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Apr 1

On the Existence of Simpler Machine Learning Models

It is almost always easier to find an accurate-but-complex model than an accurate-yet-simple model. Finding optimal, sparse, accurate models of various forms (linear models with integer coefficients, decision sets, rule lists, decision trees) is generally NP-hard. We often do not know whether the search for a simpler model will be worthwhile, and thus we do not go to the trouble of searching for one. In this work, we ask an important practical question: can accurate-yet-simple models be proven to exist, or shown likely to exist, before explicitly searching for them? We hypothesize that there is an important reason that simple-yet-accurate models often do exist. This hypothesis is that the size of the Rashomon set is often large, where the Rashomon set is the set of almost-equally-accurate models from a function class. If the Rashomon set is large, it contains numerous accurate models, and perhaps at least one of them is the simple model we desire. In this work, we formally present the Rashomon ratio as a new gauge of simplicity for a learning problem, depending on a function class and a data set. The Rashomon ratio is the ratio of the volume of the set of accurate models to the volume of the hypothesis space, and it is different from standard complexity measures from statistical learning theory. Insight from studying the Rashomon ratio provides an easy way to check whether a simpler model might exist for a problem before finding it, namely whether several different machine learning methods achieve similar performance on the data. In that sense, the Rashomon ratio is a powerful tool for understanding why and when an accurate-yet-simple model might exist. If, as we hypothesize in this work, many real-world data sets admit large Rashomon sets, the implications are vast: it means that simple or interpretable models may often be used for high-stakes decisions without losing accuracy.

  • 3 authors
·
Aug 5, 2019

Scaling Limits of Wide Neural Networks with Weight Sharing: Gaussian Process Behavior, Gradient Independence, and Neural Tangent Kernel Derivation

Several recent trends in machine learning theory and practice, from the design of state-of-the-art Gaussian Process to the convergence analysis of deep neural nets (DNNs) under stochastic gradient descent (SGD), have found it fruitful to study wide random neural networks. Central to these approaches are certain scaling limits of such networks. We unify these results by introducing a notion of a straightline tensor program that can express most neural network computations, and we characterize its scaling limit when its tensors are large and randomized. From our framework follows (1) the convergence of random neural networks to Gaussian processes for architectures such as recurrent neural networks, convolutional neural networks, residual networks, attention, and any combination thereof, with or without batch normalization; (2) conditions under which the gradient independence assumption -- that weights in backpropagation can be assumed to be independent from weights in the forward pass -- leads to correct computation of gradient dynamics, and corrections when it does not; (3) the convergence of the Neural Tangent Kernel, a recently proposed kernel used to predict training dynamics of neural networks under gradient descent, at initialization for all architectures in (1) without batch normalization. Mathematically, our framework is general enough to rederive classical random matrix results such as the semicircle and the Marchenko-Pastur laws, as well as recent results in neural network Jacobian singular values. We hope our work opens a way toward design of even stronger Gaussian Processes, initialization schemes to avoid gradient explosion/vanishing, and deeper understanding of SGD dynamics in modern architectures.

  • 1 authors
·
Feb 13, 2019

Maximizing Efficiency of Dataset Compression for Machine Learning Potentials With Information Theory

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

  • 3 authors
·
Nov 13, 2025

Grad DFT: a software library for machine learning enhanced density functional theory

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

  • 5 authors
·
Sep 22, 2023

Order Theory in the Context of Machine Learning

The paper ``Tropical Geometry of Deep Neural Networks'' by L. Zhang et al. introduces an equivalence between integer-valued neural networks (IVNN) with ReLU_{t} and tropical rational functions, which come with a map to polytopes. Here, IVNN refers to a network with integer weights but real biases, and ReLU_{t} is defined as ReLU_{t}(x)=max(x,t) for tinRcup{-infty}. For every poset with n points, there exists a corresponding order polytope, i.e., a convex polytope in the unit cube [0,1]^n whose coordinates obey the inequalities of the poset. We study neural networks whose associated polytope is an order polytope. We then explain how posets with four points induce neural networks that can be interpreted as 2times 2 convolutional filters. These poset filters can be added to any neural network, not only IVNN. Similarly to maxout, poset pooling filters update the weights of the neural network during backpropagation with more precision than average pooling, max pooling, or mixed pooling, without the need to train extra parameters. We report experiments that support our statements. We also define the structure of algebra over the operad of posets on poset neural networks and tropical polynomials. This formalism allows us to study the composition of poset neural network arquitectures and the effect on their corresponding Newton polytopes, via the introduction of the generalization of two operations on polytopes: the Minkowski sum and the convex envelope.

  • 5 authors
·
Dec 8, 2024

Leslie Population Models in Predator-prey and Competitive populations: theory and applications by machine learning

We introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

  • 5 authors
·
Dec 20, 2024

Deep Learning, Machine Learning, Advancing Big Data Analytics and Management

Advancements in artificial intelligence, machine learning, and deep learning have catalyzed the transformation of big data analytics and management into pivotal domains for research and application. This work explores the theoretical foundations, methodological advancements, and practical implementations of these technologies, emphasizing their role in uncovering actionable insights from massive, high-dimensional datasets. The study presents a systematic overview of data preprocessing techniques, including data cleaning, normalization, integration, and dimensionality reduction, to prepare raw data for analysis. Core analytics methodologies such as classification, clustering, regression, and anomaly detection are examined, with a focus on algorithmic innovation and scalability. Furthermore, the text delves into state-of-the-art frameworks for data mining and predictive modeling, highlighting the role of neural networks, support vector machines, and ensemble methods in tackling complex analytical challenges. Special emphasis is placed on the convergence of big data with distributed computing paradigms, including cloud and edge computing, to address challenges in storage, computation, and real-time analytics. The integration of ethical considerations, including data privacy and compliance with global standards, ensures a holistic perspective on data management. Practical applications across healthcare, finance, marketing, and policy-making illustrate the real-world impact of these technologies. Through comprehensive case studies and Python-based implementations, this work equips researchers, practitioners, and data enthusiasts with the tools to navigate the complexities of modern data analytics. It bridges the gap between theory and practice, fostering the development of innovative solutions for managing and leveraging data in the era of artificial intelligence.

  • 26 authors
·
Dec 3, 2024

Introduction to Machine Learning

This book introduces the mathematical foundations and techniques that lead to the development and analysis of many of the algorithms that are used in machine learning. It starts with an introductory chapter that describes notation used throughout the book and serve at a reminder of basic concepts in calculus, linear algebra and probability and also introduces some measure theoretic terminology, which can be used as a reading guide for the sections that use these tools. The introductory chapters also provide background material on matrix analysis and optimization. The latter chapter provides theoretical support to many algorithms that are used in the book, including stochastic gradient descent, proximal methods, etc. After discussing basic concepts for statistical prediction, the book includes an introduction to reproducing kernel theory and Hilbert space techniques, which are used in many places, before addressing the description of various algorithms for supervised statistical learning, including linear methods, support vector machines, decision trees, boosting, or neural networks. The subject then switches to generative methods, starting with a chapter that presents sampling methods and an introduction to the theory of Markov chains. The following chapter describe the theory of graphical models, an introduction to variational methods for models with latent variables, and to deep-learning based generative models. The next chapters focus on unsupervised learning methods, for clustering, factor analysis and manifold learning. The final chapter of the book is theory-oriented and discusses concentration inequalities and generalization bounds.

  • 1 authors
·
Sep 4, 2024

More is Better in Modern Machine Learning: when Infinite Overparameterization is Optimal and Overfitting is Obligatory

In our era of enormous neural networks, empirical progress has been driven by the philosophy that more is better. Recent deep learning practice has found repeatedly that larger model size, more data, and more computation (resulting in lower training loss) improves performance. In this paper, we give theoretical backing to these empirical observations by showing that these three properties hold in random feature (RF) regression, a class of models equivalent to shallow networks with only the last layer trained. Concretely, we first show that the test risk of RF regression decreases monotonically with both the number of features and the number of samples, provided the ridge penalty is tuned optimally. In particular, this implies that infinite width RF architectures are preferable to those of any finite width. We then proceed to demonstrate that, for a large class of tasks characterized by powerlaw eigenstructure, training to near-zero training loss is obligatory: near-optimal performance can only be achieved when the training error is much smaller than the test error. Grounding our theory in real-world data, we find empirically that standard computer vision tasks with convolutional neural tangent kernels clearly fall into this class. Taken together, our results tell a simple, testable story of the benefits of overparameterization, overfitting, and more data in random feature models.

  • 4 authors
·
Nov 24, 2023

A theory of representation learning gives a deep generalisation of kernel methods

The successes of modern deep machine learning methods are founded on their ability to transform inputs across multiple layers to build good high-level representations. It is therefore critical to understand this process of representation learning. However, standard theoretical approaches (formally NNGPs) involving infinite width limits eliminate representation learning. We therefore develop a new infinite width limit, the Bayesian representation learning limit, that exhibits representation learning mirroring that in finite-width models, yet at the same time, retains some of the simplicity of standard infinite-width limits. In particular, we show that Deep Gaussian processes (DGPs) in the Bayesian representation learning limit have exactly multivariate Gaussian posteriors, and the posterior covariances can be obtained by optimizing an interpretable objective combining a log-likelihood to improve performance with a series of KL-divergences which keep the posteriors close to the prior. We confirm these results experimentally in wide but finite DGPs. Next, we introduce the possibility of using this limit and objective as a flexible, deep generalisation of kernel methods, that we call deep kernel machines (DKMs). Like most naive kernel methods, DKMs scale cubically in the number of datapoints. We therefore use methods from the Gaussian process inducing point literature to develop a sparse DKM that scales linearly in the number of datapoints. Finally, we extend these approaches to NNs (which have non-Gaussian posteriors) in the Appendices.

  • 6 authors
·
Aug 30, 2021

Accelerating the Search for Superconductors Using Machine Learning

Prediction of critical temperature (T_c) of a superconductor remains a significant challenge in condensed matter physics. While the BCS theory explains superconductivity in conventional superconductors, there is no framework to predict T_c of unconventional, higher T_{c} superconductors. Quantum Structure Diagrams (QSD) were successful in establishing structure-property relationship for superconductors, quasicrystals, and ferroelectric materials starting from chemical composition. Building on the QSD ideas, we demonstrate that the principal component analysis of superconductivity data uncovers the clustering of various classes of superconductors. We use machine learning analysis and cleaned databases of superconductors to develop predictive models of T_c of a superconductor using its chemical composition. Earlier studies relied on datasets with inconsistencies, leading to suboptimal predictions. To address this, we introduce a data-cleaning workflow to enhance the statistical quality of superconducting databases by eliminating redundancies and resolving inconsistencies. With this improvised database, we apply a supervised machine learning framework and develop a Random Forest model to predict superconductivity and T_c as a function of descriptors motivated from Quantum Structure Diagrams. We demonstrate that this model generalizes effectively in reasonably accurate prediction of T_{c} of compounds outside the database. We further employ our model to systematically screen materials across materials databases as well as various chemically plausible combinations of elements and predict Tl_{5}Ba_{6}Ca_{6}Cu_{9}O_{29} to exhibit superconductivity with a T_{c} sim 105 K. Being based on the descriptors used in QSD's, our model bypasses structural information and predicts T_{c} merely from the chemical composition.

  • 2 authors
·
May 17, 2025

Machine Learning for Polaritonic Chemistry: Accessing chemical kinetics

Altering chemical reactivity and material structure in confined optical environments is on the rise, and yet, a conclusive understanding of the microscopic mechanisms remains elusive. This originates mostly from the fact that accurately predicting vibrational and reactive dynamics for soluted ensembles of realistic molecules is no small endeavor, and adding (collective) strong light-matter interaction does not simplify matters. Here, we establish a framework based on a combination of machine learning (ML) models, trained using density-functional theory calculations, and molecular dynamics to accelerate such simulations. We then apply this approach to evaluate strong coupling, changes in reaction rate constant, and their influence on enthalpy and entropy for the deprotection reaction of 1-phenyl-2-trimethylsilylacetylene, which has been studied previously both experimentally and using ab initio simulations. While we find qualitative agreement with critical experimental observations, especially with regard to the changes in kinetics, we also find differences in comparison with previous theoretical predictions. The features for which the ML-accelerated and ab initio simulations agree show the experimentally estimated kinetic behavior. Conflicting features indicate that a contribution of dynamic electronic polarization to the reaction process is more relevant then currently believed. Our work demonstrates the practical use of ML for polaritonic chemistry, discusses limitations of common approximations and paves the way for a more holistic description of polaritonic chemistry.

  • 4 authors
·
Nov 16, 2023

Machine learning for materials discovery: two-dimensional topological insulators

One of the main goals and challenges of materials discovery is to find the best candidates for each interest property or application. Machine learning rises in this context to efficiently optimize this search, exploring the immense materials space, consisting of simultaneously the atomic, compositional, and structural spaces. Topological insulators, presenting symmetry-protected metallic edge states, are a promising class of materials for different applications. However, further, development is limited by the scarcity of viable candidates. Here we present and discuss machine learning-accelerated strategies for searching the materials space for two-dimensional topological materials. We show the importance of detailed investigations of each machine learning component, leading to different results. Using recently created databases containing thousands of ab initio calculations of 2D materials, we train machine learning models capable of determining the electronic topology of materials, with an accuracy of over 90%. We can then generate and screen thousands of novel materials, efficiently predicting their topological character without the need for a priori structural knowledge. We discover 56 non-trivial materials, of which 17 novel insulating candidates for further investigation, for which we corroborate their topological properties with density functional theory calculations. This strategy is 10times more efficient than the trial-and-error approach while few orders of magnitude faster and is a proof of concept for guiding improved materials discovery search strategies.

  • 3 authors
·
Jul 14, 2021

Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

  • 2 authors
·
Mar 11, 2025 3

An Introduction to Electrocatalyst Design using Machine Learning for Renewable Energy Storage

Scalable and cost-effective solutions to renewable energy storage are essential to addressing the world's rising energy needs while reducing climate change. As we increase our reliance on renewable energy sources such as wind and solar, which produce intermittent power, storage is needed to transfer power from times of peak generation to peak demand. This may require the storage of power for hours, days, or months. One solution that offers the potential of scaling to nation-sized grids is the conversion of renewable energy to other fuels, such as hydrogen or methane. To be widely adopted, this process requires cost-effective solutions to running electrochemical reactions. An open challenge is finding low-cost electrocatalysts to drive these reactions at high rates. Through the use of quantum mechanical simulations (density functional theory), new catalyst structures can be tested and evaluated. Unfortunately, the high computational cost of these simulations limits the number of structures that may be tested. The use of machine learning may provide a method to efficiently approximate these calculations, leading to new approaches in finding effective electrocatalysts. In this paper, we provide an introduction to the challenges in finding suitable electrocatalysts, how machine learning may be applied to the problem, and the use of the Open Catalyst Project OC20 dataset for model training.

  • 17 authors
·
Oct 14, 2020

The CAMELS project: Cosmology and Astrophysics with MachinE Learning Simulations

We present the Cosmology and Astrophysics with MachinE Learning Simulations --CAMELS-- project. CAMELS is a suite of 4,233 cosmological simulations of (25~h^{-1}{rm Mpc})^3 volume each: 2,184 state-of-the-art (magneto-)hydrodynamic simulations run with the AREPO and GIZMO codes, employing the same baryonic subgrid physics as the IllustrisTNG and SIMBA simulations, and 2,049 N-body simulations. The goal of the CAMELS project is to provide theory predictions for different observables as a function of cosmology and astrophysics, and it is the largest suite of cosmological (magneto-)hydrodynamic simulations designed to train machine learning algorithms. CAMELS contains thousands of different cosmological and astrophysical models by way of varying Omega_m, sigma_8, and four parameters controlling stellar and AGN feedback, following the evolution of more than 100 billion particles and fluid elements over a combined volume of (400~h^{-1}{rm Mpc})^3. We describe the simulations in detail and characterize the large range of conditions represented in terms of the matter power spectrum, cosmic star formation rate density, galaxy stellar mass function, halo baryon fractions, and several galaxy scaling relations. We show that the IllustrisTNG and SIMBA suites produce roughly similar distributions of galaxy properties over the full parameter space but significantly different halo baryon fractions and baryonic effects on the matter power spectrum. This emphasizes the need for marginalizing over baryonic effects to extract the maximum amount of information from cosmological surveys. We illustrate the unique potential of CAMELS using several machine learning applications, including non-linear interpolation, parameter estimation, symbolic regression, data generation with Generative Adversarial Networks (GANs), dimensionality reduction, and anomaly detection.

  • 22 authors
·
Oct 1, 2020

Reconstructions of electron-temperature profiles from EUROfusion Pedestal Database using turbulence models and machine learning

This study uses plasma-profile data from the EUROfusion pedestal database, focusing on the electron-temperature and electron-density profiles in the edge region of H-mode ELMy JET ITER-Like-Wall (ILW) pulses. We make systematic predictions of the electron-temperature pedestal, using the density profiles and engineering parameters of the pulses as inputs. We first present a machine-learning algorithm that, given more inputs than theory-based modelling and 80\% of the database as training data, can reconstruct the remaining 20\% of temperature profiles within 20\% of the experimental values, including accurate estimates of the pedestal width and location. The most important engineering parameters for these predictions are magnetic field strength, particle fuelling rate, plasma current, and strike-point configuration. This confirms the potential of accurate pedestal prediction using large databases. Next, we take a simple theoretical approach assuming a local power-law relationship between the gradients of density (R/L_{n_e}) and temperature (R/L_{T_e}): R/L_{T_e}=Aleft(R/L_{n_e}right)^α with αapprox 0.4 fits well in the steep-gradient region. When A and α are fit independently for each pedestal, a one-to-one correlation emerges, also valid for JET-C data. For α= 1, A equiv η_e, a known control parameter for turbulence in slab-ETG theory. Measured values of η_e in the steep-gradient region lie well above the slab-ETG stability threshold, suggesting a nonlinear threshold shift or a supercritical turbulent state. Finally, we test heat-flux scalings motivated by gyrokinetic simulations, and we provide best-fit parameters for reconstructing JET-ILW pedestals. These models require additional experimental inputs to reach the accuracy of the machine-learning reconstructions.

  • 6 authors
·
Apr 24, 2025

Evolution and The Knightian Blindspot of Machine Learning

This paper claims that machine learning (ML) largely overlooks an important facet of general intelligence: robustness to a qualitatively unknown future in an open world. Such robustness relates to Knightian uncertainty (KU) in economics, i.e. uncertainty that cannot be quantified, which is excluded from consideration in ML's key formalisms. This paper aims to identify this blind spot, argue its importance, and catalyze research into addressing it, which we believe is necessary to create truly robust open-world AI. To help illuminate the blind spot, we contrast one area of ML, reinforcement learning (RL), with the process of biological evolution. Despite staggering ongoing progress, RL still struggles in open-world situations, often failing under unforeseen situations. For example, the idea of zero-shot transferring a self-driving car policy trained only in the US to the UK currently seems exceedingly ambitious. In dramatic contrast, biological evolution routinely produces agents that thrive within an open world, sometimes even to situations that are remarkably out-of-distribution (e.g. invasive species; or humans, who do undertake such zero-shot international driving). Interestingly, evolution achieves such robustness without explicit theory, formalisms, or mathematical gradients. We explore the assumptions underlying RL's typical formalisms, showing how they limit RL's engagement with the unknown unknowns characteristic of an ever-changing complex world. Further, we identify mechanisms through which evolutionary processes foster robustness to novel and unpredictable challenges, and discuss potential pathways to algorithmically embody them. The conclusion is that the intriguing remaining fragility of ML may result from blind spots in its formalisms, and that significant gains may result from direct confrontation with the challenge of KU.

  • 5 authors
·
Jan 22, 2025 2

A Benchmark for Quantum Chemistry Relaxations via Machine Learning Interatomic Potentials

Computational quantum chemistry plays a critical role in drug discovery, chemical synthesis, and materials science. While first-principles methods, such as density functional theory (DFT), provide high accuracy in modeling electronic structures and predicting molecular properties, they are computationally expensive. Machine learning interatomic potentials (MLIPs) have emerged as promising surrogate models that aim to achieve DFT-level accuracy while enabling efficient large-scale atomistic simulations. The development of accurate and transferable MLIPs requires large-scale, high-quality datasets with both energy and force labels. Critically, MLIPs must generalize not only to stable geometries but also to intermediate, non-equilibrium conformations encountered during atomistic simulations. In this work, we introduce PubChemQCR, a large-scale dataset of molecular relaxation trajectories curated from the raw geometry optimization outputs of the PubChemQC project. PubChemQCR is the largest publicly available dataset of DFT-based relaxation trajectories for small organic molecules, comprising approximately 3.5 million trajectories and over 300 million molecular conformations computed at various levels of theory. Each conformation is labeled with both total energy and atomic forces, making the dataset suitable for training and evaluating MLIPs. To provide baselines for future developments, we benchmark nine representative MLIP models on the dataset. Our resources are publicly available at https://huggingface.co/divelab

  • 11 authors
·
Jun 28, 2025

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

  • 11 authors
·
Jul 1, 2021

A Unified Perspective on Optimization in Machine Learning and Neuroscience: From Gradient Descent to Neural Adaptation

Iterative optimization is central to modern artificial intelligence (AI) and provides a crucial framework for understanding adaptive systems. This review provides a unified perspective on this subject, bridging classic theory with neural network training and biological learning. Although gradient-based methods, powered by the efficient but biologically implausible backpropagation (BP), dominate machine learning, their computational demands can hinder scalability in high-dimensional settings. In contrast, derivative-free or zeroth-order (ZO) optimization feature computationally lighter approaches that rely only on function evaluations and randomness. While generally less sample efficient, recent breakthroughs demonstrate that modern ZO methods can effectively approximate gradients and achieve performance competitive with BP in neural network models. This ZO paradigm is also particularly relevant for biology. Its core principles of random exploration (probing) and feedback-guided adaptation (reinforcing) parallel key mechanisms of biological learning, offering a mathematically principled perspective on how the brain learns. In this review, we begin by categorizing optimization approaches based on the order of derivative information they utilize, ranging from first-, second-, and higher-order gradient-based to ZO methods. We then explore how these methods are adapted to the unique challenges of neural network training and the resulting learning dynamics. Finally, we build upon these insights to view biological learning through an optimization lens, arguing that a ZO paradigm leverages the brain's intrinsic noise as a computational resource. This framework not only illuminates our understanding of natural intelligence but also holds vast implications for neuromorphic hardware, helping us design fast and energy-efficient AI systems that exploit intrinsic hardware noise.

  • 3 authors
·
Oct 21, 2025

An inorganic ABX3 perovskite materials dataset for target property prediction and classification using machine learning

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

  • 2 authors
·
Dec 18, 2023

AQCat25: Unlocking spin-aware, high-fidelity machine learning potentials for heterogeneous catalysis

Large-scale datasets have enabled highly accurate machine learning interatomic potentials (MLIPs) for general-purpose heterogeneous catalysis modeling. There are, however, some limitations in what can be treated with these potentials because of gaps in the underlying training data. To extend these capabilities, we introduce AQCat25, a complementary dataset of 13.5 million density functional theory (DFT) single point calculations designed to improve the treatment of systems where spin polarization and/or higher fidelity are critical. We also investigate methodologies for integrating new datasets, such as AQCat25, with the broader Open Catalyst 2020 (OC20) dataset to create spin-aware models without sacrificing generalizability. We find that directly tuning a general model on AQCat25 leads to catastrophic forgetting of the original dataset's knowledge. Conversely, joint training strategies prove effective for improving accuracy on the new data without sacrificing general performance. This joint approach introduces a challenge, as the model must learn from a dataset containing both mixed-fidelity calculations and mixed-physics (spin-polarized vs. unpolarized). We show that explicitly conditioning the model on this system-specific metadata, for example by using Feature-wise Linear Modulation (FiLM), successfully addresses this challenge and further enhances model accuracy. Ultimately, our work establishes an effective protocol for bridging DFT fidelity domains to advance the predictive power of foundational models in catalysis.

  • 3 authors
·
Oct 26, 2025

Rise and Fall of Anderson Localization by Lattice Vibrations: A Time-Dependent Machine Learning Approach

The intricate relationship between electrons and the crystal lattice is a linchpin in condensed matter, traditionally described by the Fr\"ohlich model encompassing the lowest-order lattice-electron coupling. Recently developed quantum acoustics, emphasizing the wave nature of lattice vibrations, has enabled the exploration of previously uncharted territories of electron-lattice interaction not accessible with conventional tools such as perturbation theory. In this context, our agenda here is two-fold. First, we showcase the application of machine learning methods to categorize various interaction regimes within the subtle interplay of electrons and the dynamical lattice landscape. Second, we shed light on a nebulous region of electron dynamics identified by the machine learning approach and then attribute it to transient localization, where strong lattice vibrations result in a momentary Anderson prison for electronic wavepackets, which are later released by the evolution of the lattice. Overall, our research illuminates the spectrum of dynamics within the Fr\"ohlich model, such as transient localization, which has been suggested as a pivotal factor contributing to the mysteries surrounding strange metals. Furthermore, this paves the way for utilizing time-dependent perspectives in machine learning techniques for designing materials with tailored electron-lattice properties.

  • 4 authors
·
May 27, 2024

MMToM-QA: Multimodal Theory of Mind Question Answering

Theory of Mind (ToM), the ability to understand people's mental states, is an essential ingredient for developing machines with human-level social intelligence. Recent machine learning models, particularly large language models, seem to show some aspects of ToM understanding. However, existing ToM benchmarks use unimodal datasets - either video or text. Human ToM, on the other hand, is more than video or text understanding. People can flexibly reason about another person's mind based on conceptual representations (e.g., goals, beliefs, plans) extracted from any available data. To address this, we introduce a multimodal Theory of Mind question answering (MMToM-QA) benchmark. MMToM-QA comprehensively evaluates machine ToM both on multimodal data and on different kinds of unimodal data about a person's activity in a household environment. To engineer multimodal ToM capacity, we propose a novel method, BIP-ALM (Bayesian Inverse Planning Accelerated by Language Models). BIP-ALM extracts unified representations from multimodal data and utilizes language models for scalable Bayesian inverse planning. We conducted a systematic comparison of human performance, BIP-ALM, and state-of-the-art models, including GPT-4. The experiments demonstrate that large language models and large multimodal models still lack robust ToM capacity. BIP-ALM, on the other hand, shows promising results, by leveraging the power of both model-based mental inference and language models.

  • 10 authors
·
Jan 16, 2024

From Garbage to Gold: A Data-Architectural Theory of Predictive Robustness

Tabular machine learning presents a paradox: modern models achieve state-of-the-art performance using high-dimensional (high-D), collinear, error-prone data, defying the "Garbage In, Garbage Out" mantra. To help resolve this, we synthesize principles from Information Theory, Latent Factor Models, and Psychometrics, clarifying that predictive robustness arises not solely from data cleanliness, but from the synergy between data architecture and model capacity. Partitioning predictor-space "noise" into "Predictor Error" and "Structural Uncertainty" (informational deficits from stochastic generative mappings), we prove that leveraging high-D sets of error-prone predictors asymptotically overcomes both types of noise, whereas cleaning a low-D set is fundamentally bounded by Structural Uncertainty. We demonstrate why "Informative Collinearity" (dependencies from shared latent causes) enhances reliability and convergence efficiency, and explain why increased dimensionality reduces the latent inference burden, enabling feasibility with finite samples. To address practical constraints, we propose "Proactive Data-Centric AI" to identify predictors that enable robustness efficiently. We also derive boundaries for Systematic Error Regimes and show why models that absorb "rogue" dependencies can mitigate assumption violations. Linking latent architecture to Benign Overfitting, we offer a first step towards a unified view of robustness to Outcome Error and predictor-space noise, while also delineating when traditional DCAI's focus on label cleaning remains powerful. By redefining data quality from item-level perfection to portfolio-level architecture, we provide a theoretical rationale for "Local Factories" -- learning from live, uncurated enterprise "data swamps" -- supporting a deployment paradigm shift from "Model Transfer" to "Methodology Transfer'' to overcome static generalizability limitations.

  • 3 authors
·
Mar 8

Unified Micromechanics Theory of Composites

We consider the matrix composite materials (CM) of either random (statistically homogeneous or inhomogeneous), periodic, or deterministic (neither random nor periodic) structures. CMs exhibit linear or nonlinear behavior, coupled or uncoupled multi-physical phenomena, locally elastic, weakly nonlocal (strain gradient and stress gradient), or strongly nonlocal (strain-type and displacement-type, peridynamics) phase properties. A modified Computational Analytical Micromechanics (CAM) approach introduces an exact Additive General Integral Equation (AGIE) for CMs of any structure and phase properties mentioned above. The unified iteration solution of static AGIEs is adapted to the body force with compact support serving as a fundamentally new universal training parameter. The approach also establishes a critical threshold for filtering out unsuitable sub-datasets of effective parameters through a novel Representative Volume Element (RVE) concept, which extends Hill's classical framework. This RVE concept eliminates sample size, boundary layer, and edge effects, making it applicable to CMs of any structure and phase properties, regardless of local or nonlocal, linear or nonlinear. Incorporating this new RVE concept into machine learning and neural network techniques enables the construction of any unpredefined surrogate nonlocal operators. The methodology is structured as a modular, block-based framework, allowing independent development and refinement of software components. This flexible, robust AGIE-CAM framework integrates data-driven, multi-scale, and multi-physics modeling, accelerating research in CM of any microtopology and phase properties considered. The AGIE-CAM framework represents a groundbreaking paradigm shift in the micromechanics of composites, redefining the very philosophy that underpins our understanding of their behavior at the microscopic level.

  • 1 authors
·
Mar 15, 2025

Digital Twins: State of the Art Theory and Practice, Challenges, and Open Research Questions

Digital Twin was introduced over a decade ago, as an innovative all-encompassing tool, with perceived benefits including real-time monitoring, simulation and forecasting. However, the theoretical framework and practical implementations of digital twins (DT) are still far from this vision. Although successful implementations exist, sufficient implementation details are not publicly available, therefore it is difficult to assess their effectiveness, draw comparisons and jointly advance the DT methodology. This work explores the various DT features and current approaches, the shortcomings and reasons behind the delay in the implementation and adoption of digital twin. Advancements in machine learning, internet of things and big data have contributed hugely to the improvements in DT with regards to its real-time monitoring and forecasting properties. Despite this progress and individual company-based efforts, certain research gaps exist in the field, which have caused delay in the widespread adoption of this concept. We reviewed relevant works and identified that the major reasons for this delay are the lack of a universal reference framework, domain dependence, security concerns of shared data, reliance of digital twin on other technologies, and lack of quantitative metrics. We define the necessary components of a digital twin required for a universal reference framework, which also validate its uniqueness as a concept compared to similar concepts like simulation, autonomous systems, etc. This work further assesses the digital twin applications in different domains and the current state of machine learning and big data in it. It thus answers and identifies novel research questions, both of which will help to better understand and advance the theory and practice of digital twins.

  • 5 authors
·
Nov 2, 2020

A Semantic Generalization of Shannon's Information Theory and Applications

Does semantic communication require a semantic information theory parallel to Shannon's information theory, or can Shannon's work be generalized for semantic communication? This paper advocates for the latter and introduces a semantic generalization of Shannon's information theory (G theory for short). The core idea is to replace the distortion constraint with the semantic constraint, achieved by utilizing a set of truth functions as a semantic channel. These truth functions enable the expressions of semantic distortion, semantic information measures, and semantic information loss. Notably, the maximum semantic information criterion is equivalent to the maximum likelihood criterion and similar to the Regularized Least Squares criterion. This paper shows G theory's applications to daily and electronic semantic communication, machine learning, constraint control, Bayesian confirmation, portfolio theory, and information value. The improvements in machine learning methods involve multilabel learning and classification, maximum mutual information classification, mixture models, and solving latent variables. Furthermore, insights from statistical physics are discussed: Shannon information is similar to free energy; semantic information to free energy in local equilibrium systems; and information efficiency to the efficiency of free energy in performing work. The paper also proposes refining Friston's minimum free energy principle into the maximum information efficiency principle. Lastly, it compares G theory with other semantic information theories and discusses its limitation in representing the semantics of complex data.

  • 1 authors
·
May 6, 2025

A Metamodel and Framework for Artificial General Intelligence From Theory to Practice

This paper introduces a new metamodel-based knowledge representation that significantly improves autonomous learning and adaptation. While interest in hybrid machine learning / symbolic AI systems leveraging, for example, reasoning and knowledge graphs, is gaining popularity, we find there remains a need for both a clear definition of knowledge and a metamodel to guide the creation and manipulation of knowledge. Some of the benefits of the metamodel we introduce in this paper include a solution to the symbol grounding problem, cumulative learning, and federated learning. We have applied the metamodel to problems ranging from time series analysis, computer vision, and natural language understanding and have found that the metamodel enables a wide variety of learning mechanisms ranging from machine learning, to graph network analysis and learning by reasoning engines to interoperate in a highly synergistic way. Our metamodel-based projects have consistently exhibited unprecedented accuracy, performance, and ability to generalize. This paper is inspired by the state-of-the-art approaches to AGI, recent AGI-aspiring work, the granular computing community, as well as Alfred Korzybski's general semantics. One surprising consequence of the metamodel is that it not only enables a new level of autonomous learning and optimal functioning for machine intelligences, but may also shed light on a path to better understanding how to improve human cognition.

  • 10 authors
·
Feb 11, 2021

The Deep Arbitrary Polynomial Chaos Neural Network or how Deep Artificial Neural Networks could benefit from Data-Driven Homogeneous Chaos Theory

Artificial Intelligence and Machine learning have been widely used in various fields of mathematical computing, physical modeling, computational science, communication science, and stochastic analysis. Approaches based on Deep Artificial Neural Networks (DANN) are very popular in our days. Depending on the learning task, the exact form of DANNs is determined via their multi-layer architecture, activation functions and the so-called loss function. However, for a majority of deep learning approaches based on DANNs, the kernel structure of neural signal processing remains the same, where the node response is encoded as a linear superposition of neural activity, while the non-linearity is triggered by the activation functions. In the current paper, we suggest to analyze the neural signal processing in DANNs from the point of view of homogeneous chaos theory as known from polynomial chaos expansion (PCE). From the PCE perspective, the (linear) response on each node of a DANN could be seen as a 1^{st} degree multi-variate polynomial of single neurons from the previous layer, i.e. linear weighted sum of monomials. From this point of view, the conventional DANN structure relies implicitly (but erroneously) on a Gaussian distribution of neural signals. Additionally, this view revels that by design DANNs do not necessarily fulfill any orthogonality or orthonormality condition for a majority of data-driven applications. Therefore, the prevailing handling of neural signals in DANNs could lead to redundant representation as any neural signal could contain some partial information from other neural signals. To tackle that challenge, we suggest to employ the data-driven generalization of PCE theory known as arbitrary polynomial chaos (aPC) to construct a corresponding multi-variate orthonormal representations on each node of a DANN to obtain Deep arbitrary polynomial chaos neural networks.

  • 6 authors
·
Jun 26, 2023

A Mathematical Theory of Deep Convolutional Neural Networks for Feature Extraction

Deep convolutional neural networks have led to breakthrough results in numerous practical machine learning tasks such as classification of images in the ImageNet data set, control-policy-learning to play Atari games or the board game Go, and image captioning. Many of these applications first perform feature extraction and then feed the results thereof into a trainable classifier. The mathematical analysis of deep convolutional neural networks for feature extraction was initiated by Mallat, 2012. Specifically, Mallat considered so-called scattering networks based on a wavelet transform followed by the modulus non-linearity in each network layer, and proved translation invariance (asymptotically in the wavelet scale parameter) and deformation stability of the corresponding feature extractor. This paper complements Mallat's results by developing a theory that encompasses general convolutional transforms, or in more technical parlance, general semi-discrete frames (including Weyl-Heisenberg filters, curvelets, shearlets, ridgelets, wavelets, and learned filters), general Lipschitz-continuous non-linearities (e.g., rectified linear units, shifted logistic sigmoids, hyperbolic tangents, and modulus functions), and general Lipschitz-continuous pooling operators emulating, e.g., sub-sampling and averaging. In addition, all of these elements can be different in different network layers. For the resulting feature extractor we prove a translation invariance result of vertical nature in the sense of the features becoming progressively more translation-invariant with increasing network depth, and we establish deformation sensitivity bounds that apply to signal classes such as, e.g., band-limited functions, cartoon functions, and Lipschitz functions.

  • 2 authors
·
Dec 19, 2015

The Gauss-Markov Adjunction: Categorical Semantics of Residuals in Supervised Learning

Enhancing the intelligibility and interpretability of machine learning is a crucial task in responding to the demand for Explicability as an AI principle, and in promoting the better social implementation of AI. The aim of our research is to contribute to this improvement by reformulating machine learning models through the lens of category theory, thereby developing a semantic framework for structuring and understanding AI systems. Our categorical modeling in this paper clarifies and formalizes the structural interplay between residuals and parameters in supervised learning. The present paper focuses on the multiple linear regression model, which represents the most basic form of supervised learning. By defining two concrete categories corresponding to parameters and data, along with an adjoint pair of functors between them, we introduce our categorical formulation of supervised learning. We show that the essential structure of this framework is captured by what we call the Gauss-Markov Adjunction. Within this setting, the dual flow of information can be explicitly described as a correspondence between variations in parameters and residuals. The ordinary least squares estimator for the parameters and the minimum residual are related via the preservation of limits by the right adjoint functor. Furthermore, we position this formulation as an instance of extended denotational semantics for supervised learning, and propose applying a semantic perspective developed in theoretical computer science as a formal foundation for Explicability in AI.

  • 1 authors
·
Jul 3, 2025 1

Learning to Optimize: A Primer and A Benchmark

Learning to optimize (L2O) is an emerging approach that leverages machine learning to develop optimization methods, aiming at reducing the laborious iterations of hand engineering. It automates the design of an optimization method based on its performance on a set of training problems. This data-driven procedure generates methods that can efficiently solve problems similar to those in the training. In sharp contrast, the typical and traditional designs of optimization methods are theory-driven, so they obtain performance guarantees over the classes of problems specified by the theory. The difference makes L2O suitable for repeatedly solving a certain type of optimization problems over a specific distribution of data, while it typically fails on out-of-distribution problems. The practicality of L2O depends on the type of target optimization, the chosen architecture of the method to learn, and the training procedure. This new paradigm has motivated a community of researchers to explore L2O and report their findings. This article is poised to be the first comprehensive survey and benchmark of L2O for continuous optimization. We set up taxonomies, categorize existing works and research directions, present insights, and identify open challenges. We also benchmarked many existing L2O approaches on a few but representative optimization problems. For reproducible research and fair benchmarking purposes, we released our software implementation and data in the package Open-L2O at https://github.com/VITA-Group/Open-L2O.

  • 7 authors
·
Mar 23, 2021

Operationalizing Serendipity: Multi-Agent AI Workflows for Enhanced Materials Characterization with Theory-in-the-Loop

The history of science is punctuated by serendipitous discoveries, where unexpected observations, rather than targeted hypotheses, opened new fields of inquiry. While modern autonomous laboratories excel at accelerating hypothesis testing, their optimization for efficiency risks overlooking these crucial, unplanned findings. To address this gap, we introduce SciLink, an open-source, multi-agent artificial intelligence framework designed to operationalize serendipity in materials research by creating a direct, automated link between experimental observation, novelty assessment, and theoretical simulations. The framework employs a hybrid AI strategy where specialized machine learning models perform quantitative analysis of experimental data, while large language models handle higher-level reasoning. These agents autonomously convert raw data from materials characterization techniques into falsifiable scientific claims, which are then quantitatively scored for novelty against the published literature. We demonstrate the framework's versatility across diverse research scenarios, showcasing its application to atomic-resolution and hyperspectral data, its capacity to integrate real-time human expert guidance, and its ability to close the research loop by proposing targeted follow-up experiments. By systematically analyzing all observations and contextualizing them, SciLink provides a practical framework for AI-driven materials research that not only enhances efficiency but also actively cultivates an environment ripe for serendipitous discoveries, thereby bridging the gap between automated experimentation and open-ended scientific exploration.

  • 7 authors
·
Aug 7, 2025

Category Theory for Quantum Natural Language Processing

This thesis introduces quantum natural language processing (QNLP) models based on a simple yet powerful analogy between computational linguistics and quantum mechanics: grammar as entanglement. The grammatical structure of text and sentences connects the meaning of words in the same way that entanglement structure connects the states of quantum systems. Category theory allows to make this language-to-qubit analogy formal: it is a monoidal functor from grammar to vector spaces. We turn this abstract analogy into a concrete algorithm that translates the grammatical structure onto the architecture of parameterised quantum circuits. We then use a hybrid classical-quantum algorithm to train the model so that evaluating the circuits computes the meaning of sentences in data-driven tasks. The implementation of QNLP models motivated the development of DisCoPy (Distributional Compositional Python), the toolkit for applied category theory of which the first chapter gives a comprehensive overview. String diagrams are the core data structure of DisCoPy, they allow to reason about computation at a high level of abstraction. We show how they can encode both grammatical structures and quantum circuits, but also logical formulae, neural networks or arbitrary Python code. Monoidal functors allow to translate these abstract diagrams into concrete computation, interfacing with optimised task-specific libraries. The second chapter uses DisCopy to implement QNLP models as parameterised functors from grammar to quantum circuits. It gives a first proof-of-concept for the more general concept of functorial learning: generalising machine learning from functions to functors by learning from diagram-like data. In order to learn optimal functor parameters via gradient descent, we introduce the notion of diagrammatic differentiation: a graphical calculus for computing the gradients of parameterised diagrams.

  • 1 authors
·
Dec 13, 2022

Transfer Learning Using Ensemble Neural Networks for Organic Solar Cell Screening

Organic Solar Cells are a promising technology for solving the clean energy crisis in the world. However, generating candidate chemical compounds for solar cells is a time-consuming process requiring thousands of hours of laboratory analysis. For a solar cell, the most important property is the power conversion efficiency which is dependent on the highest occupied molecular orbitals (HOMO) values of the donor molecules. Recently, machine learning techniques have proved to be very useful in building predictive models for HOMO values of donor structures of Organic Photovoltaic Cells (OPVs). Since experimental datasets are limited in size, current machine learning models are trained on data derived from calculations based on density functional theory (DFT). Molecular line notations such as SMILES or InChI are popular input representations for describing the molecular structure of donor molecules. The two types of line representations encode different information, such as SMILES defines the bond types while InChi defines protonation. In this work, we present an ensemble deep neural network architecture, called SINet, which harnesses both the SMILES and InChI molecular representations to predict HOMO values and leverage the potential of transfer learning from a sizeable DFT-computed dataset- Harvard CEP to build more robust predictive models for relatively smaller HOPV datasets. Harvard CEP dataset contains molecular structures and properties for 2.3 million candidate donor structures for OPV while HOPV contains DFT-computed and experimental values of 350 and 243 molecules respectively. Our results demonstrate significant performance improvement from the use of transfer learning and leveraging both molecular representations.

  • 6 authors
·
Mar 7, 2019

A Comprehensive Survey of Mixture-of-Experts: Algorithms, Theory, and Applications

Artificial intelligence (AI) has achieved astonishing successes in many domains, especially with the recent breakthroughs in the development of foundational large models. These large models, leveraging their extensive training data, provide versatile solutions for a wide range of downstream tasks. However, as modern datasets become increasingly diverse and complex, the development of large AI models faces two major challenges: (1) the enormous consumption of computational resources and deployment difficulties, and (2) the difficulty in fitting heterogeneous and complex data, which limits the usability of the models. Mixture of Experts (MoE) models has recently attracted much attention in addressing these challenges, by dynamically selecting and activating the most relevant sub-models to process input data. It has been shown that MoEs can significantly improve model performance and efficiency with fewer resources, particularly excelling in handling large-scale, multimodal data. Given the tremendous potential MoE has demonstrated across various domains, it is urgent to provide a comprehensive summary of recent advancements of MoEs in many important fields. Existing surveys on MoE have their limitations, e.g., being outdated or lacking discussion on certain key areas, and we aim to address these gaps. In this paper, we first introduce the basic design of MoE, including gating functions, expert networks, routing mechanisms, training strategies, and system design. We then explore the algorithm design of MoE in important machine learning paradigms such as continual learning, meta-learning, multi-task learning, and reinforcement learning. Additionally, we summarize theoretical studies aimed at understanding MoE and review its applications in computer vision and natural language processing. Finally, we discuss promising future research directions.

  • 2 authors
·
Mar 10, 2025

Statistical mechanics of continual learning: variational principle and mean-field potential

An obstacle to artificial general intelligence is set by continual learning of multiple tasks of different nature. Recently, various heuristic tricks, both from machine learning and from neuroscience angles, were proposed, but they lack a unified theory ground. Here, we focus on continual learning in single-layered and multi-layered neural networks of binary weights. A variational Bayesian learning setting is thus proposed, where the neural networks are trained in a field-space, rather than gradient-ill-defined discrete-weight space, and furthermore, weight uncertainty is naturally incorporated, and modulates synaptic resources among tasks. From a physics perspective, we translate the variational continual learning into Franz-Parisi thermodynamic potential framework, where previous task knowledge acts as a prior and a reference as well. We thus interpret the continual learning of the binary perceptron in a teacher-student setting as a Franz-Parisi potential computation. The learning performance can then be analytically studied with mean-field order parameters, whose predictions coincide with numerical experiments using stochastic gradient descent methods. Based on the variational principle and Gaussian field approximation of internal preactivations in hidden layers, we also derive the learning algorithm considering weight uncertainty, which solves the continual learning with binary weights using multi-layered neural networks, and performs better than the currently available metaplasticity algorithm. Our proposed principled frameworks also connect to elastic weight consolidation, weight-uncertainty modulated learning, and neuroscience inspired metaplasticity, providing a theory-grounded method for the real-world multi-task learning with deep networks.

  • 4 authors
·
Dec 6, 2022

Learning to Fly -- a Gym Environment with PyBullet Physics for Reinforcement Learning of Multi-agent Quadcopter Control

Robotic simulators are crucial for academic research and education as well as the development of safety-critical applications. Reinforcement learning environments -- simple simulations coupled with a problem specification in the form of a reward function -- are also important to standardize the development (and benchmarking) of learning algorithms. Yet, full-scale simulators typically lack portability and parallelizability. Vice versa, many reinforcement learning environments trade-off realism for high sample throughputs in toy-like problems. While public data sets have greatly benefited deep learning and computer vision, we still lack the software tools to simultaneously develop -- and fairly compare -- control theory and reinforcement learning approaches. In this paper, we propose an open-source OpenAI Gym-like environment for multiple quadcopters based on the Bullet physics engine. Its multi-agent and vision based reinforcement learning interfaces, as well as the support of realistic collisions and aerodynamic effects, make it, to the best of our knowledge, a first of its kind. We demonstrate its use through several examples, either for control (trajectory tracking with PID control, multi-robot flight with downwash, etc.) or reinforcement learning (single and multi-agent stabilization tasks), hoping to inspire future research that combines control theory and machine learning.

  • 6 authors
·
Mar 2, 2021 1

Synergistic Fusion of Multi-Source Knowledge via Evidence Theory for High-Entropy Alloy Discovery

Discovering novel high-entropy alloys (HEAs) with desirable properties is challenging due to the vast compositional space and complex phase formation mechanisms. Efficient exploration of this space requires a strategic approach that integrates heterogeneous knowledge sources. Here, we propose a framework that systematically combines knowledge extracted from computational material datasets with domain knowledge distilled from scientific literature using large language models (LLMs). A central feature of this approach is the explicit consideration of element substitutability, identifying chemically similar elements that can be interchanged to potentially stabilize desired HEAs. Dempster-Shafer theory, a mathematical framework for reasoning under uncertainty, is employed to model and combine substitutabilities based on aggregated evidence from multiple sources. The framework predicts the phase stability of candidate HEA compositions and is systematically evaluated on both quaternary alloy systems, demonstrating superior performance compared to baseline machine learning models and methods reliant on single-source evidence in cross-validation experiments. By leveraging multi-source knowledge, the framework retains robust predictive power even when key elements are absent from the training data, underscoring its potential for knowledge transfer and extrapolation. Furthermore, the enhanced interpretability of the methodology offers insights into the fundamental factors governing HEA formation. Overall, this work provides a promising strategy for accelerating HEA discovery by integrating computational and textual knowledge sources, enabling efficient exploration of vast compositional spaces with improved generalization and interpretability.

  • 9 authors
·
Feb 20, 2025

Collective eXplainable AI: Explaining Cooperative Strategies and Agent Contribution in Multiagent Reinforcement Learning with Shapley Values

While Explainable Artificial Intelligence (XAI) is increasingly expanding more areas of application, little has been applied to make deep Reinforcement Learning (RL) more comprehensible. As RL becomes ubiquitous and used in critical and general public applications, it is essential to develop methods that make it better understood and more interpretable. This study proposes a novel approach to explain cooperative strategies in multiagent RL using Shapley values, a game theory concept used in XAI that successfully explains the rationale behind decisions taken by Machine Learning algorithms. Through testing common assumptions of this technique in two cooperation-centered socially challenging multi-agent environments environments, this article argues that Shapley values are a pertinent way to evaluate the contribution of players in a cooperative multi-agent RL context. To palliate the high overhead of this method, Shapley values are approximated using Monte Carlo sampling. Experimental results on Multiagent Particle and Sequential Social Dilemmas show that Shapley values succeed at estimating the contribution of each agent. These results could have implications that go beyond games in economics, (e.g., for non-discriminatory decision making, ethical and responsible AI-derived decisions or policy making under fairness constraints). They also expose how Shapley values only give general explanations about a model and cannot explain a single run, episode nor justify precise actions taken by agents. Future work should focus on addressing these critical aspects.

  • 3 authors
·
Oct 4, 2021

Benchmarking foundation potentials against quantum chemistry methods for predicting molecular redox potentials

Computational high-throughput virtual screening is essential for identifying redox-active molecules for sustainable applications such as electrochemical carbon capture. A primary challenge in this approach is the high computational cost associated with accurate quantum chemistry calculations. Machine learning foundation potentials (FPs) trained on extensive density functional theory (DFT) calculations offer a computationally efficient alternative. Here, we benchmark the MACE-OMol-0 and UMA FPs against a hierarchy of DFT functionals for predicting experimental molecular redox potentials for both electron transfer (ET) and proton-coupled electron transfer (PCET) reactions. We find that these FPs achieve exceptional accuracy for PCET processes, rivaling their target DFT method. However, the performance is diminished for ET reactions, particularly for multi-electron transfers involving reactive ions that are underrepresented in the OMol25 training data, revealing a key out-of-distribution limitation. To overcome this, we propose an optimal hybrid workflow that uses the FPs for efficient geometry optimization and thermochemical analysis, followed by a crucial single-point DFT energy refinement and an implicit solvation correction. This pragmatic approach provides a robust and scalable strategy for accelerating high-throughput virtual screening in sustainable chemistry.

  • 4 authors
·
Oct 28, 2025

The Monge Gap: A Regularizer to Learn All Transport Maps

Optimal transport (OT) theory has been been used in machine learning to study and characterize maps that can push-forward efficiently a probability measure onto another. Recent works have drawn inspiration from Brenier's theorem, which states that when the ground cost is the squared-Euclidean distance, the ``best'' map to morph a continuous measure in P(Rd) into another must be the gradient of a convex function. To exploit that result, [Makkuva+ 2020, Korotin+2020] consider maps T=nabla f_theta, where f_theta is an input convex neural network (ICNN), as defined by Amos+2017, and fit theta with SGD using samples. Despite their mathematical elegance, fitting OT maps with ICNNs raises many challenges, due notably to the many constraints imposed on theta; the need to approximate the conjugate of f_theta; or the limitation that they only work for the squared-Euclidean cost. More generally, we question the relevance of using Brenier's result, which only applies to densities, to constrain the architecture of candidate maps fitted on samples. Motivated by these limitations, we propose a radically different approach to estimating OT maps: Given a cost c and a reference measure rho, we introduce a regularizer, the Monge gap M^c_{rho}(T) of a map T. That gap quantifies how far a map T deviates from the ideal properties we expect from a c-OT map. In practice, we drop all architecture requirements for T and simply minimize a distance (e.g., the Sinkhorn divergence) between Tsharpmu and nu, regularized by M^c_rho(T). We study M^c_{rho}, and show how our simple pipeline outperforms significantly other baselines in practice.

  • 2 authors
·
Feb 9, 2023

Distributed Methods with Compressed Communication for Solving Variational Inequalities, with Theoretical Guarantees

Variational inequalities in general and saddle point problems in particular are increasingly relevant in machine learning applications, including adversarial learning, GANs, transport and robust optimization. With increasing data and problem sizes necessary to train high performing models across various applications, we need to rely on parallel and distributed computing. However, in distributed training, communication among the compute nodes is a key bottleneck during training, and this problem is exacerbated for high dimensional and over-parameterized models. Due to these considerations, it is important to equip existing methods with strategies that would allow to reduce the volume of transmitted information during training while obtaining a model of comparable quality. In this paper, we present the first theoretically grounded distributed methods for solving variational inequalities and saddle point problems using compressed communication: MASHA1 and MASHA2. Our theory and methods allow for the use of both unbiased (such as Randk; MASHA1) and contractive (such as Topk; MASHA2) compressors. New algorithms support bidirectional compressions, and also can be modified for stochastic setting with batches and for federated learning with partial participation of clients. We empirically validated our conclusions using two experimental setups: a standard bilinear min-max problem, and large-scale distributed adversarial training of transformers.

  • 5 authors
·
Oct 7, 2021

TransICD: Transformer Based Code-wise Attention Model for Explainable ICD Coding

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

  • 3 authors
·
Mar 28, 2021

An Automated Pipeline for Character and Relationship Extraction from Readers' Literary Book Reviews on Goodreads.com

Reader reviews of literary fiction on social media, especially those in persistent, dedicated forums, create and are in turn driven by underlying narrative frameworks. In their comments about a novel, readers generally include only a subset of characters and their relationships, thus offering a limited perspective on that work. Yet in aggregate, these reviews capture an underlying narrative framework comprised of different actants (people, places, things), their roles, and interactions that we label the "consensus narrative framework". We represent this framework in the form of an actant-relationship story graph. Extracting this graph is a challenging computational problem, which we pose as a latent graphical model estimation problem. Posts and reviews are viewed as samples of sub graphs/networks of the hidden narrative framework. Inspired by the qualitative narrative theory of Greimas, we formulate a graphical generative Machine Learning (ML) model where nodes represent actants, and multi-edges and self-loops among nodes capture context-specific relationships. We develop a pipeline of interlocking automated methods to extract key actants and their relationships, and apply it to thousands of reviews and comments posted on Goodreads.com. We manually derive the ground truth narrative framework from SparkNotes, and then use word embedding tools to compare relationships in ground truth networks with our extracted networks. We find that our automated methodology generates highly accurate consensus narrative frameworks: for our four target novels, with approximately 2900 reviews per novel, we report average coverage/recall of important relationships of > 80% and an average edge detection rate of >89\%. These extracted narrative frameworks can generate insight into how people (or classes of people) read and how they recount what they have read to others.

  • 8 authors
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Apr 20, 2020

The Universality Lens: Why Even Highly Over-Parametrized Models Learn Well

A fundamental question in modern machine learning is why large, over-parameterized models, such as deep neural networks and transformers, tend to generalize well, even when their number of parameters far exceeds the number of training samples. We investigate this phenomenon through the lens of information theory, grounded in universal learning theory. Specifically, we study a Bayesian mixture learner with log-loss and (almost) uniform prior over an expansive hypothesis class. Our key result shows that the learner's regret is not determined by the overall size of the hypothesis class, but rather by the cumulative probability of all models that are close, in Kullback-Leibler divergence distance, to the true data-generating process. We refer to this cumulative probability as the weight of the hypothesis. This leads to a natural notion of model simplicity: simple models are those with large weight and thus require fewer samples to generalize, while complex models have small weight and need more data. This perspective provides a rigorous and intuitive explanation for why over-parameterized models often avoid overfitting: the presence of simple hypotheses allows the posterior to concentrate on them when supported by the data. We further bridge theory and practice by recalling that stochastic gradient descent with Langevin dynamics samples from the correct posterior distribution, enabling our theoretical learner to be approximated using standard machine learning methods combined with ensemble learning. Our analysis yields non-uniform regret bounds and aligns with key practical concepts such as flat minima and model distillation. The results apply broadly across online, batch, and supervised learning settings, offering a unified and principled understanding of the generalization behavior of modern AI systems.

  • 3 authors
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Jun 9, 2025

The Open DAC 2023 Dataset and Challenges for Sorbent Discovery in Direct Air Capture

New methods for carbon dioxide removal are urgently needed to combat global climate change. Direct air capture (DAC) is an emerging technology to capture carbon dioxide directly from ambient air. Metal-organic frameworks (MOFs) have been widely studied as potentially customizable adsorbents for DAC. However, discovering promising MOF sorbents for DAC is challenging because of the vast chemical space to explore and the need to understand materials as functions of humidity and temperature. We explore a computational approach benefiting from recent innovations in machine learning (ML) and present a dataset named Open DAC 2023 (ODAC23) consisting of more than 38M density functional theory (DFT) calculations on more than 8,400 MOF materials containing adsorbed CO_2 and/or H_2O. ODAC23 is by far the largest dataset of MOF adsorption calculations at the DFT level of accuracy currently available. In addition to probing properties of adsorbed molecules, the dataset is a rich source of information on structural relaxation of MOFs, which will be useful in many contexts beyond specific applications for DAC. A large number of MOFs with promising properties for DAC are identified directly in ODAC23. We also trained state-of-the-art ML models on this dataset to approximate calculations at the DFT level. This open-source dataset and our initial ML models will provide an important baseline for future efforts to identify MOFs for a wide range of applications, including DAC.

  • 9 authors
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Nov 1, 2023

Efficient Machine Unlearning via Influence Approximation

Due to growing privacy concerns, machine unlearning, which aims at enabling machine learning models to ``forget" specific training data, has received increasing attention. Among existing methods, influence-based unlearning has emerged as a prominent approach due to its ability to estimate the impact of individual training samples on model parameters without retraining. However, this approach suffers from prohibitive computational overhead arising from the necessity to compute the Hessian matrix and its inverse across all training samples and parameters, rendering it impractical for large-scale models and scenarios involving frequent data deletion requests. This highlights the difficulty of forgetting. Inspired by cognitive science, which suggests that memorizing is easier than forgetting, this paper establishes a theoretical link between memorizing (incremental learning) and forgetting (unlearning). This connection allows machine unlearning to be addressed from the perspective of incremental learning. Unlike the time-consuming Hessian computations in unlearning (forgetting), incremental learning (memorizing) typically relies on more efficient gradient optimization, which supports the aforementioned cognitive theory. Based on this connection, we introduce the Influence Approximation Unlearning (IAU) algorithm for efficient machine unlearning from the incremental perspective. Extensive empirical evaluations demonstrate that IAU achieves a superior balance among removal guarantee, unlearning efficiency, and comparable model utility, while outperforming state-of-the-art methods across diverse datasets and model architectures. Our code is available at https://github.com/Lolo1222/IAU.

  • 4 authors
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Jul 31, 2025 2

Replica symmetry breaking in dense neural networks

Understanding the glassy nature of neural networks is pivotal both for theoretical and computational advances in Machine Learning and Theoretical Artificial Intelligence. Keeping the focus on dense associative Hebbian neural networks, the purpose of this paper is two-fold: at first we develop rigorous mathematical approaches to address properly a statistical mechanical picture of the phenomenon of {\em replica symmetry breaking} (RSB) in these networks, then -- deepening results stemmed via these routes -- we aim to inspect the {\em glassiness} that they hide. In particular, regarding the methodology, we provide two techniques: the former is an adaptation of the transport PDE to the case, while the latter is an extension of Guerra's interpolation breakthrough. Beyond coherence among the results, either in replica symmetric and in the one-step replica symmetry breaking level of description, we prove the Gardner's picture and we identify the maximal storage capacity by a ground-state analysis in the Baldi-Venkatesh high-storage regime. In the second part of the paper we investigate the glassy structure of these networks: in contrast with the replica symmetric scenario (RS), RSB actually stabilizes the spin-glass phase. We report huge differences w.r.t. the standard pairwise Hopfield limit: in particular, it is known that it is possible to express the free energy of the Hopfield neural network as a linear combination of the free energies of an hard spin glass (i.e. the Sherrington-Kirkpatrick model) and a soft spin glass (the Gaussian or "spherical" model). This is no longer true when interactions are more than pairwise (whatever the level of description, RS or RSB): for dense networks solely the free energy of the hard spin glass survives, proving a huge diversity in the underlying glassiness of associative neural networks.

  • 4 authors
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Nov 25, 2021

LeanDojo: Theorem Proving with Retrieval-Augmented Language Models

Large language models (LLMs) have shown promise in proving formal theorems using proof assistants such as Lean. However, existing methods are difficult to reproduce or build on, due to private code, data, and large compute requirements. This has created substantial barriers to research on machine learning methods for theorem proving. This paper removes these barriers by introducing LeanDojo: an open-source Lean playground consisting of toolkits, data, models, and benchmarks. LeanDojo extracts data from Lean and enables interaction with the proof environment programmatically. It contains fine-grained annotations of premises in proofs, providing valuable data for premise selection: a key bottleneck in theorem proving. Using this data, we develop ReProver (Retrieval-Augmented Prover): the first LLM-based prover that is augmented with retrieval for selecting premises from a vast math library. It is inexpensive and needs only one GPU week of training. Our retriever leverages LeanDojo's program analysis capability to identify accessible premises and hard negative examples, which makes retrieval much more effective. Furthermore, we construct a new benchmark consisting of 96,962 theorems and proofs extracted from Lean's math library. It features challenging data split requiring the prover to generalize to theorems relying on novel premises that are never used in training. We use this benchmark for training and evaluation, and experimental results demonstrate the effectiveness of ReProver over non-retrieval baselines and GPT-4. We thus provide the first set of open-source LLM-based theorem provers without any proprietary datasets and release it under a permissive MIT license to facilitate further research.

  • 9 authors
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Jun 27, 2023

Cross Learning between Electronic Structure Theories for Unifying Molecular, Surface, and Inorganic Crystal Foundation Force Fields

Creating a single unified interatomic potential capable of attaining ab initio accuracy across all chemistry remains a long-standing challenge in computational chemistry and materials science. This work introduces a training protocol for foundation machine-learning interatomic potentials (MLIPs) that bridge molecular, surface, and materials chemistry through cross-domain learning. First, we introduce enhancements to the MACE architecture that improve its performance on chemically diverse databases by increasing weight sharing across chemical elements and introducing non-linear factors into the tensor decomposition of the product basis. Second, we develop a multi-head replay post-training methodology that enables efficient knowledge transfer across diverse chemical domains. By fine-tuning on datasets at different levels of electronic structure theory, including inorganic crystals, molecular systems, surface chemistry, and reactive organic chemistry, we demonstrate that a single unified model achieves state-of-the-art performance across several chemical domains. Comprehensive benchmarking reveals superior cross-domain transferability compared with existing specialised and multi-task models, with notable improvements in molecular and surface properties while maintaining state-of-the-art performance in materials-property prediction.

  • 8 authors
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Oct 29, 2025