arXiv subjects

Michael Kirby

Publications and source records attributed to Michael Kirby.

At least 19 recordsLinked to original sources

arXiv2025

A Granular Grassmannian Clustering Framework via the Schubert Variety of Best Fit

In many classification and clustering tasks, it is useful to compute a geometric representative for a dataset or a cluster, such as a mean or median. When datasets are represented by subspaces, these representatives become points on the Grassmann or flag manifold, with distances induced by their geometry, often via principal angles. We introduce a subspace clustering algorithm that replaces subspace means with a trainable prototype defined as a Schubert Variety of Best Fit (SVBF) - a subspace that comes as close as possible to intersecting each cluster member in at least one fixed direction. Integrated in the Linde-Buzo-Grey (LBG) pipeline, this SVBF-LBG scheme yields improved cluster purity on synthetic, image, spectral, and video action data, while retaining the mathematical structure required for downstream analysis.

cs.LG↗

arXiv2025

Fine-tuning foundational models to code diagnoses from veterinary health records

Veterinary medical records represent a large data resource for application to veterinary and One Health clinical research efforts. Use of the data is limited by interoperability challenges including inconsistent data formats and data siloing. Clinical coding using standardized medical terminologies enhances the quality of medical records and facilitates their interoperability with veterinary and human health records from other sites. Previous studies, such as DeepTag and VetTag, evaluated the application of Natural Language Processing (NLP) to automate veterinary diagnosis coding, employing long short-term memory (LSTM) and transformer models to infer a subset of Systemized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) diagnosis codes from free-text clinical notes. This study expands on these efforts by incorporating all 7,739 distinct SNOMED-CT diagnosis codes recognized by the Colorado State University (CSU) Veterinary Teaching Hospital (VTH) and by leveraging the increasing availability of pre-trained language models (LMs). 13 freely-available pre-trained LMs were fine-tuned on the free-text notes from 246,473 manually-coded veterinary patient visits included in the CSU VTH's electronic health records (EHRs), which resulted in superior performance relative to previous efforts. The most accurate results were obtained when expansive labeled data were used to fine-tune relatively large clinical LMs, but the study also showed that comparable results can be obtained using more limited resources and non-clinical LMs. The results of this study contribute to the improvement of the quality of veterinary EHRs by investigating accessible methods for automated coding and support both animal and human health research by paving the way for more integrated and comprehensive health databases that span species and institutions.

cs.CL↗

arXiv2024

Optimizing Sparse Generalized Singular Vectors for Feature Selection in Proximal Support Vector Machines with Application to Breast and Ovarian Cancer Detection

This paper presents approaches to compute sparse solutions of Generalized Singular Value Problem (GSVP). The GSVP is regularized by $\ell_1$-norm and $\ell_q$-penalty for $0<q<1$, resulting in the $\ell_1$-GSVP and $\ell_q$-GSVP formulations. The solutions of these problems are determined by applying the proximal gradient descent algorithm with a fixed step size. The inherent sparsity levels within the computed solutions are exploited for feature selection, and subsequently, binary classification with non-parallel Support Vector Machines (SVM). For our feature selection task, SVM is integrated into the $\ell_1$-GSVP and $\ell_q$-GSVP frameworks to derive the $\ell_1$-GSVPSVM and $\ell_q$-GSVPSVM variants. Machine learning applications to cancer detection are considered. We remarkably report near-to-perfect balanced accuracy across breast and ovarian cancer datasets using a few selected features.

cs.LG↗

arXiv2024

A Multi-Domain Multi-Task Approach for Feature Selection from Bulk RNA Datasets

In this paper a multi-domain multi-task algorithm for feature selection in bulk RNAseq data is proposed. Two datasets are investigated arising from mouse host immune response to Salmonella infection. Data is collected from several strains of collaborative cross mice. Samples from the spleen and liver serve as the two domains. Several machine learning experiments are conducted and the small subset of discriminative across domains features have been extracted in each case. The algorithm proves viable and underlines the benefits of across domain feature selection by extracting new subset of discriminative features which couldn't be extracted only by one-domain approach.

cs.LG↗

arXiv2023

Status of DUNE Offline Computing

We summarize the status of Deep Underground Neutrino Experiment (DUNE) Offline Software and Computing program. We describe plans for the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes in pursuit of the experiment's physics goals of precision measurements of neutrino oscillation parameters, detection of astrophysical neutrinos, measurement of neutrino interaction properties and searches for physics beyond the Standard Model. In contrast to traditional HEP computational problems, DUNE's Liquid Argon Time Projection Chamber data consist of simple but very large (many GB) data objects which share many characteristics with astrophysical images. We have successfully reconstructed and simulated data from 4% prototype detector runs at CERN. The data volume from the full DUNE detector, when it starts commissioning late in this decade will present memory management challenges in conventional processing but significant opportunities to use advances in machine learning and pattern recognition as a frontier user of High Performance Computing facilities capable of massively parallel processing. Our goal is to develop infrastructure resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves.

physics.acc-ph↗

arXiv2023

ReLU Neural Networks, Polyhedral Decompositions, and Persistent Homolog

A ReLU neural network leads to a finite polyhedral decomposition of input space and a corresponding finite dual graph. We show that while this dual graph is a coarse quantization of input space, it is sufficiently robust that it can be combined with persistent homology to detect homological signals of manifolds in the input space from samples. This property holds for a variety of networks trained for a wide range of purposes that have nothing to do with this topological application. We found this feature to be surprising and interesting; we hope it will also be useful.

math.AT↗

arXiv2023

Feature Selection using Sparse Adaptive Bottleneck Centroid-Encoder

We introduce a novel nonlinear model, Sparse Adaptive Bottleneck Centroid-Encoder (SABCE), for determining the features that discriminate between two or more classes. The algorithm aims to extract discriminatory features in groups while reconstructing the class centroids in the ambient space and simultaneously use additional penalty terms in the bottleneck layer to decrease within-class scatter and increase the separation of different class centroids. The model has a sparsity-promoting layer (SPL) with a one-to-one connection to the input layer. Along with the primary objective, we minimize the $l_{2,1}$-norm of the sparse layer, which filters out unnecessary features from input data. During training, we update class centroids by taking the Hadamard product of the centroids and weights of the sparse layer, thus ignoring the irrelevant features from the target. Therefore the proposed method learns to reconstruct the critical components of class centroids rather than the whole centroids. The algorithm is applied to various real-world data sets, including high-dimensional biological, image, speech, and accelerometer sensor data. We compared our method to different state-of-the-art feature selection techniques, including supervised Concrete Autoencoders (SCAE), Feature Selection Networks (FsNet), Stochastic Gates (STG), and LassoNet. We empirically showed that SABCE features often produced better classification accuracy than other methods on the sequester test sets, setting new state-of-the-art results.

cs.LG↗

arXiv2023

Sparse Linear Centroid-Encoder: A Convex Method for Feature Selection

We present a novel feature selection technique, Sparse Linear Centroid-Encoder (SLCE). The algorithm uses a linear transformation to reconstruct a point as its class centroid and, at the same time, uses the $\ell_1$-norm penalty to filter out unnecessary features from the input data. The original formulation of the optimization problem is nonconvex, but we propose a two-step approach, where each step is convex. In the first step, we solve the linear Centroid-Encoder, a convex optimization problem over a matrix $A$. In the second step, we only search for a sparse solution over a diagonal matrix $B$ while keeping $A$ fixed. Unlike other linear methods, e.g., Sparse Support Vector Machines and Lasso, Sparse Linear Centroid-Encoder uses a single model for multi-class data. We present an in-depth empirical analysis of the proposed model and show that it promotes sparsity on various data sets, including high-dimensional biological data. Our experimental results show that SLCE has a performance advantage over some state-of-the-art neural network-based feature selection techniques.

cs.LG↗

arXiv2023

Yet Another Algorithm for Supervised Principal Component Analysis: Supervised Linear Centroid-Encoder

We propose a new supervised dimensionality reduction technique called Supervised Linear Centroid-Encoder (SLCE), a linear counterpart of the nonlinear Centroid-Encoder (CE) \citep{ghosh2022supervised}. SLCE works by mapping the samples of a class to its class centroid using a linear transformation. The transformation is a projection that reconstructs a point such that its distance from the corresponding class centroid, i.e., centroid-reconstruction loss, is minimized in the ambient space. We derive a closed-form solution using an eigendecomposition of a symmetric matrix. We did a detailed analysis and presented some crucial mathematical properties of the proposed approach. %We also provide an iterative solution approach based solving the optimization problem using a descent method. We establish a connection between the eigenvalues and the centroid-reconstruction loss. In contrast to Principal Component Analysis (PCA) which reconstructs a sample in the ambient space, the transformation of SLCE uses the instances of a class to rebuild the corresponding class centroid. Therefore the proposed method can be considered a form of supervised PCA. Experimental results show the performance advantage of SLCE over other supervised methods.

cs.LG↗

arXiv2023

Hamming Similarity and Graph Laplacians for Class Partitioning and Adversarial Image Detection

Researchers typically investigate neural network representations by examining activation outputs for one or more layers of a network. Here, we investigate the potential for ReLU activation patterns (encoded as bit vectors) to aid in understanding and interpreting the behavior of neural networks. We utilize Representational Dissimilarity Matrices (RDMs) to investigate the coherence of data within the embedding spaces of a deep neural network. From each layer of a network, we extract and utilize bit vectors to construct similarity scores between images. From these similarity scores, we build a similarity matrix for a collection of images drawn from 2 classes. We then apply Fiedler partitioning to the associated Laplacian matrix to separate the classes. Our results indicate, through bit vector representations, that the network continues to refine class detectability with the last ReLU layer achieving better than 95\% separation accuracy. Additionally, we demonstrate that bit vectors aid in adversarial image detection, again achieving over 95\% accuracy in separating adversarial and non-adversarial images using a simple classifier.

cs.CV↗

arXiv2022

Dual Graphs of Polyhedral Decompositions for the Detection of Adversarial Attacks

Previous work has shown that a neural network with the rectified linear unit (ReLU) activation function leads to a convex polyhedral decomposition of the input space. These decompositions can be represented by a dual graph with vertices corresponding to polyhedra and edges corresponding to polyhedra sharing a facet, which is a subgraph of a Hamming graph. This paper illustrates how one can utilize the dual graph to detect and analyze adversarial attacks in the context of digital images. When an image passes through a network containing ReLU nodes, the firing or non-firing at a node can be encoded as a bit ($1$ for ReLU activation, $0$ for ReLU non-activation). The sequence of all bit activations identifies the image with a bit vector, which identifies it with a polyhedron in the decomposition and, in turn, identifies it with a vertex in the dual graph. We identify ReLU bits that are discriminators between non-adversarial and adversarial images and examine how well collections of these discriminators can ensemble vote to build an adversarial image detector. Specifically, we examine the similarities and differences of ReLU bit vectors for adversarial images, and their non-adversarial counterparts, using a pre-trained ResNet-50 architecture. While this paper focuses on adversarial digital images, ResNet-50 architecture, and the ReLU activation function, our methods extend to other network architectures, activation functions, and types of datasets.

cs.CV↗

arXiv2022

Sparse Centroid-Encoder: A Nonlinear Model for Feature Selection

Autoencoders have been widely used as a nonlinear tool for data dimensionality reduction. While autoencoders don't utilize the label information, Centroid-Encoders (CE)\cite{ghosh2022supervised} use the class label in their learning process. In this study, we propose a sparse optimization using the Centroid-Encoder architecture to determine a minimal set of features that discriminate between two or more classes. The resulting algorithm, Sparse Centroid-Encoder (SCE), extracts discriminatory features in groups using a sparsity inducing $\ell_1$-norm while mapping a point to its class centroid. One key attribute of SCE is that it can extract informative features from a multi-modal data set, i.e., data sets whose classes appear to have multiple clusters. The algorithm is applied to a wide variety of real world data sets, including single-cell data, high dimensional biological data, image data, speech data, and accelerometer sensor data. We compared our method to various state-of-the-art feature selection techniques, including supervised Concrete Autoencoders (SCAE), Feature Selection Network (FsNet), deep feature selection (DFS), Stochastic Gate (STG), and LassoNet. We empirically showed that SCE features often produced better classification accuracy than other methods on sequester test set.

cs.LG↗

arXiv2022

Portability: A Necessary Approach for Future Scientific Software

Today's world of scientific software for High Energy Physics (HEP) is powered by x86 code, while the future will be much more reliant on accelerators like GPUs and FPGAs. The portable parallelization strategies (PPS) project of the High Energy Physics Center for Computational Excellence (HEP/CCE) is investigating solutions for portability techniques that will allow the coding of an algorithm once, and the ability to execute it on a variety of hardware products from many vendors, especially including accelerators. We think without these solutions, the scientific success of our experiments and endeavors is in danger, as software development could be expert driven and costly to be able to run on available hardware infrastructure. We think the best solution for the community would be an extension to the C++ standard with a very low entry bar for users, supporting all hardware forms and vendors. We are very far from that ideal though. We argue that in the future, as a community, we need to request and work on portability solutions and strive to reach this ideal.

physics.comp-ph↗

arXiv2022

The Flag Median and FlagIRLS

Finding prototypes (e.g., mean and median) for a dataset is central to a number of common machine learning algorithms. Subspaces have been shown to provide useful, robust representations for datasets of images, videos and more. Since subspaces correspond to points on a Grassmann manifold, one is led to consider the idea of a subspace prototype for a Grassmann-valued dataset. While a number of different subspace prototypes have been described, the calculation of some of these prototypes has proven to be computationally expensive while other prototypes are affected by outliers and produce highly imperfect clustering on noisy data. This work proposes a new subspace prototype, the flag median, and introduces the FlagIRLS algorithm for its calculation. We provide evidence that the flag median is robust to outliers and can be used effectively in algorithms like Linde-Buzo-Grey (LBG) to produce improved clusterings on Grassmannians. Numerical experiments include a synthetic dataset, the MNIST handwritten digits dataset, the Mind's Eye video dataset and the UCF YouTube action dataset. The flag median is compared the other leading algorithms for computing prototypes on the Grassmannian, namely, the $\ell_2$-median and to the flag mean. We find that using FlagIRLS to compute the flag median converges in $4$ iterations on a synthetic dataset. We also see that Grassmannian LBG with a codebook size of $20$ and using the flag median produces at least a $10\%$ improvement in cluster purity over Grassmannian LBG using the flag mean or $\ell_2$-median on the Mind's Eye dataset.

stat.ML↗

arXiv2020

Locally Linear Attributes of ReLU Neural Networks

A ReLU neural network determines/is a continuous piecewise linear map from an input space to an output space. The weights in the neural network determine a decomposition of the input space into convex polytopes and on each of these polytopes the network can be described by a single affine mapping. The structure of the decomposition, together with the affine map attached to each polytope, can be analyzed to investigate the behavior of the associated neural network.

cs.LG↗

arXiv2020

The flag manifold as a tool for analyzing and comparing data sets

The shape and orientation of data clouds reflect variability in observations that can confound pattern recognition systems. Subspace methods, utilizing Grassmann manifolds, have been a great aid in dealing with such variability. However, this usefulness begins to falter when the data cloud contains sufficiently many outliers corresponding to stray elements from another class or when the number of data points is larger than the number of features. We illustrate how nested subspace methods, utilizing flag manifolds, can help to deal with such additional confounding factors. Flag manifolds, which are parameter spaces for nested subspaces, are a natural geometric generalization of Grassmann manifolds. To make practical comparisons on a flag manifold, algorithms are proposed for determining the distances between points $[A], [B]$ on a flag manifold, where $A$ and $B$ are arbitrary orthogonal matrix representatives for $[A]$ and $[B]$, and for determining the initial direction of these minimal length geodesics. The approach is illustrated in the context of (hyper) spectral imagery showing the impact of ambient dimension, sample dimension, and flag structure.

cs.CV↗

arXiv2020

Supervised Dimensionality Reduction and Visualization using Centroid-encoder

Visualizing high-dimensional data is an essential task in Data Science and Machine Learning. The Centroid-Encoder (CE) method is similar to the autoencoder but incorporates label information to keep objects of a class close together in the reduced visualization space. CE exploits nonlinearity and labels to encode high variance in low dimensions while capturing the global structure of the data. We present a detailed analysis of the method using a wide variety of data sets and compare it with other supervised dimension reduction techniques, including NCA, nonlinear NCA, t-distributed NCA, t-distributed MCML, supervised UMAP, supervised PCA, Colored Maximum Variance Unfolding, supervised Isomap, Parametric Embedding, supervised Neighbor Retrieval Visualizer, and Multiple Relational Embedding. We empirically show that centroid-encoder outperforms most of these techniques. We also show that when the data variance is spread across multiple modalities, centroid-encoder extracts a significant amount of information from the data in low dimensional space. This key feature establishes its value to use it as a tool for data visualization.

cs.LG↗

arXiv2019

More chemical detection through less sampling: amplifying chemical signals in hyperspectral data cubes through compressive sensing

Compressive sensing (CS) is a method of sampling which permits some classes of signals to be reconstructed with high accuracy even when they were under-sampled. In this paper we explore a phenomenon in which bandwise CS sampling of a hyperspectral data cube followed by reconstruction can actually result in amplification of chemical signals contained in the cube. Perhaps most surprisingly, chemical signal amplification generally seems to increase as the level of sampling decreases. In some examples, the chemical signal is significantly stronger in a data cube reconstructed from 10% CS sampling than it is in the raw, 100% sampled data cube. We explore this phenomenon in two real-world datasets including the Physical Sciences Inc. Fabry-Pérot interferometer sensor multispectral dataset and the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset. Each of these datasets contains the release of a chemical simulant, such as glacial acetic acid, triethyl phospate, and sulfur hexafluoride, and in all cases we use the adaptive coherence estimator (ACE) to detect a target signal in the hyperspectral data cube. We end the paper by suggesting some theoretical justifications for why chemical signals would be amplified in CS sampled and reconstructed hyperspectral data cubes and discuss some practical implications.

eess.IV↗