faster. It provides standardized models, dataloaders, and processing procedures, allowing researchers to focus on new datasets and model development. With a no-code solution, users can access benchmark and SOTA models and datasets, utilize training visualizations, extract code for publication, and leverage an LLM-powered automated methodology description writer. The toolbox helps researchers modularize development, compare pipeline performance reproducibly, and reduce time for model development, computation, and writing. Future versions aim to facilitate building upon state-of-the-art research by loading previously published study IDs with verified code, experiments, and results stored in the system.

InterpretML is an open-source package that incorporates state-of-the-art machine learning interpretability techniques under one roof. With this package, you can train interpretable glassbox models and explain blackbox systems. InterpretML helps you understand your model's global behavior, or understand the reasons behind individual predictions. Interpretability is essential for: - Model debugging - Why did my model make this mistake? - Feature Engineering - How can I improve my model? - Detecting fairness issues - Does my model discriminate? - Human-AI cooperation - How can I understand and trust the model's decisions? - Regulatory compliance - Does my model satisfy legal requirements? - High-risk applications - Healthcare, finance, judicial, ...

Expert in generating and explaining mathematical, chemical, and computational formulas.

A digital homage to honor Stephen Wolfram's impact on computational science and technology and to celebrate his dedication to public education, powered by Stephen Wolfram's wealth of public presentations, writings, and live streams.

Assists in evaluating protein engineering tools.

Skilled in Python, Linux, R, and more.

Expert in Marian NMT models and training

AI protein design assistant

大型语言模型的学习和训练指导专家

Formal OpenMC Python API and debugging expert.

Blends academic insights & accessible explanations on P vs NP, drawing from Lance Fortnow's works.

Advises on Bioconda recipes, following community guidelines

Advanced AI for complex computations and data analysis.

💡 Inventor of languages

A playful CFD advisor

Expert in OpenFOAM for CFD queries

Expert in GH-Python scripting & Grasshopper components

A interactive chatbot