Alcides Fonseca

Guilherme Espada, Leon Ingelse, Paulo Canelas et al. · cmu

Genetic Programming (GP) is an heuristic method that can be applied to many Machine Learning, Optimization and Engineering problems. In particular, it has been widely used in Software Engineering for Test-case generation, Program Synthesis and Improvement of Software (GI). Grammar-Guided Genetic Programming (GGGP) approaches allow the user to refine the domain of valid program solutions. Backus Normal Form is the most popular interface for describing Context-Free Grammars (CFG) for GGGP. BNF and its derivatives have the disadvantage of interleaving the grammar language and the target language of the program. We propose to embed the grammar as an internal Domain-Specific Language in the host language of the framework. This approach has the same expressive power as BNF and EBNF while using the host language type-system to take advantage of all the existing tooling: linters, formatters, type-checkers, autocomplete, and legacy code support. These tools have a practical utility in designing software in general, and GP systems in particular. We also present Meta-Handlers, user-defined overrides of the tree-generation system. This technique extends our object-oriented encoding with more practicability and expressive power than existing CFG approaches, achieving the same expressive power of Attribute Grammars, but without the grammar vs target language duality. Furthermore, we evidence that this approach is feasible, showing an example Python implementation as proof. We also compare our approach against textual BNF-representations w.r.t. expressive power and ergonomics. These advantages do not come at the cost of performance, as shown by our empirical evaluation on 5 benchmarks of our example implementation against PonyGE2. We conclude that our approach has better ergonomics with the same expressive power and performance of textual BNF-based grammar encodings.

Pedro Barbosa, Rosina Savisaar, Alcides Fonseca

Black box deep learning models trained on genomic sequences excel at predicting the outcomes of different gene regulatory mechanisms. Therefore, interpreting these models may provide novel insights into the underlying biology, supporting downstream biomedical applications. Due to their complexity, interpretable surrogate models can only be built for local explanations (e.g., a single instance). However, accomplishing this requires generating a dataset in the neighborhood of the input, which must maintain syntactic similarity to the original data while introducing semantic variability in the model's predictions. This task is challenging due to the complex sequence-to-function relationship of DNA. We propose using Genetic Programming to generate datasets by evolving perturbations in sequences that contribute to their semantic diversity. Our custom, domain-guided individual representation effectively constrains syntactic similarity, and we provide two alternative fitness functions that promote diversity with no computational effort. Applied to the RNA splicing domain, our approach quickly achieves good diversity and significantly outperforms a random baseline in exploring the search space, as shown by our proof-of-concept, short RNA sequence. Furthermore, we assess its generalizability and demonstrate scalability to larger sequences, resulting in a ~30% improvement over the baseline.

Guilherme S. Imai Aldeia, Hengzhe Zhang, Geoffrey Bomarito et al.

Symbolic Regression (SR) is a powerful technique for discovering interpretable mathematical expressions. However, benchmarking SR methods remains challenging due to the diversity of algorithms, datasets, and evaluation criteria. In this work, we present an updated version of SRBench. Our benchmark expands the previous one by nearly doubling the number of evaluated methods, refining evaluation metrics, and using improved visualizations of the results to understand the performances. Additionally, we analyze trade-offs between model complexity, accuracy, and energy consumption. Our results show that no single algorithm dominates across all datasets. We propose a call for action from SR community in maintaining and evolving SRBench as a living benchmark that reflects the state-of-the-art in symbolic regression, by standardizing hyperparameter tuning, execution constraints, and computational resource allocation. We also propose deprecation criteria to maintain the benchmark's relevance and discuss best practices for improving SR algorithms, such as adaptive hyperparameter tuning and energy-efficient implementations.

Catarina Gamboa, Paulo Alexandre Santos, Christopher S. Timperley et al.

Bugs that are detected earlier during the development lifecycle are easier and cheaper to fix, whereas bugs that are found during production are difficult and expensive to address, and may have dire consequences. Type systems are particularly effective at identifying and preventing bugs early in the development lifecycle by causing invalid programs to result in build failure. Liquid Types are more powerful than those found in mainstream programming languages, allowing the detection of more classes of bugs. However, while Liquid Types were proposed in 2008 with their integration in ML and subsequently introduced in C (2012), Javascript(2012) and Haskell(2014) through language extensions, they have yet to become widely adopted by mainstream developers. This paper investigates how Liquid Types can be integrated in a mainstream programming language, Java, by proposing a new design that aims to lower the barrier to entry and adapts to problems that Java developers commonly encounter at runtime. To promote accessibility, we conducted a series of developer surveys to design the syntax of LiquidJava, our prototype. To evaluate the prototype's usability, we conducted a user study of 30 Java developers, concluding that users intend to use LiquidJava and that it helped to find more bugs and debug faster.