Marko Djukanović

Marko Djukanović, Nikola Balaban, Christian Blum et al.

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.

Denica Kjorvezir, Marko Djukanović, Ana Gjorgjevikj et al.

Evaluating large language models (LLMs) across comprehensive benchmarks is expensive and time-consuming. We propose a graph-based prompt selection framework that models each benchmark as a similarity graph -- nodes are prompts connected if their embedding-space distance falls above a configurable threshold -- and applies Maximum Independent Set (MIS) algorithms to select a maximally diverse, non-redundant subset. We evaluate four MIS solvers (CPLEX, GREEDY, Online-MIS, ReduMIS) across six embedding models, three distance measures, six percentile thresholds, and four benchmarks (GPQA, IFEval, MMLU-Pro, Omni-MATH) covering 66 LLMs. Our central hypothesis -- that repeated selection under different random seeds yields consistent LLM rankings that may also differ from the full-benchmark baseline -- is strongly confirmed: Kendall's $W \geq 0.90$ in 99.2\% of stochastic configurations (mean $W = 0.997 \pm 0.008$), while at higher percentile thresholds selected subsets achieve 25--48\% prompt reduction on average. Ranking divergence from the full benchmark ($ρ< 0.95$) occurs in only 15.95\% of configurations, concentrated at low thresholds ($p_{10}$--$p_{20}$) and benchmarks (GPQA, IFEval), identifying overly dense graphs as the primary failure mode.

Alireza Abdi, Marko Djukanovic, Hesam Tahmasebi Boldaji et al.

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.

Maryam Gholami Shiri, Ivana Krminac, Marko Djukanović et al.

Benchmarking shortest-path algorithms is commonly based on aggregate performance over heterogeneous graph sets, which limits insight into how different search paradigms react to instance structure. We adopt an instance-landscape view of graph benchmarking by embedding graphs into a low-cost structural feature space and clustering them into regions of similar structure. Three benchmark suites are studied: weighted Erdős--Rényi graphs, random geometric (wireless) graphs, and real-world road networks. We evaluate four representative shortest-path solvers spanning uninformed exact search (Dijkstra), bidirectional exact search (bidirectional Dijkstra), heuristic-guided exact search (A$^{*}$), and deque-based strategies (DEQ). Clustering robustness is analyzed under multiple feature-selection schemes, and runtime distributions are compared across landscape regions using non-parametric tests. While generator parameters induce stable structural regions, we find that feature-space similarity does not necessarily imply performance similarity: significant runtime shifts are frequently observed even within the same landscape region. A merged-suite analysis further shows that different benchmark families occupy largely disjoint regions. These results highlight both the potential and the limits of structural landscapes for the structure-aware benchmarking of shortest-path algorithms.

Marko Djukanović, Jaume Reixach, Ana Nikolikj et al.

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.

Marko Djukanovic, Stefan Kapunac, Aleksandar Kartelj et al.

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.