arXiv subjects

Kevin R. Moon

Publications and source records attributed to Kevin R. Moon.

At least 19 recordsLinked to original sources

arXiv2026

Towards 3D Scene Understanding of Gas Plumes in LWIR Hyperspectral Images Using Neural Radiance Fields

Hyperspectral images (HSI) have many applications, ranging from environmental monitoring to national security, and can be used for material detection and identification. Longwave infrared (LWIR) HSI can be used for gas plume detection and analysis. Oftentimes, only a few images of a scene of interest are available and are analyzed individually. The ability to combine information from multiple images into a single, cohesive representation could enhance analysis by providing more context on the scene's geometry and spectral properties. Neural radiance fields (NeRFs) create a latent neural representation of volumetric scene properties that enable novel-view rendering and geometry reconstruction, offering a promising avenue for hyperspectral 3D scene reconstruction. We explore the possibility of using NeRFs to create 3D scene reconstructions from LWIR HSI and demonstrate that the model can be used for the basic downstream analysis task of gas plume detection. The physics-based DIRSIG software suite was used to generate a synthetic multi-view LWIR HSI dataset of a simple facility with a strong sulfur hexafluoride gas plume. Our method, built on the standard Mip-NeRF architecture, combines state-of-the-art methods for hyperspectral NeRFs and sparse-view NeRFs, along with a novel adaptive weighted MSE loss. Our final NeRF method requires around 50% fewer training images than the standard Mip-NeRF and achieves an average PSNR of 39.8 dB with as few as 30 training images. Gas plume detection applied to NeRF-rendered test images using the adaptive coherence estimator achieves an average AUC of 0.821 when compared with detection masks generated from ground-truth test images.

cs.CV↗

arXiv2026

Random-Forest-Induced Graph Neural Networks for Tabular Learning

Graphs are essential for modeling complex relationships and capturing structured interactions in data. Graph Neural Networks (GNNs) are particularly effective when such relational structure is explicitly available, but many real-world datasets, most notably tabular data, lack an inherent graph representation. To address this limitation, we propose RF-GNN, a framework that constructs instance-level graphs from tabular data using proximity measures induced by random forests. These proximities capture nonlinear feature interactions and data-adaptive similarity without imposing restrictive assumptions on feature geometry. The resulting graphs enable the direct application of GNNs to tabular learning problems. Extensive experiments on 36 benchmark datasets demonstrate that RF-GNN consistently outperforms strong classical baselines and recent graph-construction methods in terms of weighted F1-score. Additional ablation studies highlight the impact of proximity design choices and graph construction settings.

cs.GR↗

arXiv2026

Forest-Guided Semantic Transport for Label-Supervised Manifold Alignment

Label-supervised manifold alignment bridges the gap between unsupervised and correspondence-based paradigms by leveraging shared label information to align multimodal datasets. Still, most existing methods rely on Euclidean geometry to model intra-domain relationships. This approach can fail when features are only weakly related to the task of interest, leading to noisy, semantically misleading structure and degraded alignment quality. To address this limitation, we introduce FoSTA (Forest-guided Semantic Transport Alignment), a scalable alignment framework that leverages forest-induced geometry to denoise intra-domain structure and recover task-relevant manifolds prior to alignment. FoSTA builds semantic representations directly from label-informed forest affinities and aligns them via fast, hierarchical semantic transport, capturing meaningful cross-domain relationships. Extensive comparisons with established baselines demonstrate that FoSTA improves correspondence recovery and label transfer on synthetic benchmarks and delivers strong performance in practical single-cell applications, including batch correction and biological conservation.

cs.LG↗

arXiv2026

Revisiting Forest Proximities via Sparse Leaf-Incidence Kernels

Decision forests induce supervised similarities through the partition structure of their trees. Yet forest proximity computation is still often treated as a quadratic operation in the number of samples, which limits scalability and restricts broader use in kernel and representation-learning pipelines. We introduce a unified view of leaf-collision forest proximities through a class of Separable Weighted Leaf-Collision (SWLC) kernels, showing that most existing proximities differ only in their weighting scheme while sharing a common sparse leaf-incidence structure. This yields an explicit leaf-space representation that clarifies their kernel interpretation and leads to an exact finite-sample sparse factorization of the proximity matrix, avoiding an explicit all-pairs comparison and reducing computation to sparse linear algebra over leaf collisions. We implement this framework in a memory-efficient Python library and show, both theoretically and empirically, that exact kernel computation scales near-linearly in time and memory under standard forest regimes. Benchmarks verify the predicted scaling behavior in practice across datasets, proximity definitions, and forest settings, and show that the resulting sparse leaf-space representation can also be used directly for fast task-aware embedding.

cs.LG↗

arXiv2025

Freeze, Diffuse, Decode: Task-Aware Adaptation of Transformer Embeddings for Antimicrobial Peptide Design

Pretrained transformers provide rich, general-purpose embeddings, which are transferred to downstream tasks. However, current transfer strategies: fine-tuning and probing, either distort the pretrained geometric structure of the embeddings or lack sufficient expressivity to capture task-relevant signals. These issues become even more pronounced when supervised data are scarce. Here, we introduce Freeze, Diffuse, Decode (FDD), a novel diffusion-based framework that adapts pre-trained embeddings to downstream tasks while preserving their underlying geometric structure. FDD propagates supervised signal along the intrinsic manifold of frozen embeddings, enabling a geometry-aware adaptation of the embedding space. Applied to antimicrobial peptide design, FDD yields low-dimensional, predictive, and interpretable representations that support property prediction, retrieval, and latent-space interpolation.

cs.LG↗

arXiv2025

The Generalized Proximity Forest

Recent work has demonstrated the utility of Random Forest (RF) proximities for various supervised machine learning tasks, including outlier detection, missing data imputation, and visualization. However, the utility of the RF proximities depends upon the success of the RF model, which itself is not the ideal model in all contexts. RF proximities have recently been extended to time series by means of the distance-based Proximity Forest (PF) model, among others, affording time series analysis with the benefits of RF proximities. In this work, we introduce the generalized PF model, thereby extending RF proximities to all contexts in which supervised distance-based machine learning can occur. Additionally, we introduce a variant of the PF model for regression tasks. We also introduce the notion of using the generalized PF model as a meta-learning framework, extending supervised imputation capability to any pre-trained classifier. We experimentally demonstrate the unique advantages of the generalized PF model compared with both the RF model and the $k$-nearest neighbors model.

cs.LG↗

arXiv2025

Continuous Symmetry Discovery and Enforcement Using Infinitesimal Generators of Multi-parameter Group Actions

Symmetry-informed machine learning can exhibit advantages over machine learning which fails to account for symmetry. In the context of continuous symmetry detection, current state of the art experiments are largely limited to detecting affine transformations. Herein, we outline a computationally efficient framework for discovering infinitesimal generators of multi-parameter group actions which are not generally affine transformations. This framework accommodates the automatic discovery of the number of linearly independent infinitesimal generators. We build upon recent work in continuous symmetry discovery by extending to neural networks and by restricting the symmetry search space to infinitesimal isometries. We also introduce symmetry enforcement of smooth models using vector field regularization, thereby improving model generalization. The notion of vector field similarity is also generalized for non-Euclidean Riemannian metric tensors.

stat.ML↗

arXiv2025

Random Forest Autoencoders for Guided Representation Learning

Extensive research has produced robust methods for unsupervised data visualization. Yet supervised visualization$\unicode{x2013}$where expert labels guide representations$\unicode{x2013}$remains underexplored, as most supervised approaches prioritize classification over visualization. Recently, RF-PHATE, a diffusion-based manifold learning method leveraging random forests and information geometry, marked significant progress in supervised visualization. However, its lack of an explicit mapping function limits scalability and its application to unseen data, posing challenges for large datasets and label-scarce scenarios. To overcome these limitations, we introduce Random Forest Autoencoders (RF-AE), a neural network-based framework for out-of-sample kernel extension that combines the flexibility of autoencoders with the supervised learning strengths of random forests and the geometry captured by RF-PHATE. RF-AE enables efficient out-of-sample supervised visualization and outperforms existing methods, including RF-PHATE's standard kernel extension, in both accuracy and interpretability. Additionally, RF-AE is robust to the choice of hyperparameters and generalizes to any kernel-based dimensionality reduction method.

cs.LG↗

arXiv2025

Forest Proximities for Time Series

RF-GAP has recently been introduced as an improved random forest proximity measure. In this paper, we present PF-GAP, an extension of RF-GAP proximities to proximity forests, an accurate and efficient time series classification model. We use the forest proximities in connection with Multi-Dimensional Scaling to obtain vector embeddings of univariate time series, comparing the embeddings to those obtained using various time series distance measures. We also use the forest proximities alongside Local Outlier Factors to investigate the connection between misclassified points and outliers, comparing with nearest neighbor classifiers which use time series distance measures. We show that the forest proximities seem to exhibit a stronger connection between misclassified points and outliers than nearest neighbor classifiers.

stat.ML↗

arXiv2024

Improved Background Estimation for Gas Plume Identification in Hyperspectral Images

Longwave infrared (LWIR) hyperspectral imaging can be used for many tasks in remote sensing, including detecting and identifying effluent gases by LWIR sensors on airborne platforms. Once a potential plume has been detected, it needs to be identified to determine exactly what gas or gases are present in the plume. During identification, the background underneath the plume needs to be estimated and removed to reveal the spectral characteristics of the gas of interest. Current standard practice is to use ``global" background estimation, where the average of all non-plume pixels is used to estimate the background for each pixel in the plume. However, if this global background estimate does not model the true background under the plume well, then the resulting signal can be difficult to identify correctly. The importance of proper background estimation increases when dealing with weak signals, large libraries of gases of interest, and with uncommon or heterogeneous backgrounds. In this paper, we propose two methods of background estimation, in addition to three existing methods, and compare each against global background estimation to determine which perform best at estimating the true background radiance under a plume, and for increasing identification confidence using a neural network classification model. We compare the different methods using 640 simulated plumes. We find that PCA is best at estimating the true background under a plume, with a median of 18,000 times less MSE compared to global background estimation. Our proposed K-Nearest Segments algorithm improves median neural network identification confidence by 53.2%.

eess.IV↗

arXiv2024

Conditional Local Importance by Quantile Expectations

Global variable importance measures are commonly used to interpret the results of machine learning models. Local variable importance techniques assess how variables contribute to individual observations. Current, popular methods, including LIME and SHAP, provide useful measures of feature contribution in the prediction space, while leaving opportunities for improved characterization of local structure in the model loss space. Additionally, they are not natively adapted for multi-class classification problems. We propose a new model-agnostic method for calculating local variable importance, CLIQUE, that highlights locally dependent relationships, provides improved stability over permutation-based methods, and can be directly applied to multi-class classification problems. Simulated and real-world examples show that CLIQUE emphasizes locally dependent information, captures interaction behavior beyond what can be evaluated by correlations, and assigns zero importance in regions where the response is invariant to changes in variables.

stat.ML↗

arXiv2024

Symmetry Discovery Beyond Affine Transformations

Symmetry detection can improve various machine learning tasks. In the context of continuous symmetry detection, current state of the art experiments are limited to detecting affine transformations. Under the manifold assumption, we outline a framework for discovering continuous symmetry in data beyond the affine transformation group. We also provide a similar framework for discovering discrete symmetry. We experimentally compare our method to an existing method known as LieGAN and show that our method is competitive at detecting affine symmetries for large sample sizes and superior than LieGAN for small sample sizes. We also show our method is able to detect continuous symmetries beyond the affine group and is generally more computationally efficient than LieGAN.

cs.LG↗

arXiv2024

Training-Free Guidance for Discrete Diffusion Models for Molecular Generation

Training-free guidance methods for continuous data have seen an explosion of interest due to the fact that they enable foundation diffusion models to be paired with interchangable guidance models. Currently, equivalent guidance methods for discrete diffusion models are unknown. We present a framework for applying training-free guidance to discrete data and demonstrate its utility on molecular graph generation tasks using the discrete diffusion model architecture of DiGress. We pair this model with guidance functions that return the proportion of heavy atoms that are a specific atom type and the molecular weight of the heavy atoms and demonstrate our method's ability to guide the data generation.

stat.ML↗

arXiv2024

Enhancing Supervised Visualization through Autoencoder and Random Forest Proximities for Out-of-Sample Extension

The value of supervised dimensionality reduction lies in its ability to uncover meaningful connections between data features and labels. Common dimensionality reduction methods embed a set of fixed, latent points, but are not capable of generalizing to an unseen test set. In this paper, we provide an out-of-sample extension method for the random forest-based supervised dimensionality reduction method, RF-PHATE, combining information learned from the random forest model with the function-learning capabilities of autoencoders. Through quantitative assessment of various autoencoder architectures, we identify that networks that reconstruct random forest proximities are more robust for the embedding extension problem. Furthermore, by leveraging proximity-based prototypes, we achieve a 40% reduction in training time without compromising extension quality. Our method does not require label information for out-of-sample points, thus serving as a semi-supervised method, and can achieve consistent quality using only 10% of the training data.

cs.LG↗

arXiv2024

Noisy Data Visualization using Functional Data Analysis

Data visualization via dimensionality reduction is an important tool in exploratory data analysis. However, when the data are noisy, many existing methods fail to capture the underlying structure of the data. The method called Empirical Intrinsic Geometry (EIG) was previously proposed for performing dimensionality reduction on high dimensional dynamical processes while theoretically eliminating all noise. However, implementing EIG in practice requires the construction of high-dimensional histograms, which suffer from the curse of dimensionality. Here we propose a new data visualization method called Functional Information Geometry (FIG) for dynamical processes that adapts the EIG framework while using approaches from functional data analysis to mitigate the curse of dimensionality. We experimentally demonstrate that the resulting method outperforms a variant of EIG designed for visualization in terms of capturing the true structure, hyperparameter robustness, and computational speed. We then use our method to visualize EEG brain measurements of sleep activity.

cs.LG↗

arXiv2024

Local Background Estimation for Improved Gas Plume Identification in Hyperspectral Images

Deep learning identification models have shown promise for identifying gas plumes in Longwave IR hyperspectral images of urban scenes, particularly when a large library of gases are being considered. Because many gases have similar spectral signatures, it is important to properly estimate the signal from a detected plume. Typically, a scene's global mean spectrum and covariance matrix are estimated to whiten the plume's signal, which removes the background's signature from the gas signature. However, urban scenes can have many different background materials that are spatially and spectrally heterogeneous. This can lead to poor identification performance when the global background estimate is not representative of a given local background material. We use image segmentation, along with an iterative background estimation algorithm, to create local estimates for the various background materials that reside underneath a gas plume. Our method outperforms global background estimation on a set of simulated and real gas plumes. This method shows promise in increasing deep learning identification confidence, while being simple and easy to tune when considering diverse plumes.

cs.CV↗

arXiv2023

Geometry- and Accuracy-Preserving Random Forest Proximities

Random forests are considered one of the best out-of-the-box classification and regression algorithms due to their high level of predictive performance with relatively little tuning. Pairwise proximities can be computed from a trained random forest and measure the similarity between data points relative to the supervised task. Random forest proximities have been used in many applications including the identification of variable importance, data imputation, outlier detection, and data visualization. However, existing definitions of random forest proximities do not accurately reflect the data geometry learned by the random forest. In this paper, we introduce a novel definition of random forest proximities called Random Forest-Geometry- and Accuracy-Preserving proximities (RF-GAP). We prove that the proximity-weighted sum (regression) or majority vote (classification) using RF-GAP exactly matches the out-of-bag random forest prediction, thus capturing the data geometry learned by the random forest. We empirically show that this improved geometric representation outperforms traditional random forest proximities in tasks such as data imputation and provides outlier detection and visualization results consistent with the learned data geometry.

stat.ML↗

arXiv2022

Manifold Alignment with Label Information

Multi-domain data is becoming increasingly common and presents both challenges and opportunities in the data science community. The integration of distinct data-views can be used for exploratory data analysis, and benefit downstream analysis including machine learning related tasks. With this in mind, we present a novel manifold alignment method called MALI (Manifold alignment with label information) that learns a correspondence between two distinct domains. MALI can be considered as belonging to a middle ground between the more commonly addressed semi-supervised manifold alignment problem with some known correspondences between the two domains, and the purely unsupervised case, where no known correspondences are provided. To do this, MALI learns the manifold structure in both domains via a diffusion process and then leverages discrete class labels to guide the alignment. By aligning two distinct domains, MALI recovers a pairing and a common representation that reveals related samples in both domains. Additionally, MALI can be used for the transfer learning problem known as domain adaptation. We show that MALI outperforms the current state-of-the-art manifold alignment methods across multiple datasets.

stat.ML↗