arXiv subjects

Dmytro Matsypura

Publications and source records attributed to Dmytro Matsypura.

7 recordsLinked to original sources

arXiv2026

Designing Efficient and Reachable Routes: The $k$-Step-Central Shortest Path Problem

Designing rapid transportation routes requires balancing efficiency and reachability. Shortest-path models ensure direct, cost-efficient routes but ignore coverage, while centrality-based approaches maximize accessibility but do not enforce operational constraints. We study the problem of selecting a shortest path that maximizes reachability, measured as the number of nodes within a fixed distance of the path. To do this, we introduce the $k$-Step-Central Shortest Path problem and analyse its structural properties. We show that optimal solutions on unweighted graphs can be found in polynomial time and propose an algorithm with a novel pruning rule. We also prove that the problem becomes NP-hard when edge weights are introduced. Additionally, we show that our algorithm can be used to solve the NP-hard problem of finding the closeness-central shortest path in a graph. We demonstrate the efficiency and scalability of our algorithm on synthetic and real-world networks with up to 2,000 nodes. Our results show that improving reachability can substitute for route expansion: increasing the reach of transit lines drastically increases their coverage with shorter routes. This suggests that investments in active transport infrastructure that improve reachability can be more effective than extending primary routes, providing a data-driven basis for allocating resources in network design.

cs.DS↗

arXiv2026

An Exact Algorithm for Mixed-Integer Bilevel Stochastic Problem

We study a class of mixed-integer bilevel stochastic programs in which the leader commits to a first-stage decision before uncertainty is realized, and the follower solves a mixed-integer optimization problem for each revealed scenario. Due to the hierarchical structure and discrete variables at both levels, these problems are inherently $Σ_2^p$-hard, rendering standard single-level reformulations computationally intractable. To address this challenge, we develop an exact algorithm that combines deterministic value-function reformulations with scenario-wise decomposition. Specifically, we propose an extended single-level reformulation and a corresponding relaxation that enable scenario decomposition. We then introduce a stochastic subgradient cutting-plane scheme that dynamically generates follower optimality cuts and updates the Lagrange multipliers. We prove that, under boundedness assumptions, our algorithm converges in finite time to a global optimum and provides valid upper and lower bounds throughout its execution.

math.OC↗

arXiv2026

Learning Shortest Paths When Data is Scarce

Digital twins and other simulators are increasingly used to support routing decisions in large-scale networks. However, simulator outputs often exhibit systematic bias, while ground-truth measurements are costly and scarce. We study a stochastic shortest-path problem in which a planner has access to abundant synthetic samples, limited real-world observations, and an edge-similarity structure capturing expected behavioral similarity across links. We model the simulator-to-reality discrepancy as an unknown, edge-specific bias that varies smoothly over the similarity graph, and estimate it using Laplacian-regularized least squares. This approach yields calibrated edge cost estimates even in data-scarce regimes. We establish finite-sample error bounds, translate estimation error into path-level suboptimality guarantees, and propose a computable, data-driven certificate that verifies near-optimality of a candidate route. For cold-start settings without initial real data, we develop a bias-aware active learning algorithm that leverages the simulator and adaptively selects edges to measure until a prescribed accuracy is met. Numerical experiments on multiple road networks and traffic graphs further demonstrate the effectiveness of our methods.

cs.LG↗

arXiv2025

Centrality of shortest paths: Algorithms and complexity results

The degree centrality of a node, defined as the number of nodes adjacent to it, is often used as a measure of importance of a node to the structure of a network. This metric can be extended to paths in a network, where the degree centrality of a path is defined as the number of nodes adjacent to it. In this paper, we reconsider the problem of finding the most degree-central shortest path in an unweighted network. We propose a polynomial algorithm with the worst-case running time of $O(|E||V|^2Δ(G))$, where $|V|$ is the number of vertices in the network, $|E|$ is the number of edges in the network, and $Δ(G)$ is the maximum degree of the graph. We conduct a numerical study of our algorithm on synthetic and real-world networks and compare our results to the existing literature. In addition, we show that the same problem is NP-hard when a weighted graph is considered. Furthermore, we consider other centrality measures, such as the betweenness and closeness centrality, showing that the problem of finding the most betweenness-central shortest path is solvable in polynomial time and finding the most closeness-central shortest path is NP-hard, regardless of whether the graph is weighted or not.

cs.DS↗

arXiv2025

Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond

Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by developing a biologically informed graph-forming method to efficiently construct pathway graphs for subjects from our newly curated JR5558 mouse transcriptomics dataset. We then develop Graph-level Pseudotime Analysis (GPA) to infer graph-level trajectories that reveal how disease progresses at the population level, rather than in individual subjects. Based on the trajectories estimated by GPA, we identify the most sensitive pathways that drive disease stage transitions. In addition, we measure changes in pathway features using neural stochastic differential equations (SDEs), which enables us to formally define and compute pathway stability and disease bifurcation points (points of no return), two fundamental problems in disease progression research. We further extend our theory to the case when pathways can interact with each other, enabling a more comprehensive and multi-faceted characterization of disease phenotypes. The comprehensive experimental results demonstrate the effectiveness of our framework in reconstructing the dynamics of the pathway, identifying critical transitions, and providing novel insights into the mechanistic understanding of disease evolution.

cs.LG↗

arXiv2024

Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a major cause of blindness in older adults, severely affecting vision and quality of life. Despite advances in understanding AMD, the molecular factors driving the severity of subretinal scarring (fibrosis) remain elusive, hampering the development of effective therapies. This study introduces a machine learning-based framework to predict key genes that are strongly correlated with lesion severity and to identify potential therapeutic targets to prevent subretinal fibrosis in AMD. Using an original RNA sequencing (RNA-seq) dataset from the diseased retinas of JR5558 mice, we developed a novel and specific feature engineering technique, including pathway-based dimensionality reduction and gene-based feature expansion, to enhance prediction accuracy. Two iterative experiments were conducted by leveraging Ridge and ElasticNet regression models to assess biological relevance and gene impact. The results highlight the biological significance of several key genes and demonstrate the framework's effectiveness in identifying novel therapeutic targets. The key findings provide valuable insights for advancing drug discovery efforts and improving treatment strategies for AMD, with the potential to enhance patient outcomes by targeting the underlying genetic mechanisms of subretinal lesion development.

q-bio.GN↗

arXiv2014

Incremental Network Design with Maximum Flows

We study an incremental network design problem, where in each time period of the planning horizon an arc can be added to the network and a maximum flow problem is solved, and where the objective is to maximize the cumulative flow over the entire planning horizon. After presenting two mixed integer programming (MIP) formulations for this NP-complete problem, we describe several heuristics and prove performance bounds for some special cases. In a series of computational experiments, we compare the performance of the MIP formulations as well as the heuristics.

cs.DM↗