arXiv subjects

Behnaz Moradi-Jamei

Publications and source records attributed to Behnaz Moradi-Jamei.

5 recordsLinked to original sources

arXiv2026

FlashSpread: IO-Aware GPU Simulation of Non-Markovian Epidemic Dynamics via Kernel Fusion

Non-Markovian (renewal) epidemic simulation on multi-million-node contact networks is essential for realistic forecasting under general age-dependent holding-time distributions (log-normal, Weibull, Erlang, and similar), but the age-dependent hazard forces dense per-step updates that render the sparse event-queue strategies of standard CPU methods ineffective. We present FlashSpread, a GPU framework that consolidates the per-step renewal pipeline (CSR traversal, numerically stable erfcx-based hazard evaluation, Bernoulli tau-leaping, state transition, and next-step infectivity write-back) into a single fused Triton kernel whose intermediates never leave streaming-multiprocessor registers, with block-scalar skips that preserve CUDA Graph capture and a degree-aware CSR dispatch (thread / warp / edge-merge) that keeps the peak throughput on scale-free graphs. On an NVIDIA A100 the fused CUDA-Graph engine reaches 8.09 Giga-NUPS at N = 10^6 on a uniform-degree graph, a 217x strict hardware speedup over optimised CPU tau-leaping at the same N; on a Barabasi-Albert graph of the same size the merge-based dispatch recovers 4.5x (0.45 to 2.0 Giga-NUPS) over the default kernel, and the framework scales to N = 10^8 on a single A100 (40 GB), with a mixed-precision storage path that extends the L2-reachable scale by roughly 3x and delivers a 1.15x throughput lift at the far bandwidth-bound end. Validation against an exact non-Markovian Gillespie reference shows a structural-bias floor of approximately 6% on peak infection and approximately 7% on final attack rate that does not detectably decrease as epsilon nears 0 across two decades of tolerance, comfortably within typical epidemiological parameter uncertainty. Code: https://github.com/Shakeri-Lab/FlashSpread.

cs.DC↗

arXiv2025

A Fast Algorithm for Finding Minimum Weight Cycles in Mining Cyclic Graph Topologies

Cyclic structures are fundamental topological features in graphs, playing critical roles in network robustness, information flow, community structure, and various dynamic processes. Algorithmic tools that can efficiently probe and analyze these cyclic topologies are increasingly vital for tasks in graph mining, network optimization, bioinformatics, and social network analysis. A core primitive for quantitative analysis of cycles is finding the Minimum Weight Cycle (MWC), representing the shortest cyclic path in a weighted graph. However, computing the MWC efficiently remains a challenge, particularly compared to shortest path computations. This paper introduces a novel deterministic algorithm for finding the MWC in general weighted graphs. Our approach adapts the structure of Dijkstra's algorithm by introducing and minimizing a \textit{composite distance} metric, effectively translating the global cycle search into an iterative node-centric optimization. We provide a rigorous proof of correctness based on loop invariants. We detail two mechanisms for accelerating the search: a provable node discarding technique based on intermediate results, and a highly effective graph pruning heuristic. This heuristic dynamically restricts the search to relevant subgraphs, leveraging the principle of locality often present in complex networks to achieve significant empirical speedups, while periodic resets ensure global optimality is maintained. The efficiency of the proposed MWC algorithm enables its use as a core component in more complex analyses focused on cyclic properties. We illustrate this through a detailed application case study: accelerating the computation of the Loop Modulus, a measure of cycle richness used in advanced network characterization. Our algorithm dramatically reduces the runtime of the iterative constraint-finding bottleneck in this computation.

cs.DS↗

arXiv2021

Community Formation and Detection on GitHub Collaboration Networks

This paper studies community formation in OSS collaboration networks. While most current work examines the emergence of small-scale OSS projects, our approach draws on a large-scale historical dataset of 1.8 million GitHub users and their repository contributions. OSS collaborations are characterized by small groups of users that work closely together, leading to the presence of communities defined by short cycles in the underlying network structure. To understand the impact of this phenomenon, we apply a pre-processing step that accounts for the cyclic network structure by using Renewal-Nonbacktracking Random Walks (RNBRW) and the strength of pairwise collaborations before implementing the Louvain method to identify communities within the network. Equipping Louvain with RNBRW and the contribution strength provides a more assertive approach for detecting small-scale teams and reveals nontrivial differences in community detection such as users tendencies toward preferential attachment to more established collaboration communities. Using this method, we also identify key factors that affect community formation, including the effect of users location and primary programming language, which was determined using a comparative method of contribution activities. Overall, this paper offers several promising methodological insights for both open-source software experts and network scholars interested in studying team formation.

cs.SI↗

arXiv2019

A new method for quantifying network cyclic structure to improve community detection

A distinguishing property of communities in networks is that cycles are more prevalent within communities than across communities. Thus, the detection of these communities may be aided through the incorporation of measures of the local "richness" of the cyclic structure. In this paper, we introduce renewal non-backtracking random walks (RNBRW) as a way of quantifying this structure. RNBRW gives a weight to each edge equal to the probability that a non-backtracking random walk completes a cycle with that edge. Hence, edges with larger weights may be thought of as more important to the formation of cycles. Of note, since separate random walks can be performed in parallel, RNBRW weights can be estimated very quickly, even for large graphs. We give simulation results showing that pre-weighting edges through RNBRW may substantially improve the performance of common community detection algorithms. Our results suggest that RNBRW is especially efficient for the challenging case of detecting communities in sparse graphs.

cs.SI↗

arXiv2018

Generalization of Effective Conductance Centrality for Egonetworks

We study the popular centrality measure known as effective conductance or in some circles as information centrality. This is an important notion of centrality for undirected networks, with many applications, e.g., for random walks, electrical resistor networks, epidemic spreading, etc. In this paper, we first reinterpret this measure in terms of modulus (energy) of families of walks on the network. This modulus centrality measure coincides with the effective conductance measure on simple undirected networks, and extends it to much more general situations, e.g., directed networks as well. Secondly, we study a variation of this modulus approach in the egocentric network paradigm. Egonetworks are networks formed around a focal node (ego) with a specific order of neighborhoods. We propose efficient analytical and approximate methods for computing these measures on both undirected and directed networks. Finally, we describe a simple method inspired by the modulus point-of-view, called shell degree, which proved to be a useful tool for network science.

physics.data-an↗