The paper predicts run times for Gaussian chemistry code.
problem Accurate run time prediction for complex scientific codes.
method Characterized data set, explored regression methods.
result Promising future directions for run time prediction.
Derives symmetric and antisymmetric kernels for quantum physics and chemistry applications.
problem Efficiently handling symmetries and antisymmetries in machine learning for quantum physics and chemistry.
method Symmetrizing and antisymmetrizing conventional kernels, analyzing feature space dimensions, proving kernel properties, proposing Slater determinant representation.
result Efficient evaluation of antisymmetric Gaussian kernels even in high-dimensional state spaces, significant reduction in training data size.
A new model explains protein interactions via electron delocalization.
problem Understanding how protein interactions affect each other.
method Quantized discrete differential geometry of n-simplices.
result Allosteric regulation follows from the model of interactions.
Gaussian process regression loses locality in high dimensions, affecting molecular energy surface fitting.
problem Loss of locality in high-dimensional Gaussian process regression.
method Analysis of Matern family kernels and multi-zeta basis functions.
result The property of locality disappears in high dimensions, impacting regression quality.
A new method for joint noise removal and trend estimation from sparse signals.
problem Jointly removing noise and estimating trends from sparse signals.
method PENDANTSS combines SOOT/SPOQ penalties with BEADS algorithm in a Trust-Region block alternating variable metric forward-backward approach.
result Outperforms comparable methods in deconvolving analytical chemistry signals.
We compute Khovanov homology for tangles using TQFT.
problem Khovanov homology for tangles is not well studied or computed.
method Topological Quantum Field Theory (TQFT) construction.
result A comprehensive method for computing Khovanov homology of tangles.
ChemCrow enhances LLMs for chemistry tasks, automating complex chemical processes.
problem Limited access to computational chemistry tools for large-language models.
method Integrating 18 expert-designed chemistry tools into an LLM (ChemCrow).
result ChemCrow autonomously plans and executes chemical syntheses and discoveries.
We use matricial free energy to regularize autoencoders, producing Gaussian-like codes.
problem Generating Gaussian-like codes for autoencoders.
method Define a differentiable loss function based on singular values of the code matrix, minimizing matricial free energy.
result Minimizing matricial free energy results in Gaussian-like codes that generalize.
CRPS improves GP-based sequential design for chemical space.
problem Finding molecules with specific properties in synthetic chemistry.
method Threshold-weighted CRPS as acquisition function for GP models in sequential design.
result Improved performance in molecule research with CRPS-based strategies.
Optimized DMD for fast atmospheric chemistry forecasting.
problem Forecasting global atmospheric chemistry dynamics efficiently.
method Optimized Dynamic Mode Decomposition (DMD) for reduced order modeling.
result Significant improvement in computational speed and interpretability.
Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural netwo…
Deep QMC methods use neural networks to solve quantum chemistry problems.
problem Solving the electronic Schrödinger equation from first principles.
method Quantum Monte Carlo with neural network wavefunctions.
result Highly accurate solutions at reduced computational cost.
Unified machine learning predicts molecular wavefunctions efficiently.
problem Lack of explicit electronic structure in machine learning models for chemistry.
method Deep neural network for quantum mechanical wavefunction prediction.
result Efficient prediction of molecular wavefunctions with full electronic structure access.
Alchemy dataset benchmarks AI models in chemistry.
problem Lack of diverse molecular datasets for AI models in chemistry.
method Developed a new molecular dataset with 119,487 organic molecules and benchmarked AI models on it.
result Demonstrated the usefulness of new data in validating and developing machine learning models for chemistry.
ML4Chem offers a user-friendly platform for developing and deploying machine learning models in chemistry.
problem Developing and deploying machine learning models in chemistry and materials science.
method User-experience design, six core building blocks: data, featurization, models, model optimization, inference, and visualization.
result Ease of use and functionality of the atomistic module for neural networks and kernel ridge regression.
BERT learns molecular substructures for chemistry problems.
problem Predicting chemical properties and synthesizing molecules.
method Transformer-based BERT model on molecule string representations, attention visualization.
result BERT learns to represent functional groups and atoms for various chemical properties.
Gaussian processes model sparse data in astrophysics and chemistry.
problem Scarcity of data in high-energy astrophysics and synthetic chemistry.
method Gaussian processes for uncertainty-aware predictions and inferences.
result GPs enable predictions and model latent emission from black holes and molecules.
Study examines how taxes affect wealth inequality in economic models.
problem Reducing economic inequality in models of economic activity.
method Examined Artificial Chemistry models and various tax measures.
result Effective tax measures can reduce economic inequality.
IGNN improves GNNs by maximizing edge-state transform mutual information.
problem Optimizing GNNs for better relational information.
method Variational information maximization to learn optimal transform parameters.
result IGNN achieves state-of-the-art performance on molecular graph tasks.
Graphs predict reaction conditions for organic chemistry.
problem Predicting specific reaction conditions in organic chemistry.
method Graph Neural Networks (GNNs) for modeling reaction graphs.
result GNNs can identify specific graph features affecting reaction conditions.
BoFire optimizes chemistry experiments using Bayesian Optimization.
problem Effective deployment of Bayesian Optimization in the chemical industry.
method Combines Bayesian Optimization with DoE strategies, providing a rich feature-set.
result BoFire enables seamless integration into RESTful APIs for real-world use.
We propose the Lanczos network (LanczosNet), which uses the Lanczos algorithm to construct low rank approximations of the graph Laplacian for graph convolution. Relying on the tridiagonal decomposition of the Lanczos algorithm, we not only efficiently exploit multi-scale information via fast approximated computation of…
Paper develops a method to create accurate emulators of expensive computer codes.
problem High cost and complexity of running complex computer codes.
method Active learning with Gaussian processes to construct emulators.
result Accurate and compact emulators created for expensive codes.
Gaussian processes are powerful, yet analytically tractable models for supervised learning. A Gaussian process is characterized by a mean function and a covariance function (kernel), which are determined by a model selection criterion. The functions to be compared do not just differ in their parametrization but in thei…
End-to-end learning of codes for secure BPSK communication in Gaussian wiretap channel.
problem Secure communication in the presence of an adversary for BPSK modulation.
method Learning finite-length codes using deep neural networks (DNNs) with mutual information estimation.
result Learned codes achieve near-optimal security performance, as demonstrated by numerical results.
GEMSS discovers multiple sparse solutions in high-dimensional data.
problem Identifying multiple sparse feature combinations in high-dimensional, underdetermined systems.
method GEMSS (Gaussian Ensemble for Multiple Sparse Solutions) uses a structured spike-and-slab prior, mixture of Gaussians, and Jaccard-based penalty to optimize a single objective function via stochastic gradient descent.
result GEMSS consistently outperforms five feature selection methods on 128 experiments and real-world datasets.
Proposes Gaussian process priors on graph sets with geometric structure.
problem Defining Gaussian process priors on sets of graphs with geometric structure.
method Defines priors respecting graph geometric structure, analogous to Euclidean isotropic processes.
result Efficient computational technique for evaluating priors' kernels, making them usable in toolboxes.
This work improves chemistry modeling by jointly learning reaction progress variables and look-up models.
problem Jointly modeling turbulent combustion requires solving both chemistry and flow systems simultaneously, which is computationally expensive.
method Developed a deep neural network architecture that jointly learns reaction progress variables and look-up models, improving accuracy.
result Joint learning yields more accurate results in chemistry modeling.
Generalizes bits back coding for time-series models with latent Markov structures.
problem Efficiently compressing time-series data with latent Markov structures.
method Extends bits back coding to time-series models with latent Markov structures, including HMMs and LGSSMs.
result Effective for small scale models, promising for larger scale settings like video compression.
Review of automation's role in chemical discoveries.
problem Improving autonomous discovery in chemistry.
method Classification of discovery types, assessment of autonomy, case studies.
result Rapid advancements in automation and machine learning are transforming experimentation and modeling.
New dataset abla2DFT for drug-like molecules benchmarks neural network potentials.
problem Lack of large, diverse datasets for training neural network potentials in quantum chemistry.
method Developed a new dataset abla2DFT containing energies, forces, and molecular properties for drug-like molecules. result First dataset with relaxation trajectories for drug-like molecules.
Tutorial on information bottleneck problems with connections to coding and learning.
problem Information bottleneck problems and their connections to coding and learning.
method Information theoretic perspective, practical methods, connections to various problems.
result Optimal trade-offs between relevance and complexity in discrete and vector Gaussian frameworks.
DiffC compresses images by diffusing Gaussian noise, outperforming state-of-the-art methods.
problem Efficient lossy image compression without transform coding.
method Unconditional diffusion generative models to encode and denoise corrupted pixels.
result DiffC outperforms HiFiC on ImageNet 64x64, achieving a 3 dB gain at high bitrates.
Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tas…
One endeavour of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network to build 2D compounds and layered structures atom by atom. The algorithm takes …
Transformer-M learns molecular data in 2D or 3D formats.
problem Learning models for molecules are limited to specific data formats.
method Developed a Transformer-based model that can handle 2D and 3D molecular data.
result Transformer-M achieves strong performance on both 2D and 3D molecular tasks.
Study explains Graph Convolutional Networks decisions.
problem Difficulty in understanding Graph Network decisions.
method Gradient-based and decomposition-based techniques.
result Sets groundwork for future explainability development.
Future advancement of engineering applications is dependent on design of novel materials with desired properties. Enormous size of known chemical space necessitates use of automated high throughput screening to search the desired material. The high throughput screening uses quantum chemistry calculations to predict mat…
Paper uses RL to optimize bit-flipping decoding for binary codes.
problem Improving bit-flipping decoding for binary linear codes.
method Mapped iterative decoding algorithms to MDPs for reinforcement learning.
result Learned BF decoders offer performance-complexity trade-offs and near-optimal performance.
New entropy-based objective for sparse coding improves learning.
problem Sparse coding with probabilistic priors and non-Gaussian observables.
method Derive a solely entropy-based learning objective for sparse coding parameters.
result Fully analytical ELBO objective for sparse coding with non-trivial posterior approximations.
The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the la…
Olympus benchmarks optimization algorithms for noisy experiments.
problem Benchmarking optimization algorithms on realistic experimental scenarios is challenging.
method Introduces Olympus, a software package for benchmarking optimization algorithms on synthetic experiments.
result Mitigates barriers in benchmarking optimization algorithms on realistic experimental scenarios.
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of individual (artificial) molecules, subject of reversible, but otherwise determinist…
MedGraph learns patient visit embeddings from EMRs, capturing both attributes and temporal sequences.
problem Limited EMR embedding methods fail to capture patient demographics, utilisation, and code descriptions.
method MedGraph constructs an attributed bipartite graph and uses a point process to model temporal sequences.
result MedGraph outperforms state-of-the-art methods in medical risk prediction tasks.
Kernelized PCovR reveals structure-property relations in chemistry and materials.
problem Understanding structure-property relations in complex systems.
method Kernel Principal Covariates Regression (kernel PCovR) with sparsification.
result Kernelized PCovR effectively reveals and predicts structure-property relations.
Deep neural network predicts molecular wave functions in minimal basis.
problem Improving accuracy and efficiency in quantum chemistry calculations.
method Adapted SchNet for Orbitals (SchNOrb) model in quasi-atomic minimal basis.
result Model accurately predicts molecular orbital energies and wavefunctions for large molecules.
Graph hypernetworks improve molecule property prediction and classification.
problem Improving molecule property prediction and classification using graph neural networks.
method Replacing underlying networks with hypernetworks and addressing training instability.
result Demonstrated state-of-the-art performance in various benchmarks.
Accelerated RPCholesky speeds up kernel matrix approximations.
problem Efficiently approximating large kernel matrices.
method Accelerated randomly pivoted Cholesky (RPCholesky) with block matrix computations and rejection sampling.
result Approximates kernel matrices up to 40 times faster.