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James Chapman

Publications and source records attributed to James Chapman.

At least 19 recordsLinked to original sources
arXiv2026

TreeCCA: Canonical Correlation Analysis via Gradient-Boosted Trees

Gradient-boosted trees dominate tabular machine learning, yet canonical correlation analysis has always relied on linear or neural encoders. We propose \textbf{TreeCCA}, the first method to train gradient-boosted tree ensembles end-to-end as CCA encoders, inheriting their plug-and-play reliability: no architecture design, familiar hyperparameters, and strong performance with defaults. The technical enabler is the Eckart-Young (EY) loss, which supplies closed-form per-sample gradients that slot directly into any standard GBT library (XGBoost, LightGBM) as a custom objective. TreeCCA is the first CCA method to combine nonlinear accuracy with native interpretability: every tree split selects one feature, so gain importances reveal which inputs drive cross-view correlation at no extra cost. We demonstrate these properties on synthetic benchmarks, where TreeCCA matches or exceeds Deep CCA (2.61 vs.\ 2.43 on Signed Power; 2.93 vs.\ 2.89 on Hermite), and on a sparse benchmark with zero linear cross-view covariance, where TreeCCA recovers the true support with $\text{Precision@}S = 1.00$ at $p=50$ while PMD finds no signal. On the UCI HAR sensor-fusion benchmark, TreeCCA achieves comparable accuracy to Deep CCA at $5\times$ lower cost, while XGBoost gain importances directly validate a physics-motivated hypothesis about the data --- an interpretation not readily available with neural encoders. Across five popular tabular multi-view datasets, TreeMCCA consistently matches or exceeds linear CCA in both nonlinear correlation extraction and downstream classification accuracy.

cs.LG↗
arXiv2025

Zero-Shot Context Generalization in Reinforcement Learning from Few Training Contexts

Deep reinforcement learning (DRL) has achieved remarkable success across multiple domains, including competitive games, natural language processing, and robotics. Despite these advancements, policies trained via DRL often struggle to generalize to evaluation environments with different parameters. This challenge is typically addressed by training with multiple contexts and/or by leveraging additional structure in the problem. However, obtaining sufficient training data across diverse contexts can be impractical in real-world applications. In this work, we consider contextual Markov decision processes (CMDPs) with transition and reward functions that exhibit regularity in context parameters. We introduce the context-enhanced Bellman equation (CEBE) to improve generalization when training on a single context. We prove both analytically and empirically that the CEBE yields a first-order approximation to the Q-function trained across multiple contexts. We then derive context sample enhancement (CSE) as an efficient data augmentation method for approximating the CEBE in deterministic control environments. We numerically validate the performance of CSE in simulation environments, showcasing its potential to improve generalization in DRL.

cs.LG↗
arXiv2025

Demystifying Topological Message-Passing with Relational Structures: A Case Study on Oversquashing in Simplicial Message-Passing

Topological deep learning (TDL) has emerged as a powerful tool for modeling higher-order interactions in relational data. However, phenomena such as oversquashing in topological message-passing remain understudied and lack theoretical analysis. We propose a unifying axiomatic framework that bridges graph and topological message-passing by viewing simplicial and cellular complexes and their message-passing schemes through the lens of relational structures. This approach extends graph-theoretic results and algorithms to higher-order structures, facilitating the analysis and mitigation of oversquashing in topological message-passing networks. Through theoretical analysis and empirical studies on simplicial networks, we demonstrate the potential of this framework to advance TDL.

cs.LG↗
arXiv2024

Stratified Non-Negative Tensor Factorization

Non-negative matrix factorization (NMF) and non-negative tensor factorization (NTF) decompose non-negative high-dimensional data into non-negative low-rank components. NMF and NTF methods are popular for their intrinsic interpretability and effectiveness on large-scale data. Recent work developed Stratified-NMF, which applies NMF to regimes where data may come from different sources (strata) with different underlying distributions, and seeks to recover both strata-dependent information and global topics shared across strata. Applying Stratified-NMF to multi-modal data requires flattening across modes, and therefore loses geometric structure contained implicitly within the tensor. To address this problem, we extend Stratified-NMF to the tensor setting by developing a multiplicative update rule and demonstrating the method on text and image data. We find that Stratified-NTF can identify interpretable topics with lower memory requirements than Stratified-NMF. We also introduce a regularized version of the method and demonstrate its effects on image data.

cs.LG↗
arXiv2024

Narrative Analysis of True Crime Podcasts With Knowledge Graph-Augmented Large Language Models

Narrative data spans all disciplines and provides a coherent model of the world to the reader or viewer. Recent advancement in machine learning and Large Language Models (LLMs) have enable great strides in analyzing natural language. However, Large language models (LLMs) still struggle with complex narrative arcs as well as narratives containing conflicting information. Recent work indicates LLMs augmented with external knowledge bases can improve the accuracy and interpretability of the resulting models. In this work, we analyze the effectiveness of applying knowledge graphs (KGs) in understanding true-crime podcast data from both classical Natural Language Processing (NLP) and LLM approaches. We directly compare KG-augmented LLMs (KGLLMs) with classical methods for KG construction, topic modeling, and sentiment analysis. Additionally, the KGLLM allows us to query the knowledge base in natural language and test its ability to factually answer questions. We examine the robustness of the model to adversarial prompting in order to test the model's ability to deal with conflicting information. Finally, we apply classical methods to understand more subtle aspects of the text such as the use of hearsay and sentiment in narrative construction and propose future directions. Our results indicate that KGLLMs outperform LLMs on a variety of metrics, are more robust to adversarial prompts, and are more capable of summarizing the text into topics.

cs.CL↗
arXiv2023

Spectroscopy-Guided Discovery of Three-Dimensional Structures of Disordered Materials with Diffusion Models

The ability to rapidly develop materials with desired properties has a transformative impact on a broad range of emerging technologies. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of amorphous carbons ($a$-C) as a representative material system from the target X-ray absorption near edge structure (XANES) spectra--a common experimental technique to probe atomic structures of materials. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e., with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.

cond-mat.mtrl-sci↗
arXiv2023

Stratified-NMF for Heterogeneous Data

Non-negative matrix factorization (NMF) is an important technique for obtaining low dimensional representations of datasets. However, classical NMF does not take into account data that is collected at different times or in different locations, which may exhibit heterogeneity. We resolve this problem by solving a modified NMF objective, Stratified-NMF, that simultaneously learns strata-dependent statistics and a shared topics matrix. We develop multiplicative update rules for this novel objective and prove convergence of the objective. Then, we experiment on synthetic data to demonstrate the efficiency and accuracy of the method. Lastly, we apply our method to three real world datasets and empirically investigate their learned features.

cs.LG↗
arXiv2023

Multi-modal Variational Autoencoders for normative modelling across multiple imaging modalities

One of the challenges of studying common neurological disorders is disease heterogeneity including differences in causes, neuroimaging characteristics, comorbidities, or genetic variation. Normative modelling has become a popular method for studying such cohorts where the 'normal' behaviour of a physiological system is modelled and can be used at subject level to detect deviations relating to disease pathology. For many heterogeneous diseases, we expect to observe abnormalities across a range of neuroimaging and biological variables. However, thus far, normative models have largely been developed for studying a single imaging modality. We aim to develop a multi-modal normative modelling framework where abnormality is aggregated across variables of multiple modalities and is better able to detect deviations than uni-modal baselines. We propose two multi-modal VAE normative models to detect subject level deviations across T1 and DTI data. Our proposed models were better able to detect diseased individuals, capture disease severity, and correlate with patient cognition than baseline approaches. We also propose a multivariate latent deviation metric, measuring deviations from the joint latent space, which outperformed feature-based metrics.

cs.CV↗
arXiv2023

Unconstrained Stochastic CCA: Unifying Multiview and Self-Supervised Learning

The Canonical Correlation Analysis (CCA) family of methods is foundational in multiview learning. Regularised linear CCA methods can be seen to generalise Partial Least Squares (PLS) and be unified with a Generalized Eigenvalue Problem (GEP) framework. However, classical algorithms for these linear methods are computationally infeasible for large-scale data. Extensions to Deep CCA show great promise, but current training procedures are slow and complicated. First we propose a novel unconstrained objective that characterizes the top subspace of GEPs. Our core contribution is a family of fast algorithms for stochastic PLS, stochastic CCA, and Deep CCA, simply obtained by applying stochastic gradient descent (SGD) to the corresponding CCA objectives. Our algorithms show far faster convergence and recover higher correlations than the previous state-of-the-art on all standard CCA and Deep CCA benchmarks. These improvements allow us to perform a first-of-its-kind PLS analysis of an extremely large biomedical dataset from the UK Biobank, with over 33,000 individuals and 500,000 features. Finally, we apply our algorithms to match the performance of `CCA-family' Self-Supervised Learning (SSL) methods on CIFAR-10 and CIFAR-100 with minimal hyper-parameter tuning, and also present theory to clarify the links between these methods and classical CCA, laying the groundwork for future insights.

cs.LG↗
arXiv2023

Algebraic Reasoning About Timeliness

Designing distributed systems to have predictable performance under high load is difficult because of resource exhaustion, non-linearity, and stochastic behaviour. Timeliness, i.e., delivering results within defined time bounds, is a central aspect of predictable performance. In this paper, we focus on timeliness using the DELTA-Q Systems Development paradigm (DELTA-QSD, developed by PNSol), which computes timeliness by modelling systems observationally using so-called outcome expressions. An outcome expression is a compositional definition of a system's observed behaviour in terms of its basic operations. Given the behaviour of the basic operations, DELTA-QSD efficiently computes the stochastic behaviour of the whole system including its timeliness. This paper formally proves useful algebraic properties of outcome expressions w.r.t. timeliness. We prove the different algebraic structures the set of outcome expressions form with the different DELTA-QSD operators and demonstrate why those operators do not form richer structures. We prove or disprove the set of all possible distributivity results on outcome expressions. On our way for disproving 8 of those distributivity results, we develop a technique called properisation, which gives rise to the first body of maths for improper random variables. Finally, we also prove 14 equivalences that have been used in the past in the practice of DELTA-QSD. An immediate benefit is rewrite rules that can be used for design exploration under established timeliness equivalence. This work is part of an ongoing project to disseminate and build tool support for DELTA-QSD. The ability to rewrite outcome expressions is essential for efficient tool support.

cs.PF↗
arXiv2023

Novel Batch Active Learning Approach and Its Application to Synthetic Aperture Radar Datasets

Active learning improves the performance of machine learning methods by judiciously selecting a limited number of unlabeled data points to query for labels, with the aim of maximally improving the underlying classifier's performance. Recent gains have been made using sequential active learning for synthetic aperture radar (SAR) data arXiv:2204.00005. In each iteration, sequential active learning selects a query set of size one while batch active learning selects a query set of multiple datapoints. While batch active learning methods exhibit greater efficiency, the challenge lies in maintaining model accuracy relative to sequential active learning methods. We developed a novel, two-part approach for batch active learning: Dijkstra's Annulus Core-Set (DAC) for core-set generation and LocalMax for batch sampling. The batch active learning process that combines DAC and LocalMax achieves nearly identical accuracy as sequential active learning but is more efficient, proportional to the batch size. As an application, a pipeline is built based on transfer learning feature embedding, graph learning, DAC, and LocalMax to classify the FUSAR-Ship and OpenSARShip datasets. Our pipeline outperforms the state-of-the-art CNN-based methods.

cs.LG↗
arXiv2023

Score-based denoising for atomic structure identification

We propose an effective method for removing thermal vibrations that complicate the task of analyzing complex dynamics in atomistic simulation of condensed matter. Our method iteratively subtracts thermal noises or perturbations in atomic positions using a denoising score function trained on synthetically noised but otherwise perfect crystal lattices. The resulting denoised structures clearly reveal underlying crystal order while retaining disorder associated with crystal defects. Purely geometric, agnostic to interatomic potentials, and trained without inputs from explicit simulations, our denoiser can be applied to simulation data generated from vastly different interatomic interactions. The denoiser is shown to improve existing classification methods such as common neighbor analysis and polyhedral template matching, reaching perfect classification accuracy on a recent benchmark dataset of thermally perturbed structures up to the melting point. Demonstrated here in a wide variety of atomistic simulation contexts, the denoiser is general, robust, and readily extendable to delineate order from disorder in structurally and chemically complex materials.

cond-mat.mtrl-sci↗
arXiv2023

A Generalized EigenGame with Extensions to Multiview Representation Learning

Generalized Eigenvalue Problems (GEPs) encompass a range of interesting dimensionality reduction methods. Development of efficient stochastic approaches to these problems would allow them to scale to larger datasets. Canonical Correlation Analysis (CCA) is one example of a GEP for dimensionality reduction which has found extensive use in problems with two or more views of the data. Deep learning extensions of CCA require large mini-batch sizes, and therefore large memory consumption, in the stochastic setting to achieve good performance and this has limited its application in practice. Inspired by the Generalized Hebbian Algorithm, we develop an approach to solving stochastic GEPs in which all constraints are softly enforced by Lagrange multipliers. Then by considering the integral of this Lagrangian function, its pseudo-utility, and inspired by recent formulations of Principal Components Analysis and GEPs as games with differentiable utilities, we develop a game-theory inspired approach to solving GEPs. We show that our approaches share much of the theoretical grounding of the previous Hebbian and game theoretic approaches for the linear case but our method permits extension to general function approximators like neural networks for certain GEPs for dimensionality reduction including CCA which means our method can be used for deep multiview representation learning. We demonstrate the effectiveness of our method for solving GEPs in the stochastic setting using canonical multiview datasets and demonstrate state-of-the-art performance for optimizing Deep CCA.

cs.LG↗
arXiv2022

Hydrogen in Disordered Titania: Connecting Local Chemistry, Structure, and Stoichiometry through Accelerated Exploration

Hydrogen incorporation in native surface oxides of metal alloys often controls the onset of metal hydriding, with implications for materials corrosion and hydrogen storage. A key representative example is titania, which forms as a passivating layer on a variety of titanium alloys for structural and functional applications. These oxides tend to be structurally diverse, featuring polymorphic phases, grain boundaries, and amorphous regions that generate a disparate set of unique local environments for hydrogen. Here, we introduce a workflow that can efficiently and accurately navigate this complexity. First, a machine learning force field, trained on ab initio molecular dynamics simulations, was used to generate amorphous configurations. Density functional theory calculations were then performed on these structures to identify local oxygen environments, which were compared against experimental observations. Second, to classify subtle differences across the disordered configuration space, we employ a graph-based sampling procedure. Finally, local hydrogen binding energies are computed using exhaustive density functional theory calculations on representative configurations. We leverage this methodology to show that hydrogen binding energetics are described by local oxygen coordination, which in turn is affected by stoichiometry. Together these results imply that hydrogen incorporation and transport in TiO$_x$ can be tailored through compositional engineering, with implications for improving performance and durability of titanium-derived alloys in hydrogen environments.

cond-mat.mtrl-sci↗
arXiv2022

Quantifying Free-volume Topology in Atomistic Structures Through a Combination of Voxelization and Graph Theory

We introduce a new computational methodology for the identification and characterization of free volume within/around atomistic configurations. This scheme employs a three-stage workflow, by which spheres are iteratively grown inside of voxels, and ultimately converted to planar graphs, which are then characterized via a graph-based order parameter. Our approach is computationally efficient, physically intuitive, and universally transferable to any material system. Validation of our methodology is performed on several sets of materials problems: (1) classification of unique free volumes in various crystal phases, (2) characterization of free volume defects in metals/alloys, and (3) autonomous detection and classification of complex surface defects during epitaxial growth simulations. Our method accurately identifies and characterizes unique free volumes over a multitude of systems and length scales, indicating its potential for future use in understanding the relationship between free volume morphology and material properties under both static and dynamic conditions.

cond-mat.mtrl-sci↗
arXiv2022

Quantifying Disorder One Atom at a Time Using an Interpretable Graph Neural Network Paradigm

Quantifying the level of atomic disorder within materials is critical to understanding how evolving local structural environments dictate performance and durability. Here, we leverage graph neural networks to define a physically interpretable metric for local disorder. This metric encodes the diversity of the local atomic configurations as a continuous spectrum between the solid and liquid phases, quantified against a distribution of thermal perturbations. We apply this novel methodology to three prototypical examples with varying levels of disorder: (1) solid-liquid interfaces, (2) polycrystalline microstructures, and (3) grain boundaries. Using elemental aluminum as a case study, we show how our paradigm can track the spatio-temporal evolution of interfaces, incorporating a mathematically defined description of the spatial boundary between order and disorder. We further show how to extract physics-preserved gradients from our continuous disorder fields, which may be used to understand and predict materials performance and failure. Overall, our framework provides an intuitive and generalizable pathway to quantify the relationship between complex local atomic structure and coarse-grained materials phenomena.

cond-mat.dis-nn↗
arXiv2022

Efficient, Interpretable Graph Neural Network Representation for Angle-dependent Properties and its Application to Optical Spectroscopy

Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for describing atomic arrangements in disordered systems. In this work, we extend the recently proposed ALIGNN encoding, which incorporates bond angles, to also include dihedral angles (ALIGNN-d). This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic structures. ALIGNN-d is applied to predict the infrared optical response of dynamically disordered Cu(II) aqua complexes, leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural components. Bond and dihedral angles are found to be critical contributors to the fine structure of the absorption response, with distortions representing transitions between more common geometries exhibiting the strongest absorption intensity. Future directions for further development of ALIGNN-d are discussed.

cs.LG↗
arXiv2021

A Type and Scope Safe Universe of Syntaxes with Binding: Their Semantics and Proofs

Almost every programming language's syntax includes a notion of binder and corresponding bound occurrences, along with the accompanying notions of $α$-equivalence, capture-avoiding substitution, typing contexts, runtime environments, and so on. In the past, implementing and reasoning about programming languages required careful handling to maintain the correct behaviour of bound variables. Modern programming languages include features that enable constraints like scope safety to be expressed in types. Nevertheless, the programmer is still forced to write the same boilerplate over again for each new implementation of a scope safe operation (e.g., renaming, substitution, desugaring, printing, etc.), and then again for correctness proofs. We present an expressive universe of syntaxes with binding and demonstrate how to (1) implement scope safe traversals once and for all by generic programming; and (2) how to derive properties of these traversals by generic proving. Our universe description, generic traversals and proofs, and our examples have all been formalised in Agda and are available in the accompanying material available online at https://github.com/gallais/generic-syntax.

cs.PL↗