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We propose an effective method to improve Protein Function Prediction (PFP) utilizing hierarchical features of Gene Ontology (GO) terms. Our method consists of a language model for encoding the protein sequence and a Graph Convolutional…

Artificial Intelligence · Computer Science 2021-12-07 Kyudam Choi , Yurim Lee , Cheongwon Kim , Minsung Yoon

Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…

Neural and Evolutionary Computing · Computer Science 2019-10-24 Andrew Lensen , Bing Xue , Mengjie Zhang

Fitness landscapes in test-based program synthesis are known to be extremely rugged, with even minimal modifications of programs often leading to fundamental changes in their behavior and, consequently, fitness values. Relying on fitness as…

Machine Learning · Computer Science 2025-02-10 Piotr Wyrwiński , Krzysztof Krawiec

Traditionally, traders and quantitative analysts address alpha decay by manually crafting formulaic alphas, mathematical expressions that identify patterns or signals in financial data, through domain expertise and trial-and-error. This…

Computational Engineering, Finance, and Science · Computer Science 2026-03-05 Qizhao Chen , Hiroaki Kawashima

In response to the persistent safety challenges within coal mines, this study proposes a novel approach integrating a three-layer feedforward backpropagation artificial neural network with a genetic algorithm (GA-BP) for establishing a…

Neural and Evolutionary Computing · Computer Science 2024-12-09 Jiabin Luo , Hanzhe Pan

Classical optimization algorithms--hill climbing, simulated annealing, population-based methods--generate candidate solutions via random perturbations. We replace the random proposal generator with an LLM agent that reasons about evaluation…

Artificial Intelligence · Computer Science 2026-03-31 Yitao Li

Gene set analysis methods rely on knowledge-based representations of genetic interactions in the form of both gene set collections and protein-protein interaction (PPI) networks. Explicit representations of genetic interactions often fail…

Quantitative Methods · Quantitative Biology 2023-02-23 Henry Cousins , Taryn Hall , Yinglong Guo , Luke Tso , Kathy Tzy-Hwa Tzeng , Le Cong , Russ Altman

Within the optimization community, the question of how to generate new optimization problems has been gaining traction in recent years. Within topics such as instance space analysis (ISA), the generation of new problems can provide new…

Neural and Evolutionary Computing · Computer Science 2023-05-25 Fu Xing Long , Diederick Vermetten , Anna V. Kononova , Roman Kalkreuth , Kaifeng Yang , Thomas Bäck , Niki van Stein

One of the most significant current discussions in the field of data mining is classifying imbalanced data. In recent years, several ways are proposed such as algorithm level (internal) approaches, data level (external) techniques, and…

Machine Learning · Computer Science 2021-06-03 Maliheh Roknizadeh , Hossein Monshizadeh Naeen

This paper presents a Genetic Programming (GP) approach to solving multi-robot path planning (MRPP) problems in single-lane workspaces, specifically those easily mapped to graph representations. GP's versatility enables this approach to…

Robotics · Computer Science 2019-12-23 Alexandre Trudeau , Christopher M. Clark

Image classification is an essential task in computer vision, which aims to categorise a set of images into different groups based on some visual criteria. Existing methods, such as convolutional neural networks, have been successfully…

Neural and Evolutionary Computing · Computer Science 2019-10-01 Benjamin Patrick Evans , Harith Al-Sahaf , Bing Xue , Mengjie Zhang

The performance of GA is measured and analyzed in terms of its performance parameters against variations in its genetic operators and associated parameters. Since last four decades huge numbers of researchers have been working on the…

Neural and Evolutionary Computing · Computer Science 2013-10-07 Anagha P. Khedkar , Shaila Subbaraman

Optical focusing through scattering media has important implications for optical applications in medicine, communications, and detection. In recent years, many wavefront shaping methods have been successfully applied to the field, among…

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…

This paper implements a new way of solving a problem called the traveling salesman problem (TSP) using quantum genetic algorithm (QGA). We compared how well this new approach works to the traditional method known as a classical genetic…

Quantum Physics · Physics 2024-09-24 Yijiang Ma , Tan Chye Cheah

This paper introduces an active learning framework for manifold Gaussian Process (GP) regression, combining manifold learning with strategic data selection to improve accuracy in high-dimensional spaces. Our method jointly optimizes a…

Machine Learning · Statistics 2026-05-12 Yuanxing Cheng , Lulu Kang , Yiwei Wang , Chun Liu

With the improvement of computer performance and the development of GPU-accelerated technology, trading with machine learning algorithms has attracted the attention of many researchers and practitioners. In this research, we propose a novel…

Portfolio Management · Quantitative Finance 2021-03-23 Huanming Zhang , Zhengyong Jiang , Jionglong Su

We propose a scalable stochastic variational approach to GP classification building on Polya-Gamma data augmentation and inducing points. Unlike former approaches, we obtain closed-form updates based on natural gradients that lead to…

Machine Learning · Statistics 2018-11-28 Florian Wenzel , Theo Galy-Fajou , Christan Donner , Marius Kloft , Manfred Opper

Genetic algorithms have been widely used in many practical optimization problems. Inspired by natural selection, operators, including mutation, crossover and selection, provide effective heuristics for search and black-box optimization.…

Machine Learning · Statistics 2018-03-14 Tanmay Gangwani , Jian Peng

We develop a flexible Gaussian Process (GP) framework for learning the covariance structure of Age- and Year-specific mortality surfaces. Utilizing the additive and multiplicative structure of GP kernels, we design a genetic programming…

Machine Learning · Statistics 2024-11-20 Mike Ludkovski , Jimmy Risk
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