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SpeakerCodes | Papers | Intresting LinksJob Openings
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David Balcells
University of Oslo

Generative Machine Learning for Transition Metal Chemistry
tmQM and tmQM-L dataset and PL-MOGA genetic algorithm
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tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal Complexes | Journal of Chemical Information and Modeling
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Directional Multiobjective Optimization of Metal Complexes at the Billion-Scale with the tmQMg-L Dataset and PL-MOGA Algorithm | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage
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Repository for the tmQMg-L dataset files.
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GitHub - hkneiding/PL-MOGA: Pareto Lighthouse Multiobjective Genetic Algorithm for the de novo design of transition metal complexes.
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Volker Deringer
University of Oxford

Data-driven interatomic potentials for inorganic materials chemistry
How to validate machine-learned interatomic potentials | The Journal of Chemical Physics | AIP Publishing
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GitHub - MorrowChem/how-to-validate-potentials: Some tutorial-style examples for validating machine-learned interatomic potentials
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Eva Zurek
University at Buffalo, SUNY

Machine Learned Interatomic Potentials for Binary Carbides Trained on the AFLOW Database
XtalOpt - Zurek Lab
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RandSpg: Generate Random Crystals with Specific Spacegroups
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Matthew Carbone
Brookhaven National Laboratory

Flexible formulation of value for experiment interpretation and design
GitHub - matthewcarbone/ScientificValueAgent: The Scientific Value Agent
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Richard Hennig
University of Florida

Accelerating Materials Discovery Through Deep Learning and Ultra-Fast Potentials
Ultra-fast force field
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UF3: a python library for generating ultra-fast interatomic potentials
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Fang Liu
Emory University

Machine learning aided chemical discovery in the solution phase
GitHub - Liu-group/AutoSolvate: Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules
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Chenru Duan
Microsoft

Diffusion models on sampling rare events in chemistry
GitHub - chenruduan/OAReactDiff: An object-aware diffusion model for generating chemical reactions
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Rose Cersonsky
University of Wisconsin-Madison

Data-driven approaches to chemical and materials science:the impact of data selection, representation, and interpretability
GitHub - scikit-learn-contrib/scikit-matter: A collection of scikit-learn compatible utilities that implement methods born out of the materials science and chemistry communities
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Will Bricker
University of New Mexico

Machine-learned electron densities of nucleic acids
Predicting accurate ab initio DNA electron densities with equivariant neural networks - ScienceDirect
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Kieron Burke
University of California, Irvine

Machine Learning Density Functionals
Machine learning and density functional theory | Nature Reviews Physics
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https://pubs.rsc.org/en/content/articlelanding/2024/cp/d4cp00878b
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Gabor Csanyi
University of Cambridge

Foundation models for materials chemistry
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Mario Barbatti
Aix Marseille University, CNRS, ICR

Machine Learning Nonadiabatic Dynamics
Newton-X package for non-adibatic dynamics + ML

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The Newton-X platform for surface hopping and nuclear ensembles
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Newton-X
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Puck van Gerwen
EPFL

EquiReact: Equivariant Neural Networks for Chemical Reactions
EquiReact model and datasets

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GitHub - lcmd-epfl/EquiReact
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Comprehensive exploration of graphically defined reaction spaces | Scientific Data
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High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions | Scientific Data
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Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions | Scientific Data
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Reaction-based machine learning representations for predicting the enantioselectivity of organocatalysts
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Y Z
University of Michigan

Unusual Dynamics of Tetrahedral Liquids Caused by the Competition between Dynamic Heterogeneity and Structural Heterogeneity
LiquidLib by Z Lab (z-laboratory.github.io)
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Julien Lam
CNRS


Exploiting constrained linear models for machine-learning interaction potentials
Physical LassoLars Interactions Potential
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GitHub - LAM-GROUP/PLIP: Linear Machine learning Interatomic Potential for atomistic simulations
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Dmitry Zubarev
IBM Research


Foundational Models for Chemical Discovery
MolFormer
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Large-scale chemical language representations capture molecular structure and properties | Nature Machine Intelligence
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GitHub - IBM/molformer
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Joshua Rackers
Genentech / Prescient Design

Building Physics into AI for Drug Discovery
Equivariant NNs
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e3nn
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19. Equivariant Neural Network for Predicting Trajectories
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Structure-based drug design by denoising voxel grids
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Sakib Matin
LANL

Machine Learning Potentials with long-range Coulomb interaction: Atomistic simulations of water
HIP-NN potential with tensor sensitivity
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GitHub - lanl/hippynn: python library for atomistic machine learning
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Lightweight and effective tensor sensitivity for atomistic neural networks | The Journal of Chemical Physics | AIP Publishing
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Chiho Kim
GATech / Matmerize, Inc.

Machine Learning-Aided Design of Biodegradable Polymers
Bioplastic design using multitask deep neural networks | Communications Materials
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PolymRize TM
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Daniel Schwalbe-Koda
UCLA


Unifying Views on the Extrapolation Power of Machine Learning Potentials and Materials Thermodynamics
dskoda/quests: Quick Uncertainty and Entropy via STructural Similarity (github.com)
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Rebecca Lindsey
University of Michigan, Ann Arbor

Explaining Performance of Physics-Informed Machine-Learned Interatomic Models
ChIMES ML-IAP fitting (lsq), active learning (al), and calculator, including scripts for installation in LAMMPS
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GitHub - rk-lindsey/chimes_lsq: Tools to develop ChIMES parameter sets
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GitHub - rk-lindsey/al_driver: AI-driven framework for automated ChIMES model development
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GitHub - rk-lindsey/chimes_calculator: Tools to interface ChIMES with various external codes.
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Alexandre Tkatchenko
University of Luxembourg

Navigating Chemical Compound Space with Machine Learning
Institute for Pure & Applied Mathematics - IPAM (ucla.edu)
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QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules | Scientific Data
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“Freedom of design” in chemical compound space: towards rational in silico design of molecules with targeted quantum-mechanical properties
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[2309.00506] Enabling Inverse Design in Chemical Compound Space: Mapping Quantum Properties to Structures for Small Organic Molecules
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Nong Artrith
Debye Institute for Nanomaterials Science


Accelerated Sampling Strategies and Machine Learning Potentials for Modeling Non-Crystalline Energy Materials
atomisticnet/aenet-PyTorch: ænet-PyTorch: a GPU-supported implementation for machine learning atomic potentials training (github.com)
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GitHub - atomisticnet/aenet-lammps: Interface aenet with the LAMMPS molecular dynamics software (https://lammps.sandia.gov)
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Karel Berka
Palacky University Olomouc


MolMeDB - free database of molecules on membranes
Database of molecules on membrabes
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MolMeDB | MolMeDB (upol.cz)
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interactive session
Jason Hattrick-Simpers
University of Toronto

Tutorial on the use of LLMs in Science

LLM-Prop and LLM finetuning for materials prediction
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https://github.com/vertaix/LLM-Prop
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https://cohereai.notion.site/MRS-Fall-2023-DS04-Tutorial-Runbook-7ed8ca8fb2bf4e18937e6a119b63e3e5
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https://colab.research.google.com/drive/1Al-mweiY6fnxjHTZJGia_z7RPoKPvZfM?usp=sharing#scrollTo=gZnFnjGdyGbV
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https://vertaix.princeton.edu/
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[2310.14029] LLM-Prop: Predicting Physical And Electronic Properties Of Crystalline Solids From Their Text Descriptions
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Roberto Car
Princeton University

Deep potential models for equilibrium and near equilibrium processes
A deep potential model with long-range electrostatic interactions | The Journal of Chemical Physics | AIP Publishing
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3.14. Deep potential long-range (DPLR) — DeePMD-kit documentation
https://github.com/deepmodeling/deepmd-kit
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Alan Aspuru-Guzik
University of Toronto

Self-driving Labs
Self-driving labs, robotics for synthesis and lab chatbots
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On scientific understanding with artificial intelligence | Nature Reviews Physics
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The Matter Simulation (R)evolution | ACS Central Science
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Organa: A Robotic Assistant for Automated Chemistry Experimentation and Characterization
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[2402.05015] A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules?
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Pavlo Dral
Xiamen University

From fast potentials for dynamics to learning dynamics

TALK SLIDES
MLatom – AI-enhanced computational chemistry
http://mlatom.com/
Postdoc in method development for materials or molecular simulations
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https://xacs.xmu.edu.cn/docs/mlatom/
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Aditya Nandy
UCLA | University of Chicago

Leveraging Community Knowledge to Forge a Path Forward for Transition Metal Complex and Metal-Organic Framework Design
Generation of MOFs and metallorganic complexes
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hjkgrp/molSimplify: molSimplify code (github.com)
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Richard Messerly
LANL

Nanoreactor active learning: Discovering chemistry with a general reactive machine learning potential
Reactive ANI-1xnr potential: code/applications/data
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GitHub - atomistic-ml/ani-1xnr: Machine learning interatomic potential for condensed-phase reactive chemistry
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https://springernature.figshare.com/ndownloader/files/43190004
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Exploring the frontiers of condensed-phase chemistry with a general reactive machine learning potential
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Bakhtiyor Rasulev
North Dakota State University

Application of Mixture-type Descriptors in Machine Learning Modeling of Materials"
Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles | Nature Nanotechnology
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Development of QSAR Models on the Fouling-Release Performance of Silicone Oil-modified Siloxane Polyurethane Coatings | Polymer Science | ChemRxiv | Cambridge Open Engage
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Nina Andrejevic
Argonne National Laboratory

Advancing materials characterization through physics-guided machine learning
Welcome to e3nn! {#welcome} | e3nn
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Markus Reiher
ETH Zurich

Lifelong Machine Learning Potentials
Software for Chemical Interaction Networks - SCINE (ethz.ch)
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Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks | Journal of Chemical Theory and Computation (acs.org)
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Lifelong Machine Learning Potentials | Journal of Chemical Theory and Computation (acs.org)
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ReiherGroup/CoRe_optimizer: Continual Resilient (CoRe) Optimizer for PyTorch (github.com)
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Code/Data for Lifelong Machine Learning Potentials (zenodo.org)
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Roman Zubatyuk
Carnegie Mellon University

AIMNet2: Robust neural network potential for organic, element-organic molecules and chemical reactions
isayevlab/AIMNet2 (github.com)
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AIMNet2: A Neural Network Potential to Meet your Neutral, Charged, Organic, and Elemental-Organic Needs | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage
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Johannes Margraf
University of Bayreuth

Materials Discovery with Foundation Models
Foundation models — mace 0.1.0 documentation (mace-docs.readthedocs.io)
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TUM-DAML/gemnet_tf: GemNet model in TensorFlow, as proposed in "GemNet: Universal Directional Graph Neural Networks for Molecules" (NeurIPS 2021) (github.com)
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Matthias Rupp
Luxembourg Institute of Science and Technology (LIST)


Thermal transport via machine-learning potentials
Phys. Rev. B 108, L100302 (2023) - Heat flux for semilocal machine-learning potentials (aps.org)
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sirmarcel/gknet-archive: data and code for "heat flux for semi-local machine-learning potentials" (github.com)
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sirmarcel/glp: tools for graph-based machine-learning potentials in jax (github.com)
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uf3 - Ultra-Fast Force Fields · GitHub
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Tom Penfold
Newcastle Univeristy

Deep Neural Networks for X-ray Spectroscopy: Hero or Zero?
Codes and Datasets (penfoldgroup.co.uk)
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NNs for X-ray spectroscopy / xanesnet · GitLab
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Accurate, Affordable, and Generalisable Machine Learning Simulations of Transition Metal X-ray Absorption Spectra using the XANESNET Deep Neural Network | Theoretical and Computational Chemistry | ChemRxiv | Cambridge Open Engage
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Connor Coley
MIT


Molecular design and the intersection with synthesis
Closing the Execution Gap in Generative AI for Chemicals and Materials: Freeways or Safeguards · From Novel Chemicals to Opera (pubpub.org)
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Marivi Fernandez-Serra
Stony Brook University


Learning the exchange and correlation functional in DFT
semodi/neuralxc: Implementation of a machine learned density functional (github.com)
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semodi/libnxc: A library for using machine-learned exchange-correlation functionals for density-functional theory (github.com)
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David Yaron
Carnegie Mellon University


Quantum chemical Hamiltonians as flexible and interpretable model forms for machine learning
djyaron/DFTBML: Fitting DFTB Hamiltonians to data. (github.com)
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[2210.11682] Semiempirical Hamiltonians learned from data can have accuracy comparable to Density Functional Theory (arxiv.org)
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Treating Semiempirical Hamiltonians as Flexible Machine Learning Models Yields Accurate and Interpretable Results | Journal of Chemical Theory and Computation (acs.org)
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Jenna Pope
Pacific Northwest National Laboratory

Accelerating Atomic-scale Simulations of Molecules and Materials with Neural Network Potentials
[2312.07511] A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems (arxiv.org)
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exalearn/hydronet: HydroNet: Benchmark Tasks for Preserving Long-range Interactions and Structural Motifs in Predictive and Generative Models for Molecular Data, at the 34th Conference on Neural Information Processing Systems (NuerIPS), Workshop on Machine Learning and the Physical Sciences [https://arxiv.org/abs/2012.00131] (github.com)
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pnnl/Active-Sampling-for-Atomistic-Potentials: Active sampling for neural network potentials: Accelerated simulations of shear-induced deformation in Cu–Ni multilayers (github.com)
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pnnl/downstream_mol_gnn: Reducing Down(stream)time: Pretraining Molecular GNNs using Heterogeneous AI Accelerators (github.com)
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Jing Huang
Westlake University

DP/MM: a hybrid force field model for zinc-protein dynamics
JingHuangLab/openmm_deepmd_plugin (github.com)
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Marina Meila
University of Washington


Coordinates with physical meaning

sjkoelle/montlake: Montlake contains tools for geometric data analysis. It includes vector field group lasso and basis pursuit methods for parametric manifold learning. It also contains differentiable shape featurizations including interpoint distances, planar angles, and torsions from data positions for shape space analysis. (github.com)
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yuchaz/homology_emb (github.com)
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yuchaz/independent_coordinate_search: Repository for "Selecting the independent coordinates of manifolds with large aspect ratios" at NeurIPS'19 (github.com)
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megaman: Manifold Learning for Millions of Points — megaman 0.2 documentation (mmp2.github.io)
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Manifold Learning: What, How, and Why | Annual Reviews
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Manifold Learning 2.0: Explanations and Eigenflows - The Fields Institute Workshop on Manifold and Graph-based learning (washington.edu)
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Manifold Coordinates with Physical Meaning (jmlr.org)
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A tutorial on Manifold Learning for real data | Fields Institute for Research in Mathematical Sciences (utoronto.ca)
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Focus Program on Data Science, Approximation Theory, and Harmonic Analysis | Fields Institute for Research in Mathematical Sciences (utoronto.ca)
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