arXiv subjects

Thijs Vogels

Publications and source records attributed to Thijs Vogels.

15 recordsLinked to original sources

arXiv2026

Molecular Implementation of the Machine-Learned Skala Exchange-Correlation Functional in CP2K through GauXC

Machine-learned exchange--correlation (XC) functionals offer a route to improve Kohn--Sham density-functional theory without incurring the cost of explicitly correlated electronic-structure methods. Their use in production simulation codes, however, requires a well-defined mapping between the learned model and the host-code density representation. We formulate and implement a Skala-1.1 interface in CP2K through the external GauXC library. CP2K supplies the geometry, Gaussian basis, spin-resolved atomic-orbital density matrix, and communicator, while GauXC evaluates the XC energy, atomic-orbital potential matrix, and available nuclear derivatives. The interface accepts both all-electron and valence-only density matrices. The latter may arise from separable dual-space pseudopotentials or molecular effective-core potentials. Implementation errors are isolated from functional differences by comparing the Perdew--Burke--Ernzerhof (PBE) functional evaluated through GauXC with native CP2K PBE. The resulting interface gives consistent energies, forces validated against finite-difference total-energy checks, and force-based molecular-virial diagnostics for representative molecular cases. The dietGMTKN55 benchmark suite is evaluated with an all-electron Gaussian augmented plane-wave treatment for elements up to bromine and def2 effective-core potentials for the heavier elements. The resulting aggregate mean absolute deviation of 1.255 kcal/mol is within 0.020 kcal/mol of the corresponding Skala reference value of 1.235 kcal/mol. This work establishes a validated molecular implementation of Skala in CP2K through GauXC.

physics.chem-ph↗

arXiv2026

Accurate and scalable exchange-correlation with deep learning

Density Functional Theory (DFT) underpins much of modern computational chemistry and materials science. Yet, the reliability of DFT-derived predictions of experimentally measurable properties remains fundamentally limited by the need to approximate the unknown exchange-correlation (XC) functional. The traditional paradigm for improving accuracy has relied on increasingly elaborate hand-crafted functional forms. This approach has led to a longstanding trade-off between computational efficiency and accuracy, which remains insufficient for reliable predictive modelling of laboratory experiments. Here we introduce Skala, a deep learning-based XC functional that surpasses state-of-the-art hybrid functionals in accuracy across the main-group chemistry benchmark set GMTKN55 with an error of 2.8 kcal/mol, while retaining the lower computational cost characteristic of semi-local DFT. This demonstrated departure from the historical trade-off between accuracy and efficiency is enabled by learning non-local representations of electronic structure directly from data, bypassing the need for increasingly costly hand-engineered features. Leveraging an unprecedented volume of high-accuracy reference data from wavefunction-based methods, we establish that modern deep learning enables systematically improvable neural exchange-correlation models as training datasets expand, positioning first-principles simulations to become progressively more predictive.

physics.chem-ph↗

arXiv2026

The Python Simulations of Chemistry Framework: 10 years of an open-source quantum chemistry project

Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major advances since the previous overview in 2020, covering new modules and methodology, infrastructure changes, and performance benchmarks.

physics.chem-ph↗

arXiv2026

Accurate Chemistry Collection: Coupled cluster atomization energies for broad chemical space

Accurate thermochemical data with sub-chemical accuracy (within 1 kcal mol$^{-1}$ of the empirical ground truth) are essential for advancing computational chemistry methods. However, existing datasets that reach this level of accuracy remain limited in size or scope. This hinders the development of data-driven methods with predictive accuracy across the broad chemical space of closed-shell, neutral molecules. Here we present Microsoft Research Accurate Chemistry Collection (MSR-ACC) and its first release, MSR-ACC/TAE25, comprising 73,040 total atomization energies at the CCSD(T)/CBS level obtained with the W1-F12 thermochemical protocol. The dataset is constructed to exhaustively cover the chemical space of closed-shell, charge-neutral, covalently bound equilibrium molecular structures containing up to 5 non-hydrogen atoms drawn from elements up to argon and lacking significant multireference character. The dataset and its canonical train and validation splits are openly available on Zenodo in the QCSchema format under the CDLA Permissive 2.0 license. This first release of MSR-ACC enables data-driven approaches for developing predictive computational chemistry methods with unprecedented accuracy and scope.

physics.chem-ph↗

arXiv2024

Exponential Moving Average of Weights in Deep Learning: Dynamics and Benefits

Weight averaging of Stochastic Gradient Descent (SGD) iterates is a popular method for training deep learning models. While it is often used as part of complex training pipelines to improve generalization or serve as a `teacher' model, weight averaging lacks proper evaluation on its own. In this work, we present a systematic study of the Exponential Moving Average (EMA) of weights. We first explore the training dynamics of EMA, give guidelines for hyperparameter tuning, and highlight its good early performance, partly explaining its success as a teacher. We also observe that EMA requires less learning rate decay compared to SGD since averaging naturally reduces noise, introducing a form of implicit regularization. Through extensive experiments, we show that EMA solutions differ from last-iterate solutions. EMA models not only generalize better but also exhibit improved i) robustness to noisy labels, ii) prediction consistency, iii) calibration and iv) transfer learning. Therefore, we suggest that an EMA of weights is a simple yet effective plug-in to improve the performance of deep learning models.

cs.LG↗

arXiv2024

LASER: Linear Compression in Wireless Distributed Optimization

Data-parallel SGD is the de facto algorithm for distributed optimization, especially for large scale machine learning. Despite its merits, communication bottleneck is one of its persistent issues. Most compression schemes to alleviate this either assume noiseless communication links, or fail to achieve good performance on practical tasks. In this paper, we close this gap and introduce LASER: LineAr CompreSsion in WirEless DistRibuted Optimization. LASER capitalizes on the inherent low-rank structure of gradients and transmits them efficiently over the noisy channels. Whilst enjoying theoretical guarantees similar to those of the classical SGD, LASER shows consistent gains over baselines on a variety of practical benchmarks. In particular, it outperforms the state-of-the-art compression schemes on challenging computer vision and GPT language modeling tasks. On the latter, we obtain $50$-$64 \%$ improvement in perplexity over our baselines for noisy channels.

cs.NE↗

arXiv2023

MultiModN- Multimodal, Multi-Task, Interpretable Modular Networks

Predicting multiple real-world tasks in a single model often requires a particularly diverse feature space. Multimodal (MM) models aim to extract the synergistic predictive potential of multiple data types to create a shared feature space with aligned semantic meaning across inputs of drastically varying sizes (i.e. images, text, sound). Most current MM architectures fuse these representations in parallel, which not only limits their interpretability but also creates a dependency on modality availability. We present MultiModN, a multimodal, modular network that fuses latent representations in a sequence of any number, combination, or type of modality while providing granular real-time predictive feedback on any number or combination of predictive tasks. MultiModN's composable pipeline is interpretable-by-design, as well as innately multi-task and robust to the fundamental issue of biased missingness. We perform four experiments on several benchmark MM datasets across 10 real-world tasks (predicting medical diagnoses, academic performance, and weather), and show that MultiModN's sequential MM fusion does not compromise performance compared with a baseline of parallel fusion. By simulating the challenging bias of missing not-at-random (MNAR), this work shows that, contrary to MultiModN, parallel fusion baselines erroneously learn MNAR and suffer catastrophic failure when faced with different patterns of MNAR at inference. To the best of our knowledge, this is the first inherently MNAR-resistant approach to MM modeling. In conclusion, MultiModN provides granular insights, robustness, and flexibility without compromising performance.

cs.LG↗

arXiv2023

Beyond spectral gap (extended): The role of the topology in decentralized learning

In data-parallel optimization of machine learning models, workers collaborate to improve their estimates of the model: more accurate gradients allow them to use larger learning rates and optimize faster. In the decentralized setting, in which workers communicate over a sparse graph, current theory fails to capture important aspects of real-world behavior. First, the `spectral gap' of the communication graph is not predictive of its empirical performance in (deep) learning. Second, current theory does not explain that collaboration enables larger learning rates than training alone. In fact, it prescribes smaller learning rates, which further decrease as graphs become larger, failing to explain convergence dynamics in infinite graphs. This paper aims to paint an accurate picture of sparsely-connected distributed optimization. We quantify how the graph topology influences convergence in a quadratic toy problem and provide theoretical results for general smooth and (strongly) convex objectives. Our theory matches empirical observations in deep learning, and accurately describes the relative merits of different graph topologies. This paper is an extension of the conference paper by Vogels et. al. (2022). Code: https://github.com/epfml/topology-in-decentralized-learning.

cs.LG↗

arXiv2022

Modular Clinical Decision Support Networks (MoDN) -- Updatable, Interpretable, and Portable Predictions for Evolving Clinical Environments

Data-driven Clinical Decision Support Systems (CDSS) have the potential to improve and standardise care with personalised probabilistic guidance. However, the size of data required necessitates collaborative learning from analogous CDSS's, which are often unsharable or imperfectly interoperable (IIO), meaning their feature sets are not perfectly overlapping. We propose Modular Clinical Decision Support Networks (MoDN) which allow flexible, privacy-preserving learning across IIO datasets, while providing interpretable, continuous predictive feedback to the clinician. MoDN is a novel decision tree composed of feature-specific neural network modules. It creates dynamic personalised representations of patients, and can make multiple predictions of diagnoses, updatable at each step of a consultation. The modular design allows it to compartmentalise training updates to specific features and collaboratively learn between IIO datasets without sharing any data.

cs.LG↗

arXiv2022

Beyond spectral gap: The role of the topology in decentralized learning

In data-parallel optimization of machine learning models, workers collaborate to improve their estimates of the model: more accurate gradients allow them to use larger learning rates and optimize faster. We consider the setting in which all workers sample from the same dataset, and communicate over a sparse graph (decentralized). In this setting, current theory fails to capture important aspects of real-world behavior. First, the 'spectral gap' of the communication graph is not predictive of its empirical performance in (deep) learning. Second, current theory does not explain that collaboration enables larger learning rates than training alone. In fact, it prescribes smaller learning rates, which further decrease as graphs become larger, failing to explain convergence in infinite graphs. This paper aims to paint an accurate picture of sparsely-connected distributed optimization when workers share the same data distribution. We quantify how the graph topology influences convergence in a quadratic toy problem and provide theoretical results for general smooth and (strongly) convex objectives. Our theory matches empirical observations in deep learning, and accurately describes the relative merits of different graph topologies.

cs.LG↗

arXiv2022

RelaySum for Decentralized Deep Learning on Heterogeneous Data

In decentralized machine learning, workers compute model updates on their local data. Because the workers only communicate with few neighbors without central coordination, these updates propagate progressively over the network. This paradigm enables distributed training on networks without all-to-all connectivity, helping to protect data privacy as well as to reduce the communication cost of distributed training in data centers. A key challenge, primarily in decentralized deep learning, remains the handling of differences between the workers' local data distributions. To tackle this challenge, we introduce the RelaySum mechanism for information propagation in decentralized learning. RelaySum uses spanning trees to distribute information exactly uniformly across all workers with finite delays depending on the distance between nodes. In contrast, the typical gossip averaging mechanism only distributes data uniformly asymptotically while using the same communication volume per step as RelaySum. We prove that RelaySGD, based on this mechanism, is independent of data heterogeneity and scales to many workers, enabling highly accurate decentralized deep learning on heterogeneous data. Our code is available at http://github.com/epfml/relaysgd.

cs.LG↗

arXiv2020

PowerGossip: Practical Low-Rank Communication Compression in Decentralized Deep Learning

Lossy gradient compression has become a practical tool to overcome the communication bottleneck in centrally coordinated distributed training of machine learning models. However, algorithms for decentralized training with compressed communication over arbitrary connected networks have been more complicated, requiring additional memory and hyperparameters. We introduce a simple algorithm that directly compresses the model differences between neighboring workers using low-rank linear compressors applied on model differences. Inspired by the PowerSGD algorithm for centralized deep learning, this algorithm uses power iteration steps to maximize the information transferred per bit. We prove that our method requires no additional hyperparameters, converges faster than prior methods, and is asymptotically independent of both the network and the compression. Out of the box, these compressors perform on par with state-of-the-art tuned compression algorithms in a series of deep learning benchmarks.

cs.LG↗

arXiv2020

Optimizer Benchmarking Needs to Account for Hyperparameter Tuning

The performance of optimizers, particularly in deep learning, depends considerably on their chosen hyperparameter configuration. The efficacy of optimizers is often studied under near-optimal problem-specific hyperparameters, and finding these settings may be prohibitively costly for practitioners. In this work, we argue that a fair assessment of optimizers' performance must take the computational cost of hyperparameter tuning into account, i.e., how easy it is to find good hyperparameter configurations using an automatic hyperparameter search. Evaluating a variety of optimizers on an extensive set of standard datasets and architectures, our results indicate that Adam is the most practical solution, particularly in low-budget scenarios.

cs.LG↗

arXiv2020

PowerSGD: Practical Low-Rank Gradient Compression for Distributed Optimization

We study gradient compression methods to alleviate the communication bottleneck in data-parallel distributed optimization. Despite the significant attention received, current compression schemes either do not scale well or fail to achieve the target test accuracy. We propose a new low-rank gradient compressor based on power iteration that can i) compress gradients rapidly, ii) efficiently aggregate the compressed gradients using all-reduce, and iii) achieve test performance on par with SGD. The proposed algorithm is the only method evaluated that achieves consistent wall-clock speedups when benchmarked against regular SGD with an optimized communication backend. We demonstrate reduced training times for convolutional networks as well as LSTMs on common datasets. Our code is available at https://github.com/epfml/powersgd.

cs.LG↗

arXiv2018

Web2Text: Deep Structured Boilerplate Removal

Web pages are a valuable source of information for many natural language processing and information retrieval tasks. Extracting the main content from those documents is essential for the performance of derived applications. To address this issue, we introduce a novel model that performs sequence labeling to collectively classify all text blocks in an HTML page as either boilerplate or main content. Our method uses a hidden Markov model on top of potentials derived from DOM tree features using convolutional neural networks. The proposed method sets a new state-of-the-art performance for boilerplate removal on the CleanEval benchmark. As a component of information retrieval pipelines, it improves retrieval performance on the ClueWeb12 collection.

cs.IR↗