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ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data 29th

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ALPINE: An Interpretable Approach for Decoding Phenotypes ...

29th International Conference on Research in Computational Molecular Biology, RECOMB 2025

作者： Lee, Wei-Hao Li, Lechuan Dannenfelser, Ruth Yao, Vicky Systems Synthetic and Physical Biology Graduate Program Rice University Houston United States Department of Computer Science Rice University Houston United States Ken Kennedy Institute Rice University Houston United States Rice Synthetic Biology Institute Rice University Houston United States

ISBN: (纸本)9783031902512

Advancements in sequencing technology have expanded data availability, capturing diverse phenotypic traits and biological perturbations. However, increased resolution also raises complexity, as studies now examine multiple dimensions, including donor phenotypes, anatomical regions, cell types, and time points. Integrating datasets across studies promises insights into health and disease beyond the scope of individual experiments, but this requires methods that can separate technical artifacts from meaningful biological signals while providing interpretable insights into condition-related genetic factors. Existing approaches tend to focus on either integration or interpretability, rarely addressing both simultaneously. To overcome these challenges, we introduce ALPINE, a joint supervised-unsupervised non-negative matrix factorization framework that disentangles technical and biological variation while directly identifying condition-associated genes. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Matrix factorization

GOOSE Algorithm: A New Bio-Inspired Metaheuristic Algorithm for Solving Optimization Problems Based on Goose Behavior

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SSRN

SSRN 2023年

作者： Hamad, Rebwar Khalid Rashid, Tarik A. Department of Information Systems Engineering Erbil Technical Engineering College Erbil Polytechnic University Erbil Iraq Computer Science and Engineering Department University of Kurdistan Hewler Erbil Iraq

This study proposes the GOOSE algorithm as a novel metaheuristic algorithm based on the goose's behavior during rest and foraging. The goose stands on one leg and keeps his balance to guard and protect other individuals in the flock. The GOOSE algorithm is benchmarked on 19 well-known benchmark test functions, and the results are verified by a comparative study with genetic algorithm (GA), particle swarm optimization (PSO), dragonfly algorithm (DA), and fitness dependent optimizer (FDO). In addition, the proposed algorithm is tested on 10 modern benchmark functions, and the gained results are compared with three recent algorithms, such as the dragonfly algorithm, whale optimization algorithm (WOA), and salp swarm algorithm (SSA). Moreover, the GOOSE algorithm is tested on 5 classical benchmark functions, and the obtained results are evaluated with six algorithms, such as fitness dependent optimizer (FDO), FOX optimizer, butterfly optimization algorithm (BOA), whale optimization algorithm, dragonfly algorithm, and chimp optimization algorithm (ChOA). The achieved findings attest to the proposed algorithm's superior performance compared to the other algorithms that were utilized in the current study. The technique is then used to optimize Welded beam design and Economic Load Dispatch Problem, three renowned real-world engineering challenges, and the Pathological IgG Fraction in the Nervous System. The outcomes of the engineering case studies illustrate how well the suggested approach can optimize issues that arise in the real-world. © 2023, The Authors. All rights reserved.

关键词： Particle swarm optimization (PSO)

Multi-Modal Conformal Prediction Regions with Simple Structures by Optimizing Convex Shape Templates

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arXiv 2023年

作者： Tumu, Renukanandan Cleaveland, Matthew Mangharam, Rahul Pappas, George J. Lindemann, Lars Department of Electrical & Systems Engineering University of Pennsylvania United States Thomas Lord Department of Computer Science University of Southern California United States

Conformal prediction is a statistical tool for producing prediction regions for machine learning models that are valid with high probability. A key component of conformal prediction algorithms is a non-conformity score function that quantifies how different a model’s prediction is from the unknown ground truth value. Essentially, these functions determine the shape and the size of the conformal prediction regions. While prior work has gone into creating score functions that produce multi-model prediction regions, such regions are generally too complex for use in downstream planning and control problems. We propose a method that optimizes parameterized shape template functions over calibration data, which results in non-conformity score functions that produce prediction regions with minimum volume. Our approach results in prediction regions that are multi-modal, so they can properly capture residuals of distributions that have multiple modes, and practical, so each region is convex and can be easily incorporated into downstream tasks, such as a motion planner using conformal prediction regions. Our method applies to general supervised learning tasks, while we illustrate its use in time-series prediction. We provide a toolbox and present illustrative case studies of F16 fighter jets and autonomous vehicles, showing an up to 68% reduction in prediction region area compared to a circular baseline region. Copyright © 2023, The Authors. All rights reserved.

关键词： Forecasting

Myopically Verifiable Probabilistic Certificates for Safe Control and Learning

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arXiv 2024年

作者： Wang, Zhuoyuan Jing, Haoming Kurniawan, Christian Chern, Albert Nakahira, Yorie The Department of Electrical and Computer Engineering Carnegie Mellon Universty PA15213 United States The Information Systems Technology and Design Pillar Singapore University of Technology and Design Singapore487372 Singapore The Department of Computer Science and Engineering University of California San DiegoCA92093 United States

This paper addresses the design of safety certificates for stochastic systems, with a focus on ensuring long-term safety through fast real-time control. In stochastic environments, set invariance-based methods that restrict the probability of risk events in infinitesimal time intervals may exhibit significant long-term risks due to cumulative uncertainties/risks. On the other hand, reachability-based approaches that account for the long-term future may require prohibitive computation in real-time decision making. To overcome this challenge involving stringent long-term safety vs. computation tradeoffs, we first introduce a novel technique termed 'probabilistic invariance'. This technique characterizes the invariance conditions of the probability of interest. When the target probability is defined using long-term trajectories, this technique can be used to design myopic conditions/controllers with assured long-term safe probability. Then, we integrate this technique into safe control and learning. The proposed control methods efficiently assure long-term safety using neural networks or model predictive controllers with short outlook horizons. The proposed learning methods can be used to guarantee long-term safety during and after training. Finally, we demonstrate the performance of the proposed techniques in numerical simulations. Copyright © 2024, The Authors. All rights reserved.

关键词： Stochastic systems

Unveiling Code Clone Patterns in Open Source VR Software: An Empirical Study

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arXiv 2025年

作者： Chen, Huashan Huang, Zisheng Xu, Yifan Huang, Wenjie Chen, Jinfu Li, Haotang Peng, Kebin Liu, Feng He, Sen Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China School of Computer Science Wuhan University Wuhan China Department of Systems and Industrial Engineering University of Arizona Tucson United States Department of Computer Science East Carolina University Greenville United States

Code cloning is frequently observed in software development, often leading to a variety of maintenance and security issues. While substantial research has been conducted on code cloning in traditional software, to the best of my knowledge, there is a lack of studies on cloning in VR software that consider its unique nature, particularly the presence of numerous serialized files in conjunction with the source code. In this paper, we conduct the first large-scale quantitative empirical analysis of software clones in 345 open-source VR projects, using the NiCad detector for source code clone detection and large language models (LLMs) for identifying serialized file clones. Our study leads to a number of insights into cloning phenomena in VR software, guided by seven carefully formulated research questions. These findings, along with their implications, are anticipated to provide useful guidance for both researchers and software developers within the VR field. Copyright © 2025, The Authors. All rights reserved.

关键词： Virtual environments

Teeth Segmentation from Bite-Wing X-Ray Images by Integrating Nested Dual UNet with Swin Transformers

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Teeth Segmentation from Bite-Wing X-Ray Images by Integratin...

2024 IEEE International Conference on systems, Man, and Cybernetics, SMC 2024

作者： Li, Yubo Tian, Yibin Zhang, Zhiyuan Zhang, Xueyang Du, Bingran Zeng, Zhi School of Computer and Information Science Chongqing Normal University Chongqing401331 China College of Mechatronics and Control Engineering Shenzhen University Shenzhen518060 China Litemaze Technology Shenzhen518000 China School of Computing and Information Systems Singapore Management University Singapore487372 Singapore Shunde Hospital Department of Stomatology Foshan528000 China

ISBN: (纸本)9781665410205

In medical practice, the precision of image segmentation is crucial for diagnosis and treatment evaluations. Specifically, in dentistry, accurate teeth segmentation from bite-wing images is important for automatic and objective evaluations of root canal treatments. This study introduces Swin-U2 Net, a model merging the nested dual UNet with residual U-block and Swin Transformers. It combines the local feature extraction capability of the former and the global attention and context understanding of the latter. It has been evaluated for tooth root segmentation using 500 bite-wing dental x-ray images obtained from a root canal treatment clinic. It achieved the best segmentation outcome in terms of Intersection over Union (IOU) and the third best result in terms of Dice Similarity Coefficient (DSC) with the second least amount of network parameters among six UNet-like models, thus it is effective and efficient. © 2024 IEEE.

关键词： Image segmentation

Brain-Controlled computer Tasks for Paralyzed Persons: Framework Overview

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Brain-Controlled Computer Tasks for Paralyzed Persons: Frame...

2023 International Conference on Industry sciences and computer science Innovation, iSCSi 2023

作者： Imran, Amna Chaudhary, Haider Tariq, Maimoona Ali, Zahra Ahad, Abdul Naqvi, Hammad Coelho, Paulo Jorge Pires, Ivan Miguel Knowledge Unit of Science and Technology University of Management and Technology Sialkot Pakistan School of Software Northwestern Polytechnical University Shaanxi Xian710072 China Department of Computer Science Istanbul Technical University Turkey Polytechnic of Leiria Leiria Portugal Institute for Systems Engineering and Computers at Coimbra Coimbra Portugal Instituto de Telecomunicações Universidade da Beira Interior Covilhã Portugal

To bridge the digital barrier between those with disabilities and those without impairments, several applications can be operated by brain signals. It highlights the importance of employing brain-computer interfaces (BCI) and mentions a specific system called the "Brain-Controlled computer System" that can control a computer cursor and perform mouse actions using brain signals.. The system can control the cursor and provide mouse left/right click with brain signals using a low-cost Brainlink Lite device. Based on this system, we employed machine learning and deep learning methodologies to develop a system that classifies brain signals for cursor movement. The methodology involved gathering user input through surveys, interviews, and comparison studies, as well as utilizing pre-developed datasets collected using a mind sensor. We initially trained a model on a previous dataset, achieving approximately 70% accuracy. However, when applied to the new dataset, the accuracy dropped to 49%. To improve the results, we experimented with more complex models, including additional layers and a dropout layer to prevent overfitting. Despite these enhancements, the accuracy only reached a maximum of 52%. The research team collected a dataset tailored to their specific application. They made a groundbreaking discovery by applying a convolutional neural network (CNN), typically used for image analysis, to process continuous brainwave data. Despite this non-standard use, their hypothesis proved correct, with the CNN model achieving an impressive 80% accuracy in classifying brain signals for controlling a cursor. © 2024 The Authors. Published by ELSEVIER B.V.

关键词： Brain computer interface

Empowering Urban Accessibility: A Prototype System for People with Disability

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Empowering Urban Accessibility: A Prototype System for Peopl...

International Conference on Advanced Learning Technologies (ICALT)

作者： Arlley Dos Santos Costa Luis Carlos Costa Fonseca Sofiane Labidi Graduate Program in Computer and Systems Engineering State University of Maranhão – UEMA São Luís Brazil Bachelor of Science and Technology Program -BICT Federal University of Maranhão – UFMA São Luis Brazil

ISBN: (数字)9798350362053

ISBN: (纸本)9798350362060

This work demonstrates the development of a prototype system that could improve urban and digital accessibility for People with Disability - PwD. The research involves using an academic questionnaire to enable a wider perspective of the central subject and assessing the effectiveness of the proposed solution. The main goal is to help social integration and make the future solution implementable for smart cities through an experiment in an academic campus. The dissertation is related to technological and social issues that might be used as a resource by researchers, public or private bodies interested in more profound studies. The document recognizes the lack of studies on this subject, especially in Brazil because there are few available articles. The prototype system is designed to tackle the issues faced by persons with disability in urban settings through platforms, applications and mobile phones as it proposes a comprehensive set of solutions when addressing accessibility for PwDs. In turn, this research fosters knowledge advancements in the field of urban accessibility and provides vital recommendations for developing inclusive technologies and policies.

关键词： Smart cities Prototypes People with disabilities Mobile handsets

Fuzzy Granule Density-Based Outlier Detection with Multi-Scale Granular Balls

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arXiv 2025年

作者： Gao, Can Tan, Xiaofeng Zhou, Jie Ding, Weiping Pedrycz, Witold The College of Computer Science and Software Engineering Shenzhen University Shenzhen518060 China Guangdong Key Laboratory of Intelligent Information Processing Shenzhen518060 China The National Engineering Laboratory for Big Data System Computing Technology Shenzhen University Shenzhen518060 China The School of Artificial Intelligence and Computer Science Nantong University Nantong226019 China The Faculty of Data Science City University of Macau Macau999078 China The Department of Electrical and Computer Engineering University of Alberta Edmonton Canada Systems Research Institute Polish Academy of Sciences Warsaw Poland The Department of Electrical and Computer Engineering King Abdulaziz University Jeddah Saudi Arabia The Department of Computer Engineering Istinye University Istanbul Turkey

Outlier detection refers to the identification of anomalous samples that deviate significantly from the distribution of normal data and has been extensively studied and used in a variety of practical tasks. However, most unsupervised outlier detection methods are carefully designed to detect specified outliers, while real-world data may be entangled with different types of outliers. In this study, we propose a fuzzy rough sets-based multi-scale outlier detection method to identify various types of outliers. Specifically, a novel fuzzy rough sets-based method that integrates relative fuzzy granule density is first introduced to improve the capability of detecting local outliers. Then, a multi-scale view generation method based on granular-ball computing is proposed to collaboratively identify group outliers at different levels of granularity. Moreover, reliable outliers and inliers determined by the three-way decision are used to train a weighted support vector machine to further improve the performance of outlier detection. The proposed method innovatively transforms unsupervised outlier detection into a semi-supervised classification problem and for the first time explores the fuzzy rough sets-based outlier detection from the perspective of multi-scale granular balls, allowing for high adaptability to different types of outliers. Extensive experiments carried out on both artificial and UCI datasets demonstrate that the proposed outlier detection method significantly outperforms the state-of-the-art methods, improving the results by at least 8.48% in terms of the Area Under the ROC Curve (AUROC) index. The source codes are released at https://***/Xiaofeng-Tan/MGBOD. © 2025, CC BY.

关键词： Granulation