arXiv subjects

Gustavo K. Rohde

Publications and source records attributed to Gustavo K. Rohde.

At least 19 recordsLinked to original sources

arXiv2026

FlowLOT: Linearized Optimal Transport for Flow Cytometry Analysis

Multiparameter flow cytometry generates high-dimensional, unordered single-cell mea- surement data for disease diagnosis and monitoring, yet analysis often remains dependent on manual gating, limiting scalability and reproducibility. Existing machine-learning ap- proaches can reduce annotation burden but frequently require large training cohorts and offer limited interpretability. To address these challenges, we introduce FlowLOT , an optimal-transport-based framework that models the single-cell measurement data of a pa- tient sample as an empirical cellular distribution and maps it directly into a fixed-length feature vector. Within a single transparent architecture, FlowLOT unifies high-dimensional classification, interpretable visualization, and continuous quantitative inference. In few-shot regimes, using as few as 16 patients per class on FlowCAP-II and 8 patients per class on BLAST110, it accurately distinguishes healthy from acute myeloid leukemia (AML) sam- ples, reaching 94.3% and 98.0% balanced accuracy, respectively. The underlying embedding exposes marker-level variation driving disease-associated population shifts and enables quantitative measurable residual disease (MRD) estimation, achieving a Pearson correlation of 0.82 on held-out samples and 0.79 under cross-dataset transfer. Furthermore, at the clinically relevant 0.1% threshold for leukemia-associated immunophenotype (LAIP) residual disease, FlowLOT detects positivity with 72% sensitivity at 100% specificity. By replacing subjective manual gating and black-box deep learning with a distribution-aware framework, FlowLOT offers a sample-efficient, scalable, and interpretable solution for high- dimensional cytometry under realistic clinical and experimental constraints.

q-bio.QM↗

arXiv2026

Reduced Order Modeling of One-Dimensional Conservative PDEs via the Cumulative Distribution Transform

We propose a reduced order modeling (ROM) framework for 1D conservative PDEs based on the cumulative distribution transform (CDT). The CDT maps nonnegative, equal-mass states into a Hilbert space in which 1D Wasserstein distances become weighted $L^2$ distances and translations become affine shifts. This makes the transform especially suited for transport-dominated dynamics, where Eulerian linear-subspace ROMs often suffer from slow decay of Kolmogorov widths. We study this phenomenon for scalar conservative dynamics by analyzing the solution manifold in CDT coordinates. For linear transport, the transformed solution manifold is contained in the 2-dimensional space spanned by the transformed initial datum and the constant function, and has zero Kolmogorov $2$-width. For nonlinear hyperbolic conservation laws, we prove two complementary types of estimates: robust $O(n^{-1})$ bounds that rely only on the conservative transport structure and remain meaningful after shock formation, and sharper $O(n^{-2})$ bounds in smooth pre-shock regimes. For conservative advection-diffusion, we show that the CDT trajectory remains within distance $O(\sqrt{DT})$ of the pure-transport plane, and we also obtain sharper $O(D^2T^2)$ estimates under additional regularity or away from initial layers. In both cases, the zero 2-width behavior of linear transport is recovered as the diffusion coefficient tends to zero. Motivated by these estimates, we develop a CDT-POD numerical scheme: snapshots are mapped to CDT space, Proper Orthogonal Decomposition (POD) is performed in transformed coordinates, and the inverse CDT is used to reconstruct physical states. Numerical experiments for several transport-dominated dynamics show that CDT-POD can capture solution manifolds with substantially fewer modes than Eulerian POD.

math.AP↗

arXiv2025

An Efficient Transport-Based Dissimilarity Measure for Time Series Classification under Warping Distortions

Time Series Classification (TSC) is an important problem with numerous applications in science and technology. Dissimilarity-based approaches, such as Dynamic Time Warping (DTW), are classical methods for distinguishing time series when time deformations are confounding information. In this paper, starting from a deformation-based model for signal classes we define a problem statement for time series classification problem. We show that, under theoretically ideal conditions, a continuous version of classic 1NN-DTW method can solve the stated problem, even when only one training sample is available. In addition, we propose an alternative dissimilarity measure based on Optimal Transport and show that it can also solve the aforementioned problem statement at a significantly reduced computational cost. Finally, we demonstrate the application of the newly proposed approach in simulated and real time series classification data, showing the efficacy of the method.

cs.IT↗

arXiv2023

Data-driven Identification of Parametric Governing Equations of Dynamical Systems Using the Signed Cumulative Distribution Transform

This paper presents a novel data-driven approach to identify partial differential equation (PDE) parameters of a dynamical system. Specifically, we adopt a mathematical "transport" model for the solution of the dynamical system at specific spatial locations that allows us to accurately estimate the model parameters, including those associated with structural damage. This is accomplished by means of a newly-developed mathematical transform, the signed cumulative distribution transform (SCDT), which is shown to convert the general nonlinear parameter estimation problem into a simple linear regression. This approach has the additional practical advantage of requiring no a priori knowledge of the source of the excitation (or, alternatively, the initial conditions). By using training data, we devise a coarse regression procedure to recover different PDE parameters from the PDE solution measured at a single location. Numerical experiments show that the proposed regression procedure is capable of detecting and estimating PDE parameters with superior accuracy compared to a number of recently developed machine learning methods. Furthermore, a damage identification experiment conducted on a publicly available dataset provides strong evidence of the proposed method's effectiveness in structural health monitoring (SHM) applications. The Python implementation of the proposed system identification technique is integrated as a part of the software package PyTransKit (https://github.com/rohdelab/PyTransKit).

eess.SP↗

arXiv2023

LCOT: Linear circular optimal transport

The optimal transport problem for measures supported on non-Euclidean spaces has recently gained ample interest in diverse applications involving representation learning. In this paper, we focus on circular probability measures, i.e., probability measures supported on the unit circle, and introduce a new computationally efficient metric for these measures, denoted as Linear Circular Optimal Transport (LCOT). The proposed metric comes with an explicit linear embedding that allows one to apply Machine Learning (ML) algorithms to the embedded measures and seamlessly modify the underlying metric for the ML algorithm to LCOT. We show that the proposed metric is rooted in the Circular Optimal Transport (COT) and can be considered the linearization of the COT metric with respect to a fixed reference measure. We provide a theoretical analysis of the proposed metric and derive the computational complexities for pairwise comparison of circular probability measures. Lastly, through a set of numerical experiments, we demonstrate the benefits of LCOT in learning representations of circular measures.

cs.LG↗

arXiv2023

The Radon Signed Cumulative Distribution Transform and its applications in classification of Signed Images

Here we describe a new image representation technique based on the mathematics of transport and optimal transport. The method relies on the combination of the well-known Radon transform for images and a recent signal representation method called the Signed Cumulative Distribution Transform. The newly proposed method generalizes previous transport-related image representation methods to arbitrary functions (images), and thus can be used in more applications. We describe the new transform, and some of its mathematical properties and demonstrate its ability to partition image classes with real and simulated data. In comparison to existing transport transform methods, as well as deep learning-based classification methods, the new transform more accurately represents the information content of signed images, and thus can be used to obtain higher classification accuracies. The implementation of the proposed method in Python language is integrated as a part of the software package PyTransKit, available on Github.

cs.IT↗

arXiv2022

Learning Energy-Based Models With Adversarial Training

We study a new approach to learning energy-based models (EBMs) based on adversarial training (AT). We show that (binary) AT learns a special kind of energy function that models the support of the data distribution, and the learning process is closely related to MCMC-based maximum likelihood learning of EBMs. We further propose improved techniques for generative modeling with AT, and demonstrate that this new approach is capable of generating diverse and realistic images. Aside from having competitive image generation performance to explicit EBMs, the studied approach is stable to train, is well-suited for image translation tasks, and exhibits strong out-of-distribution adversarial robustness. Our results demonstrate the viability of the AT approach to generative modeling, suggesting that AT is a competitive alternative approach to learning EBMs.

cs.LG↗

arXiv2022

GAT: Generative Adversarial Training for Adversarial Example Detection and Robust Classification

The vulnerabilities of deep neural networks against adversarial examples have become a significant concern for deploying these models in sensitive domains. Devising a definitive defense against such attacks is proven to be challenging, and the methods relying on detecting adversarial samples are only valid when the attacker is oblivious to the detection mechanism. In this paper we propose a principled adversarial example detection method that can withstand norm-constrained white-box attacks. Inspired by one-versus-the-rest classification, in a K class classification problem, we train K binary classifiers where the i-th binary classifier is used to distinguish between clean data of class i and adversarially perturbed samples of other classes. At test time, we first use a trained classifier to get the predicted label (say k) of the input, and then use the k-th binary classifier to determine whether the input is a clean sample (of class k) or an adversarially perturbed example (of other classes). We further devise a generative approach to detecting/classifying adversarial examples by interpreting each binary classifier as an unnormalized density model of the class-conditional data. We provide comprehensive evaluation of the above adversarial example detection/classification methods, and demonstrate their competitive performances and compelling properties.

cs.LG↗

arXiv2022

Invariance encoding in sliced-Wasserstein space for image classification with limited training data

Deep convolutional neural networks (CNNs) are broadly considered to be state-of-the-art generic end-to-end image classification systems. However, they are known to underperform when training data are limited and thus require data augmentation strategies that render the method computationally expensive and not always effective. Rather than using a data augmentation strategy to encode invariances as typically done in machine learning, here we propose to mathematically augment a nearest subspace classification model in sliced-Wasserstein space by exploiting certain mathematical properties of the Radon Cumulative Distribution Transform (R-CDT), a recently introduced image transform. We demonstrate that for a particular type of learning problem, our mathematical solution has advantages over data augmentation with deep CNNs in terms of classification accuracy and computational complexity, and is particularly effective under a limited training data setting. The method is simple, effective, computationally efficient, non-iterative, and requires no parameters to be tuned. Python code implementing our method is available at https://github.com/rohdelab/mathematical_augmentation. Our method is integrated as a part of the software package PyTransKit, which is available at https://github.com/rohdelab/PyTransKit.

cs.CV↗

arXiv2022

End-to-End Signal Classification in Signed Cumulative Distribution Transform Space

This paper presents a new end-to-end signal classification method using the signed cumulative distribution transform (SCDT). We adopt a transport-based generative model to define the classification problem. We then make use of mathematical properties of the SCDT to render the problem easier in transform domain, and solve for the class of an unknown sample using a nearest local subspace (NLS) search algorithm in SCDT domain. Experiments show that the proposed method provides high accuracy classification results while being data efficient, robust to out-of-distribution samples, and competitive in terms of computational complexity with respect to the deep learning end-to-end classification methods. The implementation of the proposed method in Python language is integrated as a part of the software package PyTransKit (https://github.com/rohdelab/PyTransKit).

eess.SP↗

arXiv2022

Geodesic Properties of a Generalized Wasserstein Embedding for Time Series Analysis

Transport-based metrics and related embeddings (transforms) have recently been used to model signal classes where nonlinear structures or variations are present. In this paper, we study the geodesic properties of time series data with a generalized Wasserstein metric and the geometry related to their signed cumulative distribution transforms in the embedding space. Moreover, we show how understanding such geometric characteristics can provide added interpretability to certain time series classifiers, and be an inspiration for more robust classifiers.

cs.LG↗

arXiv2022

Cell image classification: a comparative overview

Cell image classification methods are currently being used in numerous applications in cell biology and medicine. Applications include understanding the effects of genes and drugs in screening experiments, understanding the role and subcellular localization of different proteins, as well as diagnosis and prognosis of cancer from images acquired using cytological and histological techniques. We review three different approaches for cell image classification: numerical feature extraction, end to end classification with neural networks, and transport-based morphometry. In addition, we provide comparisons on four different cell imaging datasets to highlight the relative strength of each method.

q-bio.QM↗

arXiv2022

Radon cumulative distribution transform subspace modeling for image classification

We present a new supervised image classification method applicable to a broad class of image deformation models. The method makes use of the previously described Radon Cumulative Distribution Transform (R-CDT) for image data, whose mathematical properties are exploited to express the image data in a form that is more suitable for machine learning. While certain operations such as translation, scaling, and higher-order transformations are challenging to model in native image space, we show the R-CDT can capture some of these variations and thus render the associated image classification problems easier to solve. The method -- utilizing a nearest-subspace algorithm in R-CDT space -- is simple to implement, non-iterative, has no hyper-parameters to tune, is computationally efficient, label efficient, and provides competitive accuracies to state-of-the-art neural networks for many types of classification problems. In addition to the test accuracy performances, we show improvements (with respect to neural network-based methods) in terms of computational efficiency (it can be implemented without the use of GPUs), number of training samples needed for training, as well as out-of-distribution generalization. The Python code for reproducing our results is available at https://github.com/rohdelab/rcdt_ns_classifier.

cs.CV↗

arXiv2022

Nearest Subspace Search in The Signed Cumulative Distribution Transform Space for 1D Signal Classification

This paper presents a new method to classify 1D signals using the signed cumulative distribution transform (SCDT). The proposed method exploits certain linearization properties of the SCDT to render the problem easier to solve in the SCDT space. The method uses the nearest subspace search technique in the SCDT domain to provide a non-iterative, effective, and simple to implement classification algorithm. Experiments show that the proposed technique outperforms the state-of-the-art neural networks using a very low number of training samples and is also robust to out-of-distribution examples on simulated data. We also demonstrate the efficacy of the proposed technique in real-world applications by applying it to an ECG classification problem. The python code implementing the proposed classifier can be found in PyTransKit (https://github.com/rohdelab/PyTransKit).

eess.SP↗

arXiv2022

Local Sliced-Wasserstein Feature Sets for Illumination-invariant Face Recognition

We present a new method for face recognition from digital images acquired under varying illumination conditions. The method is based on mathematical modeling of local gradient distributions using the Radon Cumulative Distribution Transform (R-CDT). We demonstrate that lighting variations cause certain types of deformations of local image gradient distributions which, when expressed in R-CDT domain, can be modeled as a subspace. Face recognition is then performed using a nearest subspace in R-CDT domain of local gradient distributions. Experiment results demonstrate the proposed method outperforms other alternatives in several face recognition tasks with challenging illumination conditions. Python code implementing the proposed method is available, which is integrated as a part of the software package PyTransKit.

cs.CV↗

arXiv2021

The Signed Cumulative Distribution Transform for 1-D Signal Analysis and Classification

This paper presents a new mathematical signal transform that is especially suitable for decoding information related to non-rigid signal displacements. We provide a measure theoretic framework to extend the existing Cumulative Distribution Transform [ACHA 45 (2018), no. 3, 616-641] to arbitrary (signed) signals on $\overline{\mathbb{R}}$. We present both forward (analysis) and inverse (synthesis) formulas for the transform, and describe several of its properties including translation, scaling, convexity, linear separability and others. Finally, we describe a metric in transform space, and demonstrate the application of the transform in classifying (detecting) signals under random displacements.

cs.IT↗

arXiv2021

Wasserstein Embedding for Graph Learning

We present Wasserstein Embedding for Graph Learning (WEGL), a novel and fast framework for embedding entire graphs in a vector space, in which various machine learning models are applicable for graph-level prediction tasks. We leverage new insights on defining similarity between graphs as a function of the similarity between their node embedding distributions. Specifically, we use the Wasserstein distance to measure the dissimilarity between node embeddings of different graphs. Unlike prior work, we avoid pairwise calculation of distances between graphs and reduce the computational complexity from quadratic to linear in the number of graphs. WEGL calculates Monge maps from a reference distribution to each node embedding and, based on these maps, creates a fixed-sized vector representation of the graph. We evaluate our new graph embedding approach on various benchmark graph-property prediction tasks, showing state-of-the-art classification performance while having superior computational efficiency. The code is available at https://github.com/navid-naderi/WEGL.

cs.LG↗

arXiv2021

Partitioning signal classes using transport transforms for data analysis and machine learning

A relatively new set of transport-based transforms (CDT, R-CDT, LOT) have shown their strength and great potential in various image and data processing tasks such as parametric signal estimation, classification, cancer detection among many others. It is hence worthwhile to elucidate some of the mathematical properties that explain the successes of these transforms when they are used as tools in data analysis, signal processing or data classification. In particular, we give conditions under which classes of signals that are created by algebraic generative models are transformed into convex sets by the transport transforms. Such convexification of the classes simplify the classification and other data analysis and processing problems when viewed in the transform domain. More specifically, we study the extent and limitation of the convexification ability of these transforms under an algebraic generative modeling framework. We hope that this paper will serve as an introduction to these transforms and will encourage mathematicians and other researchers to further explore the theoretical underpinnings and algorithmic tools that will help understand the successes of these transforms and lay the groundwork for further successful applications.

cs.LG↗