Integrating Large Language Models (LLMs) within metaheuristics opens a novel path for solving complex combinatorial optimization problems. While most existing approaches leverage LLMs for code generation to create or refine specific heuristics, they often overlook the structural properties of individual problem instances. In this work, we introduce a novel framework that integrates LLMs with a Biased Random-Key Genetic Algorithm (BRKGA) to solve the NP-hard Longest Run Subsequence problem. Our approach extends the instance-driven heuristic bias paradigm by introducing a human-LLM collaborative process to co-design and implement a set of computationally efficient metrics. The LLM analyzes these instance-specific metrics to generate a tailored heuristic bias, which steers the BRKGA toward promising areas of the search space. We conduct a comprehensive experimental evaluation, including rigorous statistical tests, convergence and behavioral analyses, and targeted ablation studies, comparing our method against a standard BRKGA baseline across 1,050 generated instances of varying complexity. Results show that our top-performing hybrid, BRKGA+Llama-4-Maverick, achieves statistically significant improvements over the baseline, particularly on the most complex instances. Our findings confirm that leveraging an LLM to produce an a priori, instance-driven heuristic bias is a valuable approach for enhancing metaheuristics in complex optimization domains.

The longest run subsequence (LRS) problem is an NP-hard combinatorial optimization problem belonging to the class of subsequence problems from bioinformatics. In particular, the problem plays a role in genome reassembly. In this paper, we present a solution to the LRS problem using a Biased Random Key Genetic Algorithm (BRKGA). Our approach places particular focus on the computational efficiency of evaluating individuals, which involves converting vectors of gray values into valid solutions to the problem. For comparison purposes, a Max-Min Ant System is developed and implemented. This is in addition to the application of the integer linear programming solver CPLEX for solving all considered problem instances. The computation results show that the proposed BRKGA is currently a state-of-the-art technique for the LRS problem. Nevertheless, the results also show that there is room for improvement, especially in the context of input strings based on large alphabet sizes.

The pseudo-likelihood method is one of the most popular algorithms for learning sparse binary pairwise Markov networks. In this paper, we formulate the $L_1$ regularized pseudo-likelihood problem as a sparse multiple logistic regression problem. In this way, many insights and optimization procedures for sparse logistic regression can be applied to the learning of discrete Markov networks. Specifically, we use the coordinate descent algorithm for generalized linear models with convex penalties, combined with strong screening rules, to solve the pseudo-likelihood problem with $L_1$ regularization. Therefore a substantial speedup without losing any accuracy can be achieved. Furthermore, this method is more stable than the node-wise logistic regression approach on unbalanced high-dimensional data when penalized by small regularization parameters. Thorough numerical experiments on simulated data and real world data demonstrate the advantages of the proposed method.