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arXiv 2024年

作者： Gao, Shanghua Fang, Ada Huang, Yepeng Giunchiglia, Valentina Noori, Ayush Schwarz, Jonathan Richard Ektefaie, Yasha Kondic, Jovana Zitnik, Marinka Department of Biomedical Informatics Harvard Medical School BostonMA United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA United States Program in Biological and Biomedical Sciences Harvard Medical School BostonMA United States Department of Brain Sciences Imperial College London London United Kingdom Harvard College CambridgeMA United States Program in Biomedical Informatics Harvard Medical School BostonMA United States Department of Electrical Engineering and Computer Science MIT CambridgeMA United States Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University MA United States Broad Institute of MIT and Harvard CambridgeMA United States Harvard Data Science Initiative CambridgeMA United States

We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI’s ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are poised to be proficient in various tasks, planning discovery workflows and performing self-assessment to identify and mitigate gaps in their knowledge. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies. © 2024, CC BY.

关键词： Adversarial machine learning

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Parameter Optimization of Support Vector Regression Using Harris Hawks Optimization

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Procedia computer science 2021年 179卷 17-24页

作者： I Nyoman Setiawan Robert Kurniawan Budi Yuniarto Rezzy Eko Caraka Bens Pardamean Computational Statistics Department Polytechnic of Statistics - STIS Jakarta 13330 Indonesia Department of Information Management College of Informatics Chaoyang University of Technology Taiwan (ROC) Bioinformatics and Data Science Research Center Bina Nusantara University Indonesia 11530 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia. 11530.

Support Vector Regression (SVR) is often used in forecasting. Adjustment of parameters in the SVR affects the results of forecasting. This study aims to analyze the SVR method that is optimized using Harris Hawks Optimization (HHO), hereinafter referred to as HHO-SVR. The HHO-SVR was evaluated using five benchmark datasets to determine the performance of this method. The HHO process is also compared based on the type of kernel and other metaheuristic algorithms. The results showed that the HHO-SVR has almost the same performance as other methods but is less efficient in terms of time. In addition, the type of kernel also affects the process and results.

关键词： SVR harris hawks optimization parameter optimization kernel forecasting

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ζ-QVAE: A Quantum Variational Autoencoder utilizing Regularized Mixed-state Latent Representations

arXiv

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arXiv 2024年

作者： Wang, Gaoyuan Warrell, Jonathan Emani, Prashant S. Gerstein, Mark Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Computer Science Yale University New HavenCT06520 United States Department of Statistics & Data Science Yale University New HavenCT06520 United States Department of Biomedical Informatics & Data Science Yale University New HavenCT06520 United States NEC Laboratories America PrincetonNJ08540 United States

A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves compressing the original data to manageable dimensions while still representing essential information for downstream analysis. In classical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representation learning for subsequent tasks, and novel data generation. However, no model has been proposed that exactly captures all of these features for direct application to quantum data on quantum computers. Some existing quantum models for data compression lack regularization of latent representations, thus preventing direct use for generation and control of generalization. Others are hybrid models with only some internal quantum components, impeding direct training on quantum data. To bridge this gap, we present a fully quantum framework, ζ-QVAE, which encompasses all the capabilities of classical VAEs and can be directly applied for both classical and quantum data compression. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodates various divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at every stage, it can utilize the full-data density matrix and allow for a"global"training objective. Doing so, in turn, makes efficient optimization possible and has potential implications for private and federated learning. In addition to exploring the theoretical properties of ζ-QVAE, we demonstrate its performance on representative genomics and synthetic data. Our results consistently indicate that ζ-QVAE exhibits similar or better performance compared to matched classical models. © 2024, CC BY-NC-ND.

关键词： Large datasets

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Local Periodicity-Based Beat Tracking for Expressive Classical Piano Music

arXiv

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arXiv 2023年

作者： Chiu, Ching-Yu Müller, Meinard Davies, Matthew E.P. Su, Alvin Wen-Yu Yang, Yi-Hsuan The Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University Academia Sinica Taiwan The International Audio Laboratories Erlangen Germany The Department of Informatics Engineering Centre for Informatics and Systems of the University of Coimbra University of Coimbra Portugal The Department of Computer Science and Information Engineering National Cheng Kung University Taiwan Yating Music Team Taiwan AI Labs Taiwan Research Center for IT Innovation Academia Sinica Taiwan

To model the periodicity of beats, state-of-the-art beat tracking systems use "post-processing trackers" (PPTs) that rely on several empirically determined global assumptions for tempo transition, which work well for music with a steady tempo. For expressive classical music, however, these assumptions can be too rigid. With two large datasets of Western classical piano music, namely the Aligned Scores and Performances (ASAP) dataset and a dataset of Chopin's Mazurkas (Maz-5), we report on experiments showing the failure of existing PPTs to cope with local tempo changes, thus calling for new methods. In this paper, we propose a new local periodicity-based PPT, called predominant local pulse-based dynamic programming (PLPDP) tracking, that allows for more flexible tempo transitions. Specifically, the new PPT incorporates a method called "predominant local pulses" (PLP) in combination with a dynamic programming (DP) component to jointly consider the locally detected periodicity and beat activation strength at each time instant. Accordingly, PLPDP accounts for the local periodicity, rather than relying on a global tempo assumption. Compared to existing PPTs, PLPDP particularly enhances the recall values at the cost of a lower precision, resulting in an overall improvement of F1-score for beat tracking in ASAP (from 0.473 to 0.493) and Maz-5 (from 0.595 to 0.838). © 2023, CC BY.

关键词： Dynamic programming

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An Efficient Algorithm to Update Incremental Attributes in Morphological Trees

SSRN

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SSRN 2022年

作者： Gobber, Charles Ferreira Hashimoto, Ronaldo Fumio Alves, Wonder Alexandre Luz Informatics and Knowledge Management Graduate Program Universidade Nove de Julho São Paulo Brazil Department of Computer Science Institute of Mathematics and Statistics Universidade de São Paulo São Paulo Brazil

Attribute Filters are powerful image simplification operators that have very good contour-preservation properties. They can be efficiently computed using morphological trees. The most common strategy to compute attribute filters using morphological trees is based on three steps: (i) tree construction: the tree is built along with its attributes;(ii) filtering: we simplify the tree by removing some of its nodes based on some attribute and a filtering rule defined on a threshold value;and (iii) image reconstruction: this is the final phase where the tree is converted back to an image leading to an attribute filter. However, after filtering a few attributes in tree may change and they must be updated, since some attribute filters are computed by filtering the simplified tree again, but with a different threshold. In this paper it is presented an efficient algorithm to update incremental attributes in morphological trees with low memory consumption and fast computation. © 2022, The Authors. All rights reserved.

关键词： Image reconstruction

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Digital Technology in Health Education Trend Mapping through Bibliometrics Analysis

Digital Technology in Health Education Trend Mapping through...

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International Conference on informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Fairuz Iqbal Maulana Dian Lestari Vandha Pradwiyasma Widartha Nirwana Haidar Wahyu Dirgantara Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Medicine Airlangga University Surabaya Indonesia Information System of Industrial Engineering Faculty Telkom University Bandung Indonesia Informatics Engineering Study Program University of Madura Pamekasan Indonesia Department of Electrical Engineering University of Merdeka Malang Malang Indonesia

ISBN: (纸本)9781665473286

This study examines the mapping of research data on digital technology in the field of health education using bibliometric analysis method. Data was collected by identifying keywords in the Scopus database and sorting them out to sort the studies from the last 10 years (2012–2021). Through this step, a total of 1482 documents were obtained (articles, journals, proceedings, books, and others). The data is then processed using the VOSViewer instrument to obtain a visualization of the mapping analysis. This study also analyzes the network types of authors and co-authors through the VOSViewer instrument. The result of this study indicates that the most document types published within ten years are Articles (66.5%), Review (22.9 % ), Conference Paper (4.2 % ), and others. The most studied subjects are Medicine (55.7%), Nursing (9.0%), Health Professions (8.2%), Social sciences (7.8%), Engineering (3.9%), computer science (2.6 % ), Environmental science (2.6 % ), Biochemistry-Genetics and Molecular Biology (2.2%), Psychology (1.6%), and Dentistry (1.3%). This study offers a written communication process and the nature and direction of developing descriptive means of counting and analyzing the various phases of communication as well as recognizing the authorship and direction of its symptoms in documents on the subject of digital technology in the health sector.

关键词： Training Pediatrics Instruments Education Bibliometrics Transportation Psychology

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Lab: An R Package for Generating Analysis-Ready Data from Laboratory Records

SSRN

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SSRN 2022年

作者： Tseng, Yi-Ju Chen, Chun Ju Chang, Chia-Wei Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan Computational Health Informatics Program Boston Children’s Hospital BostonMA United States Department of Information Management National Taiwan University Taipei Taiwan

Electronic health records (EHRs) enable physicians to understand disease progression, identify appropriate treatment, and participate in data-driven health-care decision-making. Laboratory test results, which are included in EHRs, are commonly used to predict disease progression. In addition, analyzing the temporal information in EHRs can improve outcomes, prognoses, and diagnosis monitoring and prediction. However, laboratory records contain both data on the tests ordered and test results. Furthermore, the irregular frequency of the data in these records necessitates data preprocessing when time-series analyses are performed, which increases the burden of these analyses. Therefore, we developed an open-source R package that enables analysts to easily retrieve detailed information from laboratory records by mapping local laboratory codes onto the international standard, annotating abnormal results, slicing the data into time-series windows, summarizing the data through descriptive statistics, imputing missing values, and generating analysis-ready data. The proposed lab package simplifies and speeds up the workflow of laboratory report extraction and may assist clinical data analysts in generating simple and clean script that can easily be shared and reproduced. © 2022, The Authors. All rights reserved.

关键词： Laboratories

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Constructing A Creative Service Software with Semantic Web 8

Constructing A Creative Service Software with Semantic Web

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8th International Conference on Dependable Systems and Their Applications, DSA 2021

作者： Huang, Pei-Shu Fahmi, Faisal Wang, Feng-Jian Yang, Hongji Dept. of Computer Science National Yang-Ming Chiao-Tung University Hsinchu City Taiwan EECS Int’l Graduate Program National Yang-Ming Chiao-Tung University Hsinchu City Taiwan Information and Library Science Airlangga University Surabaya City Indonesia Department of Informatics University of Leicester Leicester United Kingdom

ISBN: (纸本)9781665443913

In software development, Service Oriented Architecture (SOA) and creative computing can be adopted to utilize multiple-domain knowledges to construct service software possessing creative properties, i.e., novel, useful, and surprising. In the past, several theoretical evaluation metrics have been proposed to measure creativity of a software system. However, a systematic practical method to construct creative service software is rarely considered in current researches. In this paper, we propose a model for creative service software development based on semantic web, which is applied in two phases: domain-creative requirement specification and semantic-based service design. The model can reduce communication work between domain experts and software engineers, improve traceability of the specifications, and improve machine readability during the generation of creativity. After the model of service design is validated for completeness and consistency, the creative service software is well-designed and can be implemented and reused effectively without losing of creativity. © 2021 IEEE.

关键词： Semantic Web

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Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model

arXiv

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arXiv 2024年

作者： Zhou, Peng Wang, Jianmin Li, Chunyan Wang, Zixu Liu, Yiping Sun, Siqi Lin, Jianxin Wei, Leyi Cai, Xibao Lai, Houtim Liu, Wei Wang, Longyue Liu, Yuansheng Zeng, Xiangxiang College of Information Science and Engineering Hunan University Changsha China The Interdisciplinary Graduate Program in Integrative Biotechnology Yonsei University Incheon21983 Korea Republic of School of Informatics Yunnan Normal University Kunming650500 China Department of Computer Science University of Tsukuba Tsukuba3058577 Japan Research Institute of Intelligent Complex Systems Fudan University Shanghai200433 China Shanghai AI Laboratory Shanghai200232 China Centre for Artificial Intelligence driven Drug Discovery Faculty of Applied Science Macao Polytechnic University China School of Informatics Xiamen University Xiamen China Tencent AI Lab China

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science. Copyright © 2024, The Authors. All rights reserved.

关键词： Students

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A Multi-phase Deep Learning Approach for Predicting HCC Response to TACE using Complete Computed Tomography

A Multi-phase Deep Learning Approach for Predicting HCC Resp...

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Data science and Engineering in Healthcare, Medicine and Biology, IEEE EMBS Special Topic Conference on

作者： Shun Cheng Chang Chien Fu Liu Marta Misztal Yi Hsien Hsieh Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taiwan School of Electronic Engineering and Computer Science Queen Mary University of London UK Department of Electrical Engineering NTU Taiwan Center for Computational and Systems Biology and Center for Biotechnology NTU Taiwan Smart Medicine and Health Informatics Program NTU Taiwan

In this research study, we compare the predictive performance of two advanced deep learning-based models in order to provide a solution to TACE (Transarterial Chemoembolization) response prediction in HCC (Hepatocellular Carcinoma) patients. Using entire abdominal CT scans enabled a broader perspective available for the model, eliminating the need for segmentation during the preprocessing. Making use of both single-phase and multi-phase CT imaging, we have used DenseNet121 and have obtained an accuracy of 80% for the multi-phase *** Relevance: The ability to predict the effectiveness of TACE treatment prior to its administration makes it possible to provide a better decision-making aid for physicians and patients.

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