Vasileios Maroulas

Bernardo Ameneyro, George Siopsis, Vasileios Maroulas

Persistent homology, a powerful mathematical tool for data analysis, summarizes the shape of data through tracking topological features across changes in different scales. Classical algorithms for persistent homology are often constrained by running times and memory requirements that grow exponentially on the number of data points. To surpass this problem, two quantum algorithms of persistent homology have been developed based on two different approaches. However, both of these quantum algorithms consider a data set in the form of a point cloud, which can be restrictive considering that many data sets come in the form of time series. In this paper, we alleviate this issue by establishing a quantum Takens's delay embedding algorithm, which turns a time series into a point cloud by considering a pertinent embedding into a higher dimensional space. Having this quantum transformation of time series to point clouds, then one may use a quantum persistent homology algorithm to extract the topological features from the point cloud associated with the original times series.

Edward C. Mitchell, Brittany Story, David Boothe et al.

The brain's spatial orientation system uses different neuron ensembles to aid in environment-based navigation. Two of the ways brains encode spatial information is through head direction cells and grid cells. Brains use head direction cells to determine orientation whereas grid cells consist of layers of decked neurons that overlay to provide environment-based navigation. These neurons fire in ensembles where several neurons fire at once to activate a single head direction or grid. We want to capture this firing structure and use it to decode head direction grid cell data. Understanding, representing, and decoding these neural structures requires models that encompass higher order connectivity, more than the 1-dimensional connectivity that traditional graph-based models provide. To that end, in this work, we develop a topological deep learning framework for neural spike train decoding. Our framework combines unsupervised simplicial complex discovery with the power of deep learning via a new architecture we develop herein called a simplicial convolutional recurrent neural network. Simplicial complexes, topological spaces that use not only vertices and edges but also higher-dimensional objects, naturally generalize graphs and capture more than just pairwise relationships. Additionally, this approach does not require prior knowledge of the neural activity beyond spike counts, which removes the need for similarity measurements. The effectiveness and versatility of the simplicial convolutional neural network is demonstrated on head direction and trajectory prediction via head direction and grid cell datasets.

Vasileios Maroulas, Panagiotis Stinis

We present a novel approach for improving particle filters for multi-target tracking. The suggested approach is based on drift homotopy for stochastic differential equations. Drift homotopy is used to design a Markov Chain Monte Carlo step which is appended to the particle filter and aims to bring the particle filter samples closer to the observations. Also, we present a simple Metropolis Monte Carlo algorithm for tackling the target-observation association problem. We have used the proposed approach on the problem of multi-target tracking for both linear and nonlinear observation models. The numerical results show that the suggested approach can improve significantly the performance of a particle filter.

Vasileios Maroulas, Panagiotis Stinis

In recent work (arXiv:1006.3100v1), we have presented a novel approach for improving particle filters for multi-target tracking. The suggested approach was based on drift homotopy for stochastic differential equations. Drift homotopy was used to design a Markov Chain Monte Carlo step which is appended to the particle filter and aims to bring the particle filter samples closer to the observations. In the current work, we present an alternative way to append a Markov Chain Monte Carlo step to a particle filter to bring the particle filter samples closer to the observations. Both current and previous approaches stem from the general formulation of the filtering problem. We have used the currently proposed approach on the problem of multi-target tracking for both linear and nonlinear observation models. The numerical results show that the suggested approach can improve significantly the performance of a particle filter.

Theodore Papamarkou, Tolga Birdal, Michael Bronstein et al.

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

Patrick Gillespie, Layal Bou Hamdan, Ioannis Schizas et al.

Equipping graph neural networks with a convolution operation defined in terms of a cellular sheaf offers advantages for learning expressive representations of heterophilic graph data. The most flexible approach to constructing the sheaf is to learn it as part of the network as a function of the node features. However, this leaves the network potentially overly sensitive to the learned sheaf. As a counter-measure, we propose a variational approach to learning cellular sheaves within sheaf neural networks, yielding an architecture we refer to as a Bayesian sheaf neural network. As part of this work, we define a novel family of reparameterizable probability distributions on the rotation group $SO(n)$ using the Cayley transform. We evaluate the Bayesian sheaf neural network on several graph datasets, and show that our Bayesian sheaf models achieve leading performance compared to baseline models and are less sensitive to the choice of hyperparameters under limited training data settings.

Bernardo Ameneyro, Rebekah Herrman, George Siopsis et al.

Topological Data Analysis methods can be useful for classification and clustering tasks in many different fields as they can provide two dimensional persistence diagrams that summarize important information about the shape of potentially complex and high dimensional data sets. The space of persistence diagrams can be endowed with various metrics such as the Wasserstein distance which admit a statistical structure and allow to use these summaries for machine learning algorithms. However, computing the distance between two persistence diagrams involves finding an optimal way to match the points of the two diagrams and may not always be an easy task for classical computers. In this work we explore the potential of quantum computers to estimate the distance between persistence diagrams, in particular we propose variational quantum algorithms for the Wasserstein distance as well as the $d^{c}_{p}$ distance. Our implementation is a weighted version of the Quantum Approximate Optimization Algorithm that relies on control clauses to encode the constraints of the optimization problem.

Sarah Harkins Dayton, Layal Bou Hamdan, Ioannis D. Schizas et al.

This chapter explores neural networks, topological data analysis, and topological deep learning techniques, alongside statistical Bayesian methods, for processing images, time series, and graphs to maximize the potential of artificial intelligence in the military domain. Throughout the chapter, we highlight practical applications spanning image, video, audio, and time-series recognition, fraud detection, and link prediction for graphical data, illustrating how topology-aware and uncertainty-aware models can enhance robustness, interpretability, and generalization.

Sarah Harkins Dayton, Hayden Everett, Ioannis Schizas et al.

Convolutional neural networks (CNNs) have been established as the main workhorse in image data processing; nonetheless, they require large amounts of data to train, often produce overconfident predictions, and frequently lack the ability to quantify the uncertainty of their predictions. To address these concerns, we propose a new Bayesian topological CNN that promotes a novel interplay between topology-aware learning and Bayesian sampling. Specifically, it utilizes information from important manifolds to accelerate training while reducing calibration error by placing prior distributions on network parameters and properly learning appropriate posteriors. One important contribution of our work is the inclusion of a consistency condition in the learning cost, which can effectively modify the prior distributions to improve the performance of our novel network architecture. We evaluate the model on benchmark image classification datasets and demonstrate its superiority over conventional CNNs, Bayesian neural networks (BNNs), and topological CNNs. In particular, we supply evidence that our method provides an advantage in situations where training data is limited or corrupted. Furthermore, we show that the new model allows for better uncertainty quantification than standard BNNs since it can more readily identify examples of out-of-distribution data on which it has not been trained. Our results highlight the potential of our novel hybrid approach for more efficient and robust image classification.

Andrew Deas, Adam Spannaus, Dakotah D. Maguire et al.

The opioid crisis remains a critical public health challenge in the United States. Despite national efforts which reduced opioid prescribing rates by nearly 45\% between 2011 and 2021, opioid-related overdose deaths more than tripled during the same period. This alarming trend reflects a major shift in the crisis, with illegal opioids now driving the majority of overdose deaths instead of prescription opioids. Although much attention has been given to supply-side factors fueling this transition, the underlying structural conditions that perpetuate and exacerbate opioid misuse remain less understood. Moreover, the COVID-19 pandemic intensified the opioid crisis through widespread social isolation and record-high unemployment; consequently, understanding the underlying drivers of this epidemic has become even more crucial in recent years. To address this need, our study examines the correlation between opioid-related mortality and thirteen county-level characteristics related to population traits, economic stability, and infrastructure. Leveraging a nationwide county-level dataset spanning consecutive years from 2010 to 2022, this study integrates empirical insights from exploratory data analysis with feature importance metrics derived from machine learning models. Our findings highlight critical regional characteristics strongly correlated with opioid-related mortality, emphasizing their potential roles in worsening the epidemic when their levels are high and mitigating it when their levels are low.

Jared Deighton, Wyatt Mackey, Ioannis Schizas et al.

Mammalian spatial navigation relies on specialized neurons, such as place and grid cells, which encode position based on self-motion and environmental cues. While extensive research has explored the computational role of grid cells, the principles underlying efficient place cell coding remain less understood. Existing spatial information rate measures primarily assess single-neuron encoding, limiting insights into population-level representations, while, the role of correlation in neural coding remains a subject of considerable debate. To address this, we introduce novel, correlation-aware information-theoretic measures that quantify the encoding efficiency of multiple neurons, including the joint stimulus information rate for neuron pairs and the spectral-stimulus information for arbitrary sized populations. The spectral-stimulus information, defined as the leading eigenvalue of the stimulus information matrix, is maximized when neurons exhibit localized, non-overlapping firing fields, mirroring place cell and head direction cell activity. We apply these measures to neural data recorded in mice and monkeys, elucidating differences in encoding efficiency across neuronal pairs and populations. Then, we demonstrate that these measures can be used to train recurrent neural networks (RNNs) via self-supervised learning, leading to the emergence of place cells and head direction cells. Our findings highlight how neural populations collectively encode stimuli, offering a more comprehensive framework for understanding stimulus encoding and optimizing artificial navigation systems in novel environments.

Wyatt Mackey, Ioannis Schizas, Jared Deighton et al.

A common technique for ameliorating the computational costs of running large neural models is sparsification, or the pruning of neural connections during training. Sparse models are capable of maintaining the high accuracy of state of the art models, while functioning at the cost of more parsimonious models. The structures which underlie sparse architectures are, however, poorly understood and not consistent between differently trained models and sparsification schemes. In this paper, we propose a new technique for sparsification of recurrent neural nets (RNNs), called moduli regularization, in combination with magnitude pruning. Moduli regularization leverages the dynamical system induced by the recurrent structure to induce a geometric relationship between neurons in the hidden state of the RNN. By making our regularizing term explicitly geometric, we provide the first, to our knowledge, a priori description of the desired sparse architecture of our neural net, as well as explicit end-to-end learning of RNN geometry. We verify the effectiveness of our scheme under diverse conditions, testing in navigation, natural language processing, and addition RNNs. Navigation is a structurally geometric task, for which there are known moduli spaces, and we show that regularization can be used to reach 90% sparsity while maintaining model performance only when coefficients are chosen in accordance with a suitable moduli space. Natural language processing and addition, however, have no known moduli space in which computations are performed. Nevertheless, we show that moduli regularization induces more stable recurrent neural nets, and achieves high fidelity models above 90% sparsity.

Theodore Papamarkou, Farzana Nasrin, Austin Lawson et al.

Topological data analysis (TDA) studies the shape patterns of data. Persistent homology is a widely used method in TDA that summarizes homological features of data at multiple scales and stores them in persistence diagrams (PDs). In this paper, we propose a random persistence diagram generator (RPDG) method that generates a sequence of random PDs from the ones produced by the data. RPDG is underpinned by a model based on pairwise interacting point processes, and a reversible jump Markov chain Monte Carlo (RJ-MCMC) algorithm. A first example, which is based on a synthetic dataset, demonstrates the efficacy of RPDG and provides a comparison with another method for sampling PDs. A second example demonstrates the utility of RPDG to solve a materials science problem given a real dataset of small sample size.

Mustafa Hajij, Ghada Zamzmi, Theodore Papamarkou et al.

Simplicial complexes form an important class of topological spaces that are frequently used in many application areas such as computer-aided design, computer graphics, and simulation. Representation learning on graphs, which are just 1-d simplicial complexes, has witnessed a great attention in recent years. However, there has not been enough effort to extend representation learning to higher dimensional simplicial objects due to the additional complexity these objects hold, especially when it comes to entire-simplicial complex representation learning. In this work, we propose a method for simplicial complex-level representation learning that embeds a simplicial complex to a universal embedding space in a way that complex-to-complex proximity is preserved. Our method uses our novel geometric message passing schemes to learn an entire simplicial complex representation in an end-to-end fashion. We demonstrate the proposed model on publicly available mesh dataset. To the best of our knowledge, this work presents the first method for learning simplicial complex-level representation.

Adam Spannaus, Kody J. H. Law, Piotr Luszczek et al.

Significant progress in many classes of materials could be made with the availability of experimentally-derived large datasets composed of atomic identities and three-dimensional coordinates. Methods for visualizing the local atomic structure, such as atom probe tomography (APT), which routinely generate datasets comprised of millions of atoms, are an important step in realizing this goal. However, state-of-the-art APT instruments generate noisy and sparse datasets that provide information about elemental type, but obscure atomic structures, thus limiting their subsequent value for materials discovery. The application of a materials fingerprinting process, a machine learning algorithm coupled with topological data analysis, provides an avenue by which here-to-fore unprecedented structural information can be extracted from an APT dataset. As a proof of concept, the material fingerprint is applied to high-entropy alloy APT datasets containing body-centered cubic (BCC) and face-centered cubic (FCC) crystal structures. A local atomic configuration centered on an arbitrary atom is assigned a topological descriptor, with which it can be characterized as a BCC or FCC lattice with near perfect accuracy, despite the inherent noise in the dataset. This successful identification of a fingerprint is a crucial first step in the development of algorithms which can extract more nuanced information, such as chemical ordering, from existing datasets of complex materials.

Ephy R. Love, Benjamin Filippenko, Vasileios Maroulas et al.

This work introduces the Topological CNN (TCNN), which encompasses several topologically defined convolutional methods. Manifolds with important relationships to the natural image space are used to parameterize image filters which are used as convolutional weights in a TCNN. These manifolds also parameterize slices in layers of a TCNN across which the weights are localized. We show evidence that TCNNs learn faster, on less data, with fewer learned parameters, and with greater generalizability and interpretability than conventional CNNs. We introduce and explore TCNN layers for both image and video data. We propose extensions to 3D images and 3D video.

Vasileios Maroulas, Cassie Putman Micucci, Farzana Nasrin

Actin cytoskeleton networks generate local topological signatures due to the natural variations in the number, size, and shape of holes of the networks. Persistent homology is a method that explores these topological properties of data and summarizes them as persistence diagrams. In this work, we analyze and classify these filament networks by transforming them into persistence diagrams whose variability is quantified via a Bayesian framework on the space of persistence diagrams. The proposed generalized Bayesian framework adopts an independent and identically distributed cluster point process characterization of persistence diagrams and relies on a substitution likelihood argument. This framework provides the flexibility to estimate the posterior cardinality distribution of points in a persistence diagram and the posterior spatial distribution simultaneously. We present a closed form of the posteriors under the assumption of Gaussian mixtures and binomials for prior intensity and cardinality respectively. Using this posterior calculation, we implement a Bayes factor algorithm to classify the actin filament networks and benchmark it against several state-of-the-art classification methods.

Farzana Nasrin, Christopher Oballe, David L. Boothe et al.

Investigation of human brain states through electroencephalograph (EEG) signals is a crucial step in human-machine communications. However, classifying and analyzing EEG signals are challenging due to their noisy, nonlinear and nonstationary nature. Current methodologies for analyzing these signals often fall short because they have several regularity assumptions baked in. This work provides an effective, flexible and noise-resilient scheme to analyze EEG by extracting pertinent information while abiding by the 3N (noisy, nonlinear and nonstationary) nature of data. We implement a topological tool, namely persistent homology, that tracks the evolution of topological features over time intervals and incorporates individual's expectations as prior knowledge by means of a Bayesian framework to compute posterior distributions. Relying on these posterior distributions, we apply Bayes factor classification to noisy EEG measurements. The performance of this Bayesian classification scheme is then compared with other existing methods for EEG signals.

Vasileios Maroulas, Cassie Putman Micucci, Adam Spannaus

This work incorporates topological features via persistence diagrams to classify point cloud data arising from materials science. Persistence diagrams are multisets summarizing the connectedness and holes of given data. A new distance on the space of persistence diagrams generates relevant input features for a classification algorithm for materials science data. This distance measures the similarity of persistence diagrams using the cost of matching points and a regularization term corresponding to cardinality differences between diagrams. Establishing stability properties of this distance provides theoretical justification for the use of the distance in comparisons of such diagrams. The classification scheme succeeds in determining the crystal structure of materials on noisy and sparse data retrieved from synthetic atom probe tomography experiments.