arXiv subjects

Jose Guadalupe Hernandez

Publications and source records attributed to Jose Guadalupe Hernandez.

12 recordsLinked to original sources

arXiv2026

Automating Parent Selection Configuration in Genetic Programming with Agentic AI

We investigate whether agentic artificial intelligence can automate parts of the process of designing genetic programming systems by introducing an agentic framework that identifies and implements parent selection algorithms using large language model (LLM) reasoning and retrieval-augmented generation. Using symbolic regression as a test bed, we first conduct an ablation study across four LLM types to evaluate the effects of agentic reasoning and retrieval on generated algorithm categories, validity, implementation similarity, and downstream performance. Results show that these components substantially influence the types of algorithms generated, but their downstream performance largely depends on the underlying LLM. The strongest configuration, the full agentic setup with 5 mini (5 mini--AR), consistently generated established $ε$-lexicase implementations while maintaining competitive downstream performance. We then benchmark this configuration against fixed implementations of tournament selection and semi-dynamic MAD $ε$-lexicase. Across six symbolic regression problems, 5 mini--AR performed similarly to $ε$-lexicase while generally outperforming tournament selection. These findings demonstrate the potential of agentic AI to translate domain knowledge into generating executable components, providing a step toward automated configuration and design of evolutionary systems.

cs.NE↗

arXiv2026

The impact of objective interactions on the performance of massive objective optimization algorithms

Many-objective optimization has been a field of interest over the past two decades and several evolutionary optimization algorithms have been introduced to tackle these problems; yet two fundamental questions remain underexplored: (i) What happens when the number of objectives grows beyond the typical many-objective regime of about fifteen and becomes massive? (ii) How do problem characteristics, such as the nature of interactions between objectives, influence algorithmic performance? To answer these questions we employ a diagnostic benchmark suite that allows control over problem characteristics and can be scaled to extremely high objective counts. Using this framework we evaluate several state-of-the-art evolutionary algorithms including NSGA-II, NSGA-III, MOEA/D and lexicase selection across a range of dimensionalities and diagnostic problem landscapes. Our experiments reveal that problem characteristics significantly affect algorithm performance. In particular, the nature of interactions between objectives appears important. These results highlight the importance of understanding these properties before selecting an algorithm for a specific problem. We also show that lexicase selection, an algorithm originally designed for genetic programming, compares favorably with state-of-the-art many-objective optimization algorithms while avoiding the dependence on predefined reference directions.

cs.NE↗

arXiv2026

Ablation Study of a Fairness Auditing Agentic System for Bias Mitigation in Early-Onset Colorectal Cancer Detection

Artificial intelligence (AI) is increasingly used in clinical settings, yet limited oversight and domain expertise can allow algorithmic bias and safety risks to persist. This study evaluates whether an agentic AI system can support auditing biomedical machine learning models for fairness in early-onset colorectal cancer (EO-CRC), a condition with documented demographic disparities. We implemented a two-agent architecture consisting of a Domain Expert Agent that synthesizes literature on EO-CRC disparities and a Fairness Consultant Agent that recommends sensitive attributes and fairness metrics for model evaluation. An ablation study compared three Ollama large language models (8B, 20B, and 120B parameters) across three configurations: pretrained LLM-only, Agent without Retrieval-Augmented Generation (RAG), and Agent with RAG. Across models, the Agent with RAG achieved the highest semantic similarity to expert-derived reference statements, particularly for disparity identification, suggesting agentic systems with retrieval may help scale fairness auditing in clinical AI.

cs.MA↗

arXiv2026

Evolved Sample Weights for Bias Mitigation: Effectiveness Depends on the Fairness Objective

Machine learning models trained on real-world data may inadvertently make biased predictions that negatively impact marginalized communities. Reweighting, which assigns a weight to each data point used during model training, can mitigate such bias, though sometimes at the cost of predictive accuracy. In this paper, we investigated this trade-off by comparing three methods for generating these weights: (1) evolving them using a Genetic Algorithm (GA), (2) computing them using only dataset characteristics, and (3) assigning equal weights to all data points. Model performance under each strategy was evaluated using paired predictive and fairness metrics. We used two predictive metrics (accuracy and area under the Receiver Operating Characteristic curve) and two fairness metrics (demographic parity and subgroup false negative fairness). By conducting experiments on eleven publicly available datasets (including two medical datasets), we show that evolved sample weights can produce models that achieve better trade-offs between fairness and predictive performance than alternative weighting methods. However, the magnitude of these benefits depends strongly on the choice of fairness objective. Our experiments reveal that the evolved weights were most effective when optimizing for demographic parity-independent of choice of the performance objective-yielding better performance than other weighting strategies on the largest number of datasets.

cs.LG↗

arXiv2025

GP and LLMs for Program Synthesis: No Clear Winners

Genetic programming (GP) and large language models (LLMs) differ in how program specifications are provided: GP uses input-output examples, and LLMs use text descriptions. In this work, we compared the ability of PushGP and GPT-4o to synthesize computer programs for tasks from the PSB2 benchmark suite. We used three prompt variants with GPT-4o: input-output examples (data-only), textual description of the task (text-only), and a combination of both textual descriptions and input-output examples (data-text). Additionally, we varied the number of input-output examples available for building programs. For each synthesizer and task combination, we compared success rates across all program synthesizers, as well as the similarity between successful GPT-4o synthesized programs. We found that the combination of PushGP and GPT-4o with data-text prompting led to the greatest number of tasks solved (23 of the 25 tasks), even though several tasks were solved exclusively by only one of the two synthesizers. We also observed that PushGP and GPT-4o with data-only prompting solved fewer tasks with the decrease in the training set size, while the remaining synthesizers saw no decrease. We also detected significant differences in similarity between the successful programs synthesized for GPT-4o with text-only and data-only prompting. With there being no dominant program synthesizer, this work highlights the importance of different optimization techniques used by PushGP and LLMs to synthesize programs.

cs.NE↗

arXiv2025

StarBASE-GP: Biologically-Guided Automated Machine Learning for Genotype-to-Phenotype Association Analysis

We present the Star-Based Automated Single-locus and Epistasis analysis tool - Genetic Programming (StarBASE-GP), an automated framework for discovering meaningful genetic variants associated with phenotypic variation in large-scale genomic datasets. StarBASE-GP uses a genetic programming-based multi-objective optimization strategy to evolve machine learning pipelines that simultaneously maximize explanatory power (r2) and minimize pipeline complexity. Biological domain knowledge is integrated at multiple stages, including the use of nine inheritance encoding strategies to model deviations from additivity, a custom linkage disequilibrium pruning node that minimizes redundancy among features, and a dynamic variant recommendation system that prioritizes informative candidates for pipeline inclusion. We evaluate StarBASE-GP on a cohort of Rattus norvegicus (brown rat) to identify variants associated with body mass index, benchmarking its performance against a random baseline and a biologically naive version of the tool. StarBASE-GP consistently evolves Pareto fronts with superior performance, yielding higher accuracy in identifying both ground truth and novel quantitative trait loci, highlighting relevant targets for future validation. By incorporating evolutionary search and relevant biological theory into a flexible automated machine learning framework, StarBASE-GP demonstrates robust potential for advancing variant discovery in complex traits.

cs.NE↗

arXiv2024

Lexicase Selection Parameter Analysis: Varying Population Size and Test Case Redundancy with Diagnostic Metrics

Lexicase selection is a successful parent selection method in genetic programming that has outperformed other methods across multiple benchmark suites. Unlike other selection methods that require explicit parameters to function, such as tournament size in tournament selection, lexicase selection does not. However, if evolutionary parameters like population size and number of generations affect the effectiveness of a selection method, then lexicase's performance may also be impacted by these `hidden' parameters. Here, we study how these hidden parameters affect lexicase's ability to exploit gradients and maintain specialists using diagnostic metrics. By varying the population size with a fixed evaluation budget, we show that smaller populations tend to have greater exploitation capabilities, whereas larger populations tend to maintain more specialists. We also consider the effect redundant test cases have on specialist maintenance, and find that high redundancy may hinder the ability to optimize and maintain specialists, even for larger populations. Ultimately, we highlight that population size, evaluation budget, and test cases must be carefully considered for the characteristics of the problem being solved.

cs.NE↗

arXiv2024

Lexidate: Model Evaluation and Selection with Lexicase

Automated machine learning streamlines the task of finding effective machine learning pipelines by automating model training, evaluation, and selection. Traditional evaluation strategies, like cross-validation (CV), generate one value that averages the accuracy of a pipeline's predictions. This single value, however, may not fully describe the generalizability of the pipeline. Here, we present Lexicase-based Validation (lexidate), a method that uses multiple, independent prediction values for selection. Lexidate splits training data into a learning set and a selection set. Pipelines are trained on the learning set and make predictions on the selection set. The predictions are graded for correctness and used by lexicase selection to identify parent pipelines. Compared to 10-fold CV, lexicase reduces the training time. We test the effectiveness of three lexidate configurations within the Tree-based Pipeline Optimization Tool 2 (TPOT2) package on six OpenML classification tasks. In one configuration, we detected no difference in the accuracy of the final model returned from TPOT2 on most tasks compared to 10-fold CV. All configurations studied here returned similar or less complex final pipelines compared to 10-fold CV.

cs.NE↗

arXiv2023

A suite of diagnostic metrics for characterizing selection schemes

Benchmark suites are crucial for assessing the performance of evolutionary algorithms, but the constituent problems are often too complex to provide clear intuition about an algorithm's strengths and weaknesses. To address this gap, we introduce DOSSIER ("Diagnostic Overview of Selection Schemes In Evolutionary Runs"), a diagnostic suite initially composed of eight handcrafted metrics. These metrics are designed to empirically measure specific capacities for exploitation, exploration, and their interactions. We consider exploitation both with and without constraints, and we divide exploration into two aspects: diversity exploration (the ability to simultaneously explore multiple pathways) and valley-crossing exploration (the ability to cross wider and wider fitness valleys). We apply DOSSIER to six popular selection schemes: truncation, tournament, fitness sharing, lexicase, nondominated sorting, and novelty search. Our results confirm that simple schemes (e.g., tournament and truncation) emphasized exploitation. For more sophisticated schemes, however, our diagnostics revealed interesting dynamics. Lexicase selection performed moderately well across all diagnostics that did not incorporate valley crossing, but faltered dramatically whenever valleys were present, performing worse than even random search. Fitness sharing was the only scheme to effectively contend with valley crossing but it struggled with the other diagnostics. Our study highlights the utility of using diagnostics to gain nuanced insights into selection scheme characteristics, which can inform the design of new selection methods.

cs.NE↗

arXiv2023

Phylogeny-informed fitness estimation

Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the step-by-step process by which any solutions evolve. Thus far, phylogenetic analyses have primarily been applied as post-hoc analyses used to deepen our understanding of existing evolutionary algorithms. Here, we investigate whether phylogenetic analyses can be used at runtime to augment parent selection procedures during an evolutionary search. Specifically, we propose phylogeny-informed fitness estimation, which exploits a population's phylogeny to estimate fitness evaluations. We evaluate phylogeny-informed fitness estimation in the context of the down-sampled lexicase and cohort lexicase selection algorithms on two diagnostic analyses and four genetic programming (GP) problems. Our results indicate that phylogeny-informed fitness estimation can mitigate the drawbacks of down-sampled lexicase, improving diversity maintenance and search space exploration. However, the extent to which phylogeny-informed fitness estimation improves problem-solving success for GP varies by problem, subsampling method, and subsampling level. This work serves as an initial step toward improving evolutionary algorithms by exploiting runtime phylogenetic analysis.

cs.NE↗

arXiv2021

What can phylogenetic metrics tell us about useful diversity in evolutionary algorithms?

It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research has measured diversity using the richness and/or evenness of a particular genotypic or phenotypic property. While these metrics are informative, we hypothesize that other diversity metrics are more strongly predictive of success. Phylogenetic diversity metrics are a class of metrics popularly used in biology, which take into account the evolutionary history of a population. Here, we investigate the extent to which 1) these metrics provide different information than those traditionally used in evolutionary computation, and 2) these metrics better predict the long-term success of a run of evolutionary computation. We find that, in most cases, phylogenetic metrics behave meaningfully differently from other diversity metrics. Moreover, our results suggest that phylogenetic diversity is indeed a better predictor of success.

cs.NE↗

arXiv2021

An Exploration of Exploration: Measuring the ability of lexicase selection to find obscure pathways to optimality

Parent selection algorithms (selection schemes) steer populations through a problem's search space, often trading off between exploitation and exploration. Understanding how selection schemes affect exploitation and exploration within a search space is crucial to tackling increasingly challenging problems. Here, we introduce an "exploration diagnostic" that diagnoses a selection scheme's capacity for search space exploration. We use our exploration diagnostic to investigate the exploratory capacity of lexicase selection and several of its variants: epsilon lexicase, down-sampled lexicase, cohort lexicase, and novelty-lexicase. We verify that lexicase selection out-explores tournament selection, and we show that lexicase selection's exploratory capacity can be sensitive to the ratio between population size and the number of test cases used for evaluating candidate solutions. Additionally, we find that relaxing lexicase's elitism with epsilon lexicase can further improve exploration. Both down-sampling and cohort lexicase -- two techniques for applying random subsampling to test cases -- degrade lexicase's exploratory capacity; however, we find that cohort partitioning better preserves lexicase's exploratory capacity than down-sampling. Finally, we find evidence that novelty-lexicase's addition of novelty test cases can degrade lexicase's capacity for exploration. Overall, our findings provide hypotheses for further exploration and actionable insights and recommendations for using lexicase selection. Additionally, this work demonstrates the value of selection scheme diagnostics as a complement to more conventional benchmarking approaches to selection scheme analysis.

cs.NE↗