arXiv subjects

Tenindra Abeywickrama

Publications and source records attributed to Tenindra Abeywickrama.

3 recordsLinked to original sources

arXiv2026

Identifying Multi-Hit Cancer Drivers Without Massive Parallelization: A CP, MIP, and Column Generation Framework

Cancer is often driven by specific combinations of an estimated two to nine gene mutations, known as multi-hit combinations. Identifying these multi-hit combinations of gene mutations that drive cancer is critical for understanding carcinogenesis and designing targeted therapies. We formalize this challenge as the Multi-Hit Cancer Driver Set Cover Problem (MHCDSCP), optimizing the selection of gene combinations to maximize tumor coverage while strictly minimizing normal sample misclassification. While existing approaches rely on exhaustive enumeration and massive parallelization, we introduce fast heuristics based on constraint programming and mixed integer programming formulations. Evaluated on real-world cancer genomics data, our framework matches state-of-the-art supercomputing methods using a single commodity CPU in under a minute. We also propose a price-and-branch heuristic which, by solving the root node to optimality, provides the first provably optimal solutions for over half of the benchmark instances, thereby verifying the near-optimality of our fast heuristics. These findings demonstrate that on real-world problem instances, the MHCDSCP is far less computationally demanding than previously believed, providing an accessible baseline that enables the exploration of previously intractable multi-hit modeling assumptions.

math.OC↗

arXiv2026

COL-Trees: Efficient Hierarchical Object Search in Road Networks

Location-based services rely heavily on efficient methods that search for relevant points-of-interest (POIs) near a given location. A k Nearest Neighbor (kNN) query is one such example that finds the k closest POIs from an agent's location. While most existing techniques focus on retrieving nearby POIs for a single agent, these search heuristics do not translate to many other applications. For example, Aggregate k Nearest Neighbor (AkNN) queries require POIs that are close to multiple agents. k Farthest Neighbor (kFN) queries require POIs that are the antithesis of nearest. Such problems naturally benefit from a hierarchical approach, but existing methods rely on Euclidean-based heuristics, which have diminished effectiveness in graphs such as road networks. We propose a novel data structure, COL-Tree (Compacted Object-Landmark Tree), to address this gap by enabling efficient hierarchical graph traversal using a more accurate landmark-based heuristic. We then present query algorithms that utilize COL-Trees to efficiently answer AkNN, kFN, and other queries. In our experiments on real-world and synthetic datasets, we demonstrate that our techniques significantly outperform existing approaches, achieving up to 4 orders of magnitude improvement. Moreover, this comes at a small pre-processing overhead in both theory and practice.

cs.DB↗

arXiv2016

k-Nearest Neighbors on Road Networks: A Journey in Experimentation and In-Memory Implementation

A k nearest neighbor (kNN) query on road networks retrieves the k closest points of interest (POIs) by their network distances from a given location. Today, in the era of ubiquitous mobile computing, this is a highly pertinent query. While Euclidean distance has been used as a heuristic to search for the closest POIs by their road network distance, its efficacy has not been thoroughly investigated. The most recent methods have shown significant improvement in query performance. Earlier studies, which proposed disk-based indexes, were compared to the current state-of-the-art in main memory. However, recent studies have shown that main memory comparisons can be challenging and require careful adaptation. This paper presents an extensive experimental investigation in main memory to settle these and several other issues. We use efficient and fair memory-resident implementations of each method to reproduce past experiments and conduct additional comparisons for several overlooked evaluations. Notably we revisit a previously discarded technique (IER) showing that, through a simple improvement, it is often the best performing technique.

cs.DS↗