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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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consexpressionR: an R package for consensus differential gene expression analysis

arXiv

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arXiv 2025年

作者： Costa-Silva, Juliana Menotti, David Lopes, Fabricio M. Department of Informatics Federal University of Paraná Rua Coronel Francisco Heráclito dos Santos 100 Paraná81531-990 Brazil Department of Computer Science Bioinformatics Graduate Program Federal University of Technology - Paraná Av. Alberto Carazzai 1640 - Cornélio Procópio ParanáPostal code: 86300-000 Brazil

Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have been developed for each stage of the identification of differentially expressed genes. Nevertheless, there are few studies exploring the association between different types of methods. In this study, we evaluated the impact of the association of methodologies in the results of differential expression analysis. By adopting two data sets with qPCR data (to gold-standard reference), seven methods were implemented and assessed in R packages (EBSeq, edgeR, DESeq2, limma, SAMseq, NOISeq, and Knowseq), which was performed and assessed separately and in association. The results were evaluated considering the adopted qPCR data. Results: Here, we introduce consexpressionR, an R package that automates differential expression analysis using consensus of at least seven methodologies, producing more assertive results with a significant reduction in false positives. Availability: consexpressionR is an R package available via Source code and support are available at GitHub (https://***/costasilvati/consexpressionR). © 2025, CC BY-NC-ND.

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A GRAPH MODEL FOR SOFTWARE EVOLUTION

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 1990年第8期16卷 917-927页

作者： LUQI Department of Computer Science. Naval Post-graduate School. Monterey. CA 93943

This paper presents a graph model of software evolution. We seek to formalize the objects and activities involved in software evolution in sufficient detail to enable automatic assistance for maintaining the consistency and integrity of an evolving software system. This includes automated support for propagating the consequences of a change to a software system. [ABSTRACT FROM AUTHOR]

关键词： consistency Index Terms: Configuration control maintenance management software evolution

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AgriField3D: A Curated 3D Point Cloud and Procedural Model Dataset of Field-Grown Maize from a Diversity Panel

arXiv

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arXiv 2025年

作者： Kimara, Elvis Hadadi, Mozhgan Godbersen, Jackson Balu, Aditya Jubery, Talukder Li, Yawei Krishnamurthy, Adarsh Schnable, Patrick S. Ganapathysubramanian, Baskar Department of Computer Science Iowa State University Ames United States Translational AI Research and Education Center Ames United States Department of Mechanical Engineering Iowa State University Ames United States Plant Science Institute Iowa State University Ames United States Interdepartmental Genetics and Genomics Graduate Program Iowa State University Ames United States Department of Agronomy Iowa State University Ames United States

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (website), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research. © 2025, CC BY-NC-SA.

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Nonsaturated large magnetoresistance and transport dynamics in a n-doped cryogenic WSe2 field-effect device

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Physical Review B 2025年第12期111卷 125307-125307页

作者： Wei-Chen Lin Ching-Chen Yeh Jia-Zhu Zou Nhat Anh Nguyen Phan Inayat Uddin Hai Yen Le Thi Kenji Watanabe Takashi Taniguchi Gil-Ho Kim Department of Engineering and System Science National Tsing Hua University Hsinchu 300 Taiwan Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Department of Physics National Taiwan University Taipei 106 Taiwan Department of Electrical and Computer Engineering Sungkyunkwan University (SKKU) Suwon 164 Republic of Korea Sungkyunkwan Advanced Institute of Nano Technology (SAINT) Sungkyunkwan University (SKKU) Suwon 16419 Republic of Korea Research Center for Electronic and Optical Materials National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan Research Center for Materials Nanoarchitectonics National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan

Interest in the two-dimensional (2D) semiconducting transition metal dichalcogenides (TMDs) continues to intensify, driven by their suitable band gaps to supplant silicon as next-generation semiconductor materials. Among various TMDs, tungsten diselenide (WSe2) is renowned for its superior electrical properties in carrier density and mobility under ambient conditions. Despite its notable attributes, the behavior of monolayer WSe2 in the electron-doped regime under cryogenic conditions remains largely uncharted, particularly concerning its magnetotransport properties. In this study, we reveal the transport mechanisms of monolayer WSe2 from high temperatures down to the cryogenic regime. As evident by Efros–Shklovskii variable-range hopping (E-S VRH) in the cryogenic regime, strong Coulomb interactions arise between electrons. Above 8 K, an uncommon nonsaturated quadratic large magnetoresistance (MR) can be explained by the wave-function shrinkage model, which is consistent with the E-S VRH transport mechanism. Notably, the nonsaturated quadratic large MR shows a magnitude up to 1740% at 13 T. These findings underscore the potential applications for monolayer WSe2 in cryogenic field-effect devices, magnetic sensors, and memory devices and mark a significant advance in magnetotransport research.

关键词： Monolayers

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Assistive technology with device for self-inflating bag in neonatology

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Research on Biomedical Engineering 2025年第2期41卷

作者： Marcelino, Ana Carolina Rodovanski, Giovana Pascoali Bonetti, Karoline Panes, Caio Rabinovich de Almeida Martins, Fernando Moran, Cristiane Aparecida Araranguá Brazil Graduate Program in Neurosciences and Behavior Department of Experimental Psychology of the Institute of Psychology-University of São Paulo Sao Paulo Brazil Araranguá Brazil Computer Engineering Instituto Mauá de Tecnologia São Caetano do Sul Brazil Electronic Engineering and Computing with Emphasis on Electronic Devices and Systems at Instituto Tecnológico de Aeronáutica–ITA São Caetano do Sul Brazil Department of Physiotheraphy and at the Postgraduate Program in Rehabilitation Science of the Federal University of Santa Catarina-UFCS Ararangua Brazil

Purpose: The objectives of this study were to create a device with technological development of the self-inflating bag (SIB) equipment to measure the variables tidal volume, peak inspiratory pressure, and inspiratory flow and to evaluate the knowledge of undergraduate students in handling the SIB. To reduce the risks of mortality, length of hospital stay, and infections, SIB is a resource used to ventilate the patient through the inflation of the device, but it is not capable of measuring the ventilatory parameters. Excess ventilation and incorrect handling of the bag can cause lung injury in newborns. Therefore, measuring these parameters can prevent lung injury resulting from inadequate ventilation. Method: This is a cross-sectional and experimental study, with the development of a device SIB that allows the evaluation of variables of neonatal respiratory mechanics that were tested with an artificial lung. It was approved by the Research Ethics Committee and the research was developed in three stages: the first represents the search for scientific articles for the consensus of neonatal ventilatory variables for the construction of the SIB parameters;the second stage depicts the technological development of a device capable of monitoring such variables through the SIB. In the third stage, the content validation of the device with the handling of the SIB was carried out by students of medicine and physiotherapy courses of Brazil. Results: In this work, a device that analyzes the values of the main ventilatory parameters in neonatology was developed and to generate a safety range for the use of the device, curves with a tolerance of 10% up and down were created. All electronic components were coupled to the equipment, with a display that transmits the parameter values. The web page can be used on a cell phone, tablet, computer, or SmartTv, as long as it is connected to the "RespiratorIoT_AP" network. Among the 29 participants in the study, 8 said they were familiar w

关键词： Students

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PERFORMANCE MODELING AND ANALYSIS OF BLOOD FLOW IN ELASTIC ARTERIES

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Applied Mathematics and Mechanics(English Edition) 2005年第3期26卷 345-354页

作者： Anil Kumar C.L.Varshney G.C.Sharma Department of Post-Graduate Studies and Research in Mathematics &Computer Science S.Varshney College Aligarh-202001 IndiaDepartment of Post-Graduate Studies and Research in Mathematics &Computer Science S.Varshney College Aligarh-202001 IndiaInstitute of Basic Science Khandari Agra-282002 India

Two different non_Newtonian models for blood flow are considered,first a simple power law model displaying shear thinning viscosity,and second a generalized Maxwell model displaying both shear thinning viscosity and oscillating flow viscous_*** models are used along with a Newtonian model to study sinusoidal flow of blood in rigid and elastic straight arteries in the presence of magnetic *** elasticity of blood does not appear to influence its flow behavior under physiological conditions in the large arteries,purely viscous shear thinning model should be quite realistic for simulating blood flow under these *** using the power law model with high shear rate for sinusoidal flow simulation in elastic arteries,the mean and amplitude of the flow rate were found to be lower for a power law fluid compared to Newtonian fluid for the same pressure *** governing equations have been solved by Crank_Niclson *** results are interpreted in the context of blood in the elastic arteries keeping the magnetic effects in *** physiological flow simulation in the aorta,an increase in mean wall shear stress,but a reduction in peak wall shear stress were observed for power law model compared to a Newtonian fluid model for matched flow rate wave *** flow in the presence of transverse magnetic field in an elastic artery is investigated and the influence of factors such as morphology and surface irregularity is evaluated.

关键词： elastic artery model Crank-Niclson scheme non-Newtonian fluid wall shear stress

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COMPUTATIONAL TECHNIQUE FOR FLOW IN BLOODVESSELS WITH POROUS EFFECTS

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Applied Mathematics and Mechanics(English Edition) 2005年第1期26卷 63-72页

A finite element solution for the Navier-Stokes equations for steady flow under the porosity effects through a double branched two-dimensional section of a three-dimensional model of a canine aorta was obtained. The numerical solution involves transforming a physical coordinates to a curvilinear boundary fitted coordinate *** steady flow,branch flow and shear stress under the porous effects were discussed in detail. The shear stress at the wall was calculated for Reynolds number of 1 000 with branch to main aortic flow rate ratio as a parameter. The results are compared with earlier works involving experimental data and it has been observed that our results are very close to the exact *** work is in fact an improvement of the work of Sharma et al. (2001) in the sense that computational technique is economic and (Reynolds) number is large.

关键词： wall shear stress porosity Galerkin's technique blood vessel

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TODIM and TOPSIS with Z-numbers

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Frontiers of Information Technology & Electronic Engineering 2019年第2期20卷 283-291页

作者： Renato A.KROHLING André G.C.PACHECO Guilherme A.dos SANTOS Department of Production Engineering Federal University of Espirito Santo Graduate Program in Computer Science Federal University of Espirito Santo

In this paper, we present an approach that can handle Z-numbers in the context of multi-criteria decision-making problems. The concept of Z-number as an ordered pair Z=(A, B) of fuzzy numbers A and B is used, where A is a linguistic value of a variable of interest and B is a linguistic value of the probability measure of A. As human beings, we communicate with each other by means of natural language using sentences like "the journey from home to university most likely takes about half an hour." The Z-numbers are converted to fuzzy numbers. Then the Z-TODIM and Z-TOPSIS are presented as a direct extension of the fuzzy TODIM and fuzzy TOPSIS, respectively. The proposed methods are applied to two case studies and compared with the standard approach using crisp values. The results obtained show the feasibility of the approach.

关键词： Multi-criteria decision-making TODIM TOPSIS Fuzzy number Z-number

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Fusion of Frequency Domain Features of Face and Iris Traits for Person Identification

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Journal of The Institution of Engineers (India): Series B 2021年第5期102卷 987-996页

作者： Kagawade, Vishwanath C. Angadi, Shanmukhappa A. Department of Computer Applications Basaveshwar Engineering College Bagalkot India Department of Computer Science and Engineering Centre for Post Graduate Studies VTU Belagavi India

In this study, we present a new approach for person recognition through feature level fusion of face and iris traits. The strength of the multimodal biometric system relies much more on the consistency to determine relevant features from the individual biometric traits and fusion technique employed for integration. Hence, this paper presents a new feature extraction approach for a face–iris multimodal biometric system. The face and iris feature extraction is performed by employing Polar Fast Fourier Transform to obtain textural information in diverse scales and orientations of the face and eye images. The Canonical Correlation Analysis method is employed to integrate face and iris traits features, which reduces the new feature vector length than the input feature vectors. The proposed approach is capable to obtain and improve the discriminative power for person recognition from multi-feature data of face and iris traits. The effectiveness of the proposed model is illustrated through the use of both artificial and genuine face and iris multimodal databases, along with comparisons involving existing state-of-the-art techniques. © 2021, The Institution of Engineers (India).

关键词： Feature extraction

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