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Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…

Data Structures and Algorithms · Computer Science 2019-02-25 Damir Hasic , Eric Tannier

Previously, the exploding gradient problem has been explained to be central in deep learning and model-based reinforcement learning, because it causes numerical issues and instability in optimization. Our experiments in model-based…

Machine Learning · Computer Science 2019-02-06 Paavo Parmas , Carl Edward Rasmussen , Jan Peters , Kenji Doya

The study of the classifier's design and it's usage is one of the most important machine learning areas. With the development of automatic machine learning methods, various approaches are used to build a robust classifier model. Due to some…

Machine Learning · Computer Science 2021-01-22 Ivan Gridin

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…

Quantitative Methods · Quantitative Biology 2025-05-09 Changxi Chi , Jun Xia , Jingbo Zhou , Jiabei Cheng , Chang Yu , Stan Z. Li

We study fundamental block-structured integer programs called tree-fold and multi-stage IPs. Tree-fold IPs admit a constraint matrix with independent blocks linked together by few constraints in a recursive pattern; and transposing their…

Computational Complexity · Computer Science 2024-02-28 Christoph Hunkenschröder , Kim-Manuel Klein , Martin Koutecký , Alexandra Lassota , Asaf Levin

This paper analyses the feasible sets structure of general mixed integer linear programs (MIPs) and its relationship with the existence of a finite cardinality test set which can be applied in augmentation algorithms. We derive and…

Optimization and Control · Mathematics 2025-09-30 Justo Puerto , Jose A. Ruiz-Alba

The linear ordering problem (LOP), which consists in ordering M objects from their pairwise comparisons, is commonly applied in many areas of research. While efforts have been made to devise efficient LOP algorithms, verification of whether…

Machine Learning · Computer Science 2023-05-23 Leszek Szczecinski , Harsh Sukheja

The generalized eigenvalue problem (GEP) serves as a cornerstone in a wide range of applications in numerical linear algebra and scientific computing. However, traditional approaches that aim to maximize the classical Rayleigh quotient…

Optimization and Control · Mathematics 2025-07-04 Xiaozhi Liu , Yong Xia

Using evolutionary computation algorithms to solve multiple tasks with knowledge sharing is a promising approach. Image feature learning can be considered as a multitask problem because different tasks may have a similar feature space.…

Computer Vision and Pattern Recognition · Computer Science 2021-07-16 Ying Bi , Bing Xue , Mengjie Zhang

The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…

Neural and Evolutionary Computing · Computer Science 2019-03-11 Shalin Shah

Evolutionary algorithms rely very heavily on randomized behavior. Execution speed, therefore, depends strongly on how we implement randomness, such as our choice of pseudorandom number generator, or the algorithms used to map pseudorandom…

Neural and Evolutionary Computing · Computer Science 2024-12-04 Vincent A. Cicirello

We propose a genetic algorithm powered evolution (GAPE) method to create deep learning solutions for energy and position estimation for reactor antineutrino interactions in the Precision Reactor Oscillation and Spectrum Experiment…

Generalization is the core objective when training optimizers from data. However, limited training instances often constrain the generalization capability of the trained optimizers. Co-evolutionary approaches address this challenge by…

Neural and Evolutionary Computing · Computer Science 2025-11-19 Zhiyuan Wang , Shengcai Liu , Peng Yang , Ke Tang

Probabilistic inferences distill knowledge from graphs to aid human make important decisions. Due to the inherent uncertainty in the model and the complexity of the knowledge, it is desirable to help the end-users understand the inference…

Social and Information Networks · Computer Science 2019-08-21 Chao Chen , Yifei Liu , Xi Zhang , Sihong Xie

Missing data has a ubiquitous presence in real-life applications of machine learning techniques. Imputation methods are algorithms conceived for restoring missing values in the data, based on other entries in the database. The choice of the…

Machine Learning · Computer Science 2017-08-16 Unai Garciarena , Roberto Santana , Alexander Mendiburu

This paper examines the Evolutionary programming (EP) method for optimizing PID parameters. PID is the most common type of regulator within control theory, partly because it's relatively simple and yields stable results for most…

Neural and Evolutionary Computing · Computer Science 2017-09-28 Adam Nyberg

Context: Evolutionary algorithms typically require a large number of evaluations (of solutions) to converge - which can be very slow and expensive to evaluate.Objective: To solve search-based software engineering (SE) problems, using fewer…

Software Engineering · Computer Science 2017-09-19 Jianfeng Chen , Vivek Nair , Tim Menzies

Dynamic scheduling in real-world environments often struggles to adapt to unforeseen disruptions, making traditional static scheduling methods and human-designed heuristics inadequate. This paper introduces an innovative approach that…

Artificial Intelligence · Computer Science 2025-08-06 Xinan Chen , Rong Qu , Jing Dong , Ruibin Bai , Yaochu Jin

Graphical models capture relations between entities in a wide range of applications including social networks, biology, and natural language processing, among others. Graph neural networks (GNN) are neural models that operate over graphs,…

Machine Learning · Computer Science 2024-02-08 Xu Zheng , Farhad Shirani , Tianchun Wang , Shouwei Gao , Wenqian Dong , Wei Cheng , Dongsheng Luo

In Symbolic Regression (SR), achieving a proper balance between accuracy and interpretability remains a key challenge. The Genetic Programming variant of the Gene-pool Optimal Mixing Evolutionary Algorithm (GP-GOMEA) is of particular…

Neural and Evolutionary Computing · Computer Science 2025-07-08 Joe Harrison , Tanja Alderliesten. Peter A. N. Bosman