arXiv subjects

Aleksandar Kartelj

Publications and source records attributed to Aleksandar Kartelj.

11 recordsLinked to original sources

arXiv2026

Longest Filled Common Subsequence for Song Identification from Degraded Audio via Construct--Merge--Solve--Adapt Optimization

This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including exact, metaheuristic, and approximation algorithms, have primarily been evaluated on small instances, which provide limited insight into their scalability. In this work, we introduce a new benchmark dataset with significantly larger instances and demonstrate that existing datasets lack the discriminative power needed to meaningfully assess algorithm performance at scale. To solve large instances efficiently, we utilize an adaptive Construct, Merge, Solve, Adapt (CMSA) framework that iteratively generates promising subproblems via component-based construction and refines them using feedback from prior iterations. Subproblems are solved using an external black-box solver. Extensive experiments on both standard and newly introduced set of large-sized instances prove that the designed adaptive CMSA achieves state-of-the-art performance, outperforming four known approaches. Notably, among 1,510 problem instances with known optimal solutions, our approach matches the proven optimum on 1,486 instances---corresponding to 98.4\% of these instances. These results demonstrate substantially improved scalability on large problem instances. As an engineering contribution, we propose a novel application of LFCS to song identification from degraded audio excerpts, using real-world energy-profile instances derived from popular music. Finally, we conduct an empirical explainability analysis to identify critical feature combinations influencing algorithm performance, revealing the key problem features associated with the success or failure of the approaches across different instance types.

cs.SD↗

arXiv2026

Neuro-Evolved Heuristics for Variable Gapped Common Subsequence Identification

This study addresses the Variable Gapped Longest Common Subsequence Problem (VGLCSP), a variant of the classical longest common subsequence problem with additional gap constraints and applications in sequence alignment and time-series analysis. While the two-sequence version has been widely studied using dynamic programming, the generalized multi-sequence form is usually solved with beam search-based heuristics, whose hand-crafted designs often lack robustness. To overcome this limitation, we propose a learning-based approach for automatically designing more effective data-driven heuristics. The heuristics are represented by a neural network with predefined architecture, whose weights are optimized by a genetic algorithm within a neuro-evolutionary framework. The learning process alternates between weight optimization and evaluation within an iterative multi-source beam search procedure, a state-of-the-art method for the problem. Rather than constructing solutions directly, the neural network learns to guide the search process, producing a neuro-evolved heuristic. We further introduce an ensemble heuristic that combines the scores of learned and the best-performing hand-crafted heuristic. Integrated into the iterative multi-source beam search framework, the resulting hybrid approach outperforms existing methods on both synthetic benchmark instances and newly introduced real-world instances with data-driven gap constraints.

cs.AI↗

arXiv2026

On Solving the Multiple Variable Gapped Longest Common Subsequence Problem

This paper addresses the Variable Gapped Longest Common Subsequence (VGLCS) problem, a generalization of the classical LCS problem involving flexible gap constraints between consecutive solutions' characters. The problem arises in molecular sequence comparison, where structural distance constraints between residues must be respected, and in time-series analysis where events are required to occur within specified temporal delays. We propose a search framework based on the root-based state graph representation, in which the state space comprises a generally large number of rooted state subgraphs. To cope with the resulting combinatorial explosion, an iterative beam search strategy is employed, dynamically maintaining a global pool of promising candidate root nodes, enabling effective control of diversification across iterations. To exploit the search for high-quality solutions, several known heuristics from the LCS literature are utilized into the standalone beam search procedure. To the best of our knowledge, this is the first comprehensive computational study on the VGLCS problem comprising 320 synthetic instances with up to 10 input sequences and up to 500 characters. Experimental results show robustness of the designed approach over the baseline beam search in comparable runtimes.

cs.AI↗

arXiv2025

Twenty Years of Personality Computing: Threats, Challenges and Future Directions

Personality Computing is a field at the intersection of Personality Psychology and Computer Science. Started in 2005, research in the field utilizes computational methods to understand and predict human personality traits. The expansion of the field has been very rapid and, by analyzing digital footprints (text, images, social media, etc.), it helped to develop systems that recognize and even replicate human personality. While offering promising applications in talent recruiting, marketing and healthcare, the ethical implications of Personality Computing are significant. Concerns include data privacy, algorithmic bias, and the potential for manipulation by personality-aware Artificial Intelligence. This paper provides an overview of the field, explores key methodologies, discusses the challenges and threats, and outlines potential future directions for responsible development and deployment of Personality Computing technologies.

cs.CL↗

arXiv2024

A Learning Search Algorithm for the Restricted Longest Common Subsequence Problem

This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for identifying similarities and discovering mutual patterns and important motifs among DNA, RNA, and protein sequences. Building on recent advancements in solving this problem through a general search framework, this paper introduces two novel heuristic approaches designed to enhance the search process by steering it towards promising regions in the search space. The first heuristic employs a probabilistic model to evaluate partial solutions during the search process. The second heuristic is based on a neural network model trained offline using a genetic algorithm. A key aspect of this approach is extracting problem-specific features of partial solutions and the complete problem instance. An effective hybrid method, referred to as the learning beam search, is developed by combining the trained neural network model with a beam search framework. An important contribution of this paper is found in the generation of real-world instances where scientific abstracts serve as input strings, and a set of frequently occurring academic words from the literature are used as restricted patterns. Comprehensive experimental evaluations demonstrate the effectiveness of the proposed approaches in solving the RLCS problem. Finally, an empirical explainability analysis is applied to the obtained results. In this way, key feature combinations and their respective contributions to the success or failure of the algorithms across different problem types are identified.

cs.AI↗

arXiv2024

A Three-Stage Algorithm for the Closest String Problem on Artificial and Real Gene Sequences

The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and designing degenerated primers, among others. There are efficient exact algorithms that have reached high-quality solutions for binary sequences. However, there is still room for improvement concerning the quality of solutions over DNA and protein sequences. In this paper, we introduce a three-stage algorithm that comprises the following process: first, we apply a novel alphabet pruning method to reduce the search space for effectively finding promising search regions. Second, a variant of beam search to find a heuristic solution is employed. This method utilizes a newly developed guiding function based on an expected distance heuristic score of partial solutions. Last, we introduce a local search to improve the quality of the solution obtained from the beam search. Furthermore, due to the lack of real-world benchmarks, two real-world datasets are introduced to verify the robustness of the method. The extensive experimental results show that the proposed method outperforms the previous approaches from the literature.

cs.AI↗

arXiv2024

Graph Protection under Multiple Simultaneous Attacks: A Heuristic Approach

This work focuses on developing an effective meta-heuristic approach to protect against simultaneous attacks on nodes of a network modeled using a graph. Specifically, we focus on the $k$-strong Roman domination problem, a generalization of the well-known Roman domination problem on graphs. This general problem is about assigning integer weights to nodes that represent the number of field armies stationed at each node in order to satisfy the protection constraints while minimizing the total weights. These constraints concern the protection of a graph against any simultaneous attack consisting of $k \in \mathbb{N}$ nodes. An attack is considered repelled if each node labeled 0 can be defended by borrowing an army from one of its neighboring nodes, ensuring that the neighbor retains at least one army for self-defense. The $k$-SRD problem has practical applications in various areas, such as developing counter-terrorism strategies or managing supply chain disruptions. The solution to this problem is notoriously difficult to find, as even checking the feasibility of the proposed solution requires an exponential number of steps. We propose a variable neighborhood search algorithm in which the feasibility of the solution is checked by introducing the concept of quasi-feasibility, which is realized by careful sampling within the set of all possible attacks. Extensive experimental evaluations show the scalability and robustness of the proposed approach compared to the two exact approaches from the literature. Experiments are conducted with random networks from the literature and newly introduced random wireless networks as well as with real-world networks. A practical application scenario, using real-world networks, involves applying our approach to graphs extracted from GeoJSON files containing geographic features of hundreds of cities or larger regions.

cs.AI↗

arXiv2022

Solving the signed Roman domination and signed total Roman domination problems with exact and heuristic methods

In this paper we deal with the signed Roman domination and signed total Roman domination problems. For each problem we propose two integer linear programming (ILP) formulations, the constraint programming (CP) formulation and variable neighborhood search (VNS) method. We present proofs for the correctness of the ILP formulations and a polyhedral study in which we show that the polyhedrons of the two model relaxations are equivalent. VNS uses specifically designed penalty function that allows the appearance of slightly infeasible solutions. The acceptance of these solutions directs the overall search process to the promising areas in the long run. All proposed approaches are tested on the large number of instances. Experimental results indicate that all of them reach optimal solutions for the most of small and middle scale instances. Both ILP models have proven to be more successful than the other two methods.

math.OC↗

arXiv2020

Topologically sensitive metaheuristics

This paper proposes topologically sensitive metaheuristics, and describes conceptual design of topologically sensitive Variable Neighborhood Search method (TVNS) and topologically sensitive Electromagnetism Metaheuristic (TEM).

cs.AI↗

arXiv2019

An Integer Linear Programming Formulation for the Convex Dominating Set Problems

Due to their importance in practice, dominating set problems in graphs have been greatly studied in past and different formulations of these problems are presented in literature. This paper's focus is on two problems: weakly convex dominating set problem (WCVXDSP) and convex dominating set problem (CVXDSP). It introduces two integer linear programming (ILP) formulation for CVXDSP and one ILP mode for WCVXDSP, as well as proof for equivalency between ILP models for CVXDSP. The proof of correctness for all introduced ILP formulations is provided by showing that optimal solution to the each ILP formulation is equal to the optimal solution of the original problem.

math.OC↗

arXiv2018

Variable neighborhood search for partitioning sparse biological networks into the maximum edge-weighted $k$-plexes

In a network, a $k$-plex represents a subset of $n$ vertices where the degree of each vertex in the subnetwork induced by this subset is at least $n-k$. The maximum edge-weight $k$-plex partitioning problem (Max-EkPP) is to find the $k$-plex partitioning in edge-weighted network, such that the sum of edge weights is maximal. The Max-EkPP has an important role in discovering new information in large sparse biological networks. We propose a variable neighborhood search (VNS) algorithm for solving Max-EkPP. The VNS implements a local search based on the 1-swap first improvement strategy and the objective function that takes into account the degree of every vertex in each partition. The objective function favors feasible solutions, also enabling a gradual increase in terms of objective function value when moving from slightly infeasible to barely feasible solutions. A comprehensive experimental computation is performed on real metabolic networks and other benchmark instances from literature. Comparing to the integer linear programming method from literature, our approach succeeds to find all known optimal solutions. For all other instances, the VNS either reaches previous best known solution or improves it. The proposed VNS is also tested on a large-scaled dataset which was not previously considered in literature.

cs.DS↗