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Predicting Dry Matter Intake in Lactating Crossbred Cows Under Semi-Arid Conditions Using an Error-Based Evolving Takagi-Sugeno Fuzzy Model

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IEEE Access 2025年 13卷 71521-71529页

作者： Leal, Dijair B. Soares, Rafael A. Junior, Vicente R. Rocha Moncao, Flavio P. Camargos, Murilo O. D'Angelo, Marcos F. S. V. Miralles-Pechuan, Luis UNIMONTES Graduate Program in Animal Science Montes Claros39401-089 Brazil UNIMONTES Graduate Program in Computer Modeling and Systems Montes Claros39401-089 Brazil UNIMONTES Department of Agricultural Sciences Minas Gerais Montes Claros39401-089 Brazil UNIMONTES Department of Computer Science Minas Gerais Montes Claros39401-089 Brazil Technological University Dublin School of Computer Science Dublin 8 D07 EWV4 Ireland

Accurately predicting dry matter intake (DMI) in lactating crossbred cows under semi-arid conditions is a critical challenge in dairy farming. Precise DMI predictions are essential for optimizing nutrient utilization and enhancing animal performance, particularly in semi-arid environments, where complex and dynamic conditions prevail. This paper introduces a novel Error-Based Evolving Takagi-Sugeno (EBETS) Fuzzy Model designed to address these challenges by dynamically adapting to real-time data and leveraging both current and historical information to enhance prediction accuracy. The EBETS model employs fuzzy set theory and multivariate Gaussian functions to model complex, nonlinear relationships between variables, offering a more robust and flexible approach to DMI prediction. In experiments involving data from 114 crossbred cows under semi-arid conditions, the EBETS model was compared to traditional models and an artificial neural network. It achieved a mean squared error of 0.25, which is more than 90% lower than that of all the other models, while demonstrating a higher correlation coefficient with the expected values, indicating superior predictive performance and reliability. These results underscore the EBETS model’s substantial superiority over existing methods, highlighting its potential to significantly improve dairy farming productivity by providing precise and reliable DMI predictions in challenging environmental conditions. The model’s ability to continuously learn and adapt to changing conditions makes it a promising tool for various applications in agricultural science. © 2013 IEEE.

关键词： Prediction models

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Survey and Improvement Strategies for Gene Prioritization with Large Language Models

arXiv

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arXiv 2025年

作者： Neeley, Matthew B. Qi, Guantong Wang, Guanchu Tang, Ruixiang Mao, Dongxue Liu, Chaozhong Pasupuleti, Sasidhar Yuan, Bo Xia, Fan Liu, Pengfei Liu, Zhandong Hu, Xia Jan and Dan Duncan Neurological Research Institute Texas Children’s Hospital Houston United States Graduate School of Biomedical Sciences Program in Quantitative and Computational Biosciences Baylor College of Medicine Houston United States Graduate School of Biomedical Sciences Program in Genetics and Genomics Baylor College of Medicine Houston United States Department of Computer Science Rice University Houston United States Department of Computer Science Rutgers University NJ United States Department of Pediatrics Baylor College of Medicine Houston United States Department of Molecular and Human Genetics Baylor College of Medicine Houston United States Human Genome Sequencing Center Baylor College of Medicine Houston United States Baylor Genetics Houston United States

Background Rare diseases can be difficult to diagnose due to limited patient data and broad genetic diversity. Despite the advances in variant prioritization tools, many rare disease cases remain undiagnosed. While large language models (LLMs) have performed well in medical exams, their accuracy in diagnosing rare genetic diseases has not yet been evaluated. Methods To identify causal genes for genetic diseases, we benchmarked various LLMs for gene prioritization. We employed multi-agent and Human Phenotype Ontology (HPO) classification approaches to identify patient case groups based on phenotypes categorizing them into different levels of solvability. To address LLM limitations in ranking large gene sets, we used a divide-and-conquer strategy to break down the ranking task into smaller subsets. Mini-batching inputs and limiting the number of generated tokens improved efficiency. Results In its vanilla form, GPT-4 consistently outperformed the other LLMs with an accuracy around 30%. Multi-agent and HPO classification approaches aided us in distinguishing between confidently-solved and challenging cases. In addition, we observed bias towards well-studied genes and input order sensitivity which are drawbacks of LLMs in disease-causal gene prioritization. Our divide-and-conquer strategy enhanced accuracy by overcoming positional and gene frequency biases in literature. This framework, based on benchmarking insights and novel techniques, significantly optimizes the overall process when identifying disease-causal genes for genetic diseases when compared to our baseline evaluation, and thereby better enables the development of targeted diagnostic and therapeutic interventions. Conclusions Using HPO classification and our novel multi-agent techniques, and our LLM divide-and-conquer strategy (1) highlighted the importance of accounting for differences in patient case solvability and (2) yielded improved performance in identifying causal genes for rare diseases when compare

关键词： Gene Ontology

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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State of the Art Models for Fake News Detection Tasks

State of the Art Models for Fake News Detection Tasks

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2020 IEEE International Conference on Informatics, IoT, and Enabling Technologies, ICIoT 2020

作者： Antoun, Wissam Baly, Fady Achour, Rim Hussein, Amir Hajj, Hazem American University of Beirut Electrical and Computer Engineering Department Beirut Lebanon Graduate Program in Computational Science American University of Beirut Beirut Lebanon

ISBN: (数字)9781728148212

ISBN: (纸本)9781728148212

This paper presents state of the art methods for addressing three important challenges in automated fake news detection: fake news detection, domain identification, and bot identification in tweets. The proposed solutions achieved first place in a recent international competition on fake news. For fake news detection, we present two models. The winning model in the competition combines similarity between the embedding of each article's title and the embedding of the top five corresponding google search results. The new model relies on advances in Natural Language Understanding (NLU) end to end deep learning models to identify stylistic differences between legitimate and fake news articles. This second model was developed after the competition and outperforms the winning approach. For news domain detection, the winning model is a hybrid approach composed of named entity features concatenated with semantic embeddings derived from end to end models. For twitter bot detection, we propose to use the following features: duration between account creation and tweet date, presence of a tweet's link, presence of user's location, other tweet's features, and the tweets' metadata. Experiments include insights into the importance of the different features and the results indicate the superior performances of all proposed models. © 2020 IEEE.

关键词： Competition

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Replacing the FitzHugh-Nagumo Electrophysiology Model by Physics-Informed Neural Networks 23rd

Replacing the FitzHugh-Nagumo Electrophysiology Model by P...

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23rd International Conference on computational science, ICCS 2023

作者： Werneck, Yan Barbosa dos Santos, Rodrigo Weber Rocha, Bernardo Martins Oliveira, Rafael Sachetto Graduate Program in Computational Modeling Federal University of Juiz de Fora Juiz de Fora Brazil Graduate Program in Computer Science Federal University of São Jõao del Rei São Jão del Rei Brazil

ISBN: (纸本)9783031360206

This paper presents a novel approach to replace the FitzHugh-Nagumo (FHN) model with physics-informed neural networks (PINNs). The FHN model, a system of two ordinary differential equations, is widely used in electrophysiology and neurophysiology to simulate cell action potentials. However, in tasks such as whole-organ electrophysiology modeling and drug testing, the numerical solution of millions of cell models is computationally expensive. To address this, we propose using PINNs to accurately approximate the two variables of the FHN model at any time instant, any initial condition, and a wide range of parameters. In particular, this eliminates the need for causality after training. We employed time window marching and increased point cloud density on transition regions to improve the training of the neural network due to nonlinearity, sharp transitions, unstable equilibrium, and bifurcations of parameters. The PINNs were generated using NVIDIA’s Modulus framework, allowing efficient deployment on modern GPUs. Our results show that the generated PINNs could reproduce FHN solutions with average numerical errors below 0.5%, making them a promising lightweight computational model for electrophysiology and neurophysiology research. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Electrophysiology

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An information theoretic framework for eukaryotic gradient sensing 19

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20th Annual Conference on Neural Information Processing Systems, NIPS 2006

作者： Kimmel, Joseph M. Salter, Richard M. Thomas, Peter J. Computer Science Program Oberlin College Oberlin OH 44074 United States Department of Mathematics Biology and Cognitive Science Case Western Reserve University Cleveland OH 44106 United States Computational Neuroscience Graduate Program University of Chicago United States Center for Computation and Modeling United States

ISBN: (纸本)9780262195683

Chemical reaction networks by which individual cells gather and process information about their chemical environments have been dubbed "signal transduction" networks. Despite this suggestive terminology, there have been few attempts to analyze chemical signaling systems with the quantitative tools of information theory. Gradient sensing in the social amoeba Dictyostelium discoideum is a well characterized signal transduction system in which a cell estimates the direction of a source of diffusing chemoattractant molecules based on the spatiotemporal sequence of ligand-receptor binding events at the cell membrane. Using Monte Carlo techniques (MCell) we construct a simulation in which a collection of individual ligand particles undergoing Brownian diffusion in a three-dimensional volume interact with receptors on the surface of a static amoeboid cell. Adapting a method for estimation of spike train entropies described by Victor (originally due to Kozachenko and Leonenko), we estimate lower bounds on the mutual information between the transmitted signal (direction of ligand source) and the received signal (spatiotemporal pattern of receptor binding/unbinding events). Hence we provide a quantitative framework for addressing the question: how much could the cell know, and when could it know it? We show that the time course of the mutual information between the cell's surface receptors and the (unknown) gradient direction is consistent with experimentally measured cellular response times. We find that the acquisition of directional information depends strongly on the time constant at which the intracellular response is filtered.

关键词： Ligands

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Comparing CUDA, OpenCL and OpenGL implementations of the cardiac monodomain equations

Comparing CUDA, OpenCL and OpenGL implementations of the car...

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9th International Conference on Parallel Processing and Applied Mathematics, PPAM 2011

作者： Sachetto Oliveira, Rafael Rocha, Bernardo Martins Amorim, Ronan Mendonça Campos, Fernando Otaviano Meira Jr., Wagner Toledo, Elson Magalhães Dos Santos, Rodrigo Weber Federal University of São João del Rey Department of Computer Science Brazil Federal University of Minas Gerais Department of Computer Science Brazil Federal University of Juiz de Fora Department of Computer Science Computational Modeling Program Brazil National Laboratory of Scientific Computing Brazil Medical University of Graz Institute of Biophysics Austria

ISBN: (纸本)9783642314995

computer simulations of cardiac electrophysiology are a helpful tool in the study of bioelectric activity of the heart. The cardiac monodomain model comprises a nonlinear system of partial differential equations and its numerical solution represents a very intensive computational task due to the required fine spatial and temporal resolution. Recent studies have shown that the use of GPU as a general purpose processor can greatly improve the performance of simulations. The aim of this work is to study the performance of different GPU programming interfaces for the solution of the cardiac monodomain equations. Three different GPU implementations are compared, OpenGL, NVIDIA CUDA and OpenCL, to a CPU multicore implementation that uses OpenMP. The OpenGL approach showed to be the fastest with a speedup of 446 (compared to the multicore implementation) for the solution of the nonlinear system of ordinary differential equations (ODEs) associated to the solution of the cardiac model, whereas CUDA was the fastest for the numerical solution of the parabolic partial differential equation with a speedup of 8. Although OpenCL provides code portability between different accelerators, the OpenCL version was slower for the solution of the parabolic equation and as fast as CUDA for the solution of the system of ODEs, showing to be a portable way of programming scientific applications but not as efficient as CUDA when running on Nvidia GPUs. © 2012 Springer-Verlag.

关键词： Nonlinear systems

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A node placement optimization method for watershed underwater sensor networks 9

A node placement optimization method for watershed underwate...

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9th ACM International Conference on Underwater Networks and Systems, WUWNet 2014

作者： Barbosa, Gentil V. Letouze, Patrick Xavier, Adilson E. Department of Computer Science UFT - Universidade Federal do Tocantins PESC Brazil Department of Computer Science UFT - Universidade Federal do Tocantins MCS - Postgraduate Program of System's Computational Modeling Brazil PESC - Postgraduate Program of System's Engineering and Computation UFRJ - Universidade Federal do Rio de Janeiro Brazil

ISBN: (纸本)9781450332774

Given a set of underwater sensors coordinates that are usually determined by a specialist for the design of a watershed monitoring system, where should be placed the sinks and the base station? The answer may be the minimization of the Variable Internode Distance. In such cases, a two dimensional architecture is acceptable because it is a shallow water system. Hence, in this paper, it is proposed a two-level node distance minimization for Underwater Wireless Sensor Network for monitoring systems. The mathematical method employed for optimization is the Hyperbolic Smoothing approach and the proposed method includes the placement of the base-station in the algorithm. Copyright 2014 ACM.

关键词： Base stations

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Adaptive Time Step for Cardiac Myocyte Models

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Procedia computer science 2011年 4卷 1092-1100页

作者： Ricardo Silva Campos Marcelo Lobosco Rodrigo Weber dos Santos Department of Computer Science and Master Program in Computational Modeling Federal University of Juiz de Fora Juiz de Fora Brazil

The modeling of the electrical activity of the heart is of great medical and scientific interest as it provides a way to better understand the underlying biophysical phenomena, supports the development of new techniques for diagnoses and serves as a platform for drug tests. At cellular level, the electrical activity of cardiac myocytes may be simulated by solving a system of ordinary di_erential equations (ODEs) describing the electrical behavior of the cell membrane. Because the biophysical processes underlying this phenomenon are non-linear and change very rapidly, the ODE system is challenging to solve numerically. Furthermore, the implementation of these models is a hard task. This paper presents a tool to describe models using Ordinary Differential Equations. It is based on CellML standard and automatically generates C++ source-code, with numerical methods to solve the model's equations. The aim of this work is to present a numerical method with adaptive time step based on the Euler Method and Second Order Runge-Kutta method. The proposed method accelerated the execution and kept numerical errors under control. Preliminary results suggest this adaptive method is up to 25 times faster than the explicit Euler method with fixed time step.

关键词： Adaptive Time Step Cardiac modeling

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A quadratic approximation-based local search operator for handling two equality constraints in continuous optimization problems

A quadratic approximation-based local search operator for ha...

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Congress on Evolutionary Computation

作者： Carlos H. Fonseca Elizabeth Fialho Wanner Post-graduate Program in Mathematical and Computational Modeling MG Brasil Department of Computer Engineering MG Brasil

This work presents extensions of the general methodology of employing quadratic approximations of the objective function and constraints for handling non-linear equality constraints in single-objective optimization problems. The methodology does not require any extra function evaluation since the quadratic approximations are constructed using only information that would be already obtained in the course of the optimization algorithms. The methodology is coupled with the Real Biased Genetic Algorithm to tackle non-linear single-objective optimization problems with two equality constraints. The modified algorithm is tested with a set of analytical problems. The results show the modified algorithm finds the constrained optima with enhanced precision and faster convergence. Considering that the new technique does not impose any additional cost to the algorithms, it can be stated that the technique is also suitable for costly black-box problems.

关键词： Optimization Approximation algorithms Linear programming Search problems Genetic algorithms Symmetric matrices Convergence

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