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Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

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Nature computational science 2023年第7期3卷 658页

作者： Gengjie Jia Yu Li Xue Zhong Kanix Wang Milton Pividori Rabab Alomairy Aniello Esposito Hatem Ltaief Chikashi Terao Masato Akiyama Koichi Matsuda David E Keyes Hae Kyung Im Takashi Gojobori Yoichiro Kamatani Michiaki Kubo Nancy J Cox James Evans Xin Gao Andrey Rzhetsky Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China. jiagengjie@***. Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong People's Republic of China. Department of Medicine and Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN US. Department of Medicine Institute of Genomics and Systems Biology Committee on Genomics Genetics and Systems Biology University of Chicago Chicago IL US. Department of Operations Business Analytics and Information Systems University of Cincinnati Cincinnati OH US. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA US. Extreme Computing Research Center Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. College of Computer Science and Engineering University of Jeddah Jeddah Saudi Arabia. HPE HPC/AI EMEA Research Laboratory Bristol UK. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Clinical Research Center Shizuoka General Hospital Shizuoka Japan. Department of Applied Genetics The School of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan. Department of Ophthalmology Graduate School of Medical Sciences Kyushu University Fukuoka Japan. Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan. Biological and Environmenta

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Self-adaptive Evolutionary Algorithm for DNA Codeword Design

Self-adaptive Evolutionary Algorithm for DNA Codeword Design

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Congress on Evolutionary Computation

作者： Jeisson Prieto Elizabeth León Max H. Garzon Computing Systems and Industrial Engineering Department Universidad Nacional de Colombia Bogotá Colombia Department of Computer Science and the Bioinformatics Program University of Memphis Memphis USA

DNA has emerged as a new computational resource for data encoding and processing. The fundamental problem of DNA Codeword Design (CWD) calls for finding effective ways to encode and process data in DNA. The problem has shown to be of interest in other areas as well, including computational memories, self-assembly and phylogenetic analysis, among others. In prior work, a framework to analyze this problem has been developed and simple versions of CWD have been shown to be NP-complete using any single reasonable metric that approximates the Gibbs energy, thus practically making it very difficult to find a general procedure for finding optimal efficient encodings. We present a Self-adaptive Evolutionary Algorithm for CWD (SaEA-CWD) as an extension of the Hybrid Adaptive Evolutionary algorithm (HAEA). SaEA-CWD is a parameter adaptation technique that automatically adapts the rates of its genetic operator applications to exploit structural properties of the search space to improve the speed and quality of the solutions. An implementation and preliminary results are evaluated in spaces where searches are already prohibitive to ordinary methods (such as 8- and 10-mers) due to the combinatorial explosion of the solution DNA space. Applications to other problems are suggested, such as a general technique for dimensionality reduction based on SaEA-CWD.

关键词： DNA Evolutionary computation Encoding Extraterrestrial measurements Self-assembly

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SAMENESS ENTICES, BUT NOVELTY ENCHANTS IN FANFICTION ONLINE

arXiv

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arXiv 2019年

作者： Jing, Elise DeDeo, Simon Wright, Devin Robert Ahn, Yong-Yeol Center for Complex Networks and Systems Research Luddy School of Informatics Computing and Engineering Indiana University Bloomington United States Social and Decision Sciences Dietrich College Carnegie Mellon University United States Sirius XM United States Cognitive Science Program Indiana University Bloomington United States Indiana University Network Science Institute Indiana University Bloomington United States

Cultural evolution is driven by how we choose what to consume and share with others. A common belief is that the cultural artifacts that succeed are ones that balance novelty and conventionality. This balance theory suggests that people prefer works that are familiar, but not so familiar as to be boring;novel, but not so novel as to violate the expectations of their genre. We test this idea using a large dataset of fanfiction. We apply a multiple regression model and a generalized additive model to examine how the recognition a work receives varies with its novelty, estimated through a Latent Dirichlet Allocation topic model, in the context of existing works. We find the opposite pattern of what the balance theory predicts—overall success decline almost monotonically with novelty and exhibits a U-shaped, instead of an inverse U-shaped, curve. This puzzle is resolved by teasing out two competing forces: sameness attracts the mass whereas novelty provides enjoyment. Taken together, even though the balance theory holds in terms of expressed enjoyment, the overall success can show the opposite pattern due to the dominant role of sameness to attract the audience. Under these two "forces", cultural evolution may have to work against inertia—the appetite for consuming the familiar—and may resemble a punctuated equilibrium, marked by occasional leaps. Copyright © 2019, The Authors. All rights reserved.

关键词： Large dataset

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10 quick tips for making your software outlive your job

arXiv

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arXiv 2025年

作者： Littauer, Richard Wilson, Greg Ainali, Jan AlOmar, Eman Abdullah Arabas, Sylwester Saibene, Yanina Bellini Bubendorfer, Kris Champion, Kaylea Dillon, Clare Helske, Jouni Huybrechts, Pieter Katz, Daniel S. Liao, Chang Lippert, David Liu, Fang Marshall, Pierre McCloy, Daniel R. McInerney, Ian Mkaouer, Mohamed Wiem Ojha, Priyanka Treude, Christoph White, Ethan P. CURIOSS SustainOSS GNOME Foundation Te Herenga Waka Victoria University of Wellington Te Whanganui-a-Tara Aotearoa Wellington New Zealand Third Bit TorontoON Canada Open By Default Italy Department of Systems and Enterprises Stevens Institute of Technology HobokenNJ United States AGH University of Krakow Poland rOpenSci LP Santa Rosa Argentina Te Herenga Waka Victoria University of Wellington Wellington New Zealand Computing and Software Systems University of Washington Bothell BothellWA United States CURIOSS Lero University of Galway Ireland INVEST Research Flagship Centre University of Turku Finland Brussels Belgium University of Illinois Urbana-ChampaignIL United States Pacific Northwest National Laboratory RichlandWA United States Open Source Program Office George Washington University WashingtonDC United States Georgia Institute of Technology GA United States Oxford University United Kingdom Institute for Learning & Brain Sciences University of Washington SeattleWA United States Department of Mechanical Engineering Imperial College London London United Kingdom Department of Computer Science University of Michigan-Flint FlintMI United States Singapore Management University Singapore Department of Wildlife Ecology and Conservation University of Florida GainesvilleFL United States

Loss of key personnel has always been a risk for research software projects. Key members of the team may have to step away due to illness or burnout, to care for a family member, from a loss of financial support, or because their career is going in a new direction. Today, though, political and financial changes are putting large numbers of researchers out of work simultaneously, potentially leaving large amounts of research software abandoned. This article presents ten tips to help researchers ensure that the software they have built will continue to be usable after they have left their present job—whether in the course of voluntary career moves or researcher mobility, but particularly in cases of involuntary departure due to political or institutional changes. © 2025, CC BY-SA.

关键词： Human engineering

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StBlocks: Visual programming for data structures 18

StBlocks: Visual programming for data structures

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18th Annual Conference on Information Technology Education, SIGITE 2017

作者： Almanza, Daniel F. Del Toro, Manuel F. Urrego, Ricardo A. Feijóo, Pedro G. De La Rosa, Fernando Program of Systems Engineering Universidad El Bosque Bogotá D.C. Colombia Systems and Computing Engineering Department Universidad de los Andes Bogotá D.C. Colombia

ISBN: (纸本)9781450351003

The Data Structures course is common in systems engineering and Computer Science programs, providing a fundamental basis for professional training in these disciplines. This course presents a great pedagogical challenge, due to the high complexity in the algorithms studied and the levels of abstraction that it requires. Considering that the traditional pedagogical approach is sometimes not adequate to ease understanding of the structures covered in the course, we propose the development of DStBlocks as a playful and visual tool for the design and programming of data structures. Through this document we emphasize the context to be intervened and the problem to be solved, indicating the progress corresponding to the project. At the end we present the work which will be held in a near future, indicating how we are going to measure learning variables according to the project's objectives. © 2017 Copyright is held by the owner/author(s).

关键词： Data structures

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Speech Emotion Recognition using Convolutional Neural Network with Audio Word-based Embedding

Speech Emotion Recognition using Convolutional Neural Networ...

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International Symposium on Chinese Spoken Language Processing

作者： Kun-Yi Huang Chung-Hsien Wu Qian-Bei Hong Ming-Hsiang Su Yuan-Rong Zeng Department of Computer Science and Information Engineering National Cheng Kung University Taiwan PhD Program for Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Taiwan

ISBN: (纸本)9781538656280;9781538656273

A complete emotional expression typically contains a complex temporal course in a natural conversation. Related research on utterance-level, segment-level and multi-level processing lacks understanding of the underlying relation of emotional speech. In this work, a convolutional neural network (CNN) with audio word-based embedding is proposed for emotion modeling. In this study, vector quantization is first applied to convert the low level features of each speech frame into audio words using k-means algorithm. Word2vec is adopted to convert an input speech utterance into the corresponding audio word vector sequence. Finally, the audio word vector sequences of the training emotional speech data with emotion annotation are used to construct the CNN- based emotion model. The NCKU-ES database, containing seven emotion categories: happiness, boredom, anger, anxiety, sadness, surprise and disgust, was collected and five-fold cross validation was used to evaluate the performance of the proposed CNN-based method for speech emotion recognition. Experimental results show that the proposed method achieved an emotion recognition accuracy of 82.34%, improving by 8.7% compared to the Long Short Term Memory (LSTM)- based method, which faced the challenging issue of long input sequence. Comparing with raw features, the audio word-based embedding achieved an improvement of 3.4% for speech emotion recognition.

关键词： Emotion recognition Feature extraction Speech recognition Acoustics Training Databases Neural networks

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Exploring Macroscopic Fluctuation of Facial Expression for Mood Disorder Classification

Exploring Macroscopic Fluctuation of Facial Expression for M...

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Asian Conference on Affective computing and Intelligent Interaction (ACII Asia)

作者： Qian-Bei Hong Chung-Hsien Wu Ming-Hsiang Su Kun-Yi Huang Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Tainan Taiwan Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan

ISBN: (纸本)9781538653128

In clinical diagnosis of mood disorder, a large portion of bipolar disorder patients (BDs) are misdiagnosed as unipolar depression (UDs). Clinicians have confirmed that BDs generally show "reduced affect'' during clinical treatment. Thus, it is expected to build an objective and one-time diagnosis system for diagnosis assistance by using machine-learning techniques. In this study, facial expressions of BD, UD and control group (C) elicited by emotional video clips are collected for exploring temporal fluctuation characteristics of intensities of facial muscles expression among the three groups. The differences of facial expressions among mood disorders are investigated by observing macroscopic fluctuations. To deal with these problems, the corresponding methods for feature extraction and modeling are proposed. From the viewpoint of macroscopic facial expression, action unit (AU) is applied for describing the temporal transformation of muscles. Then, modulation spectrum is used for extracting short-term variation of AU. The multilayer perceptron (MLP)-based disorder prediction model is then applied to obtain the prediction results. For evaluation of the proposed method, 12 subjects for three group are included in the K-fold (K=12) cross validation experiments. The experiment results reached 61.1% classification accuracy, and outperformed the other baseline methods.

关键词： Mood Gold Fluctuations Databases Feature extraction Modulation Predictive models

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LSTM-based Text Emotion Recognition Using Semantic and Emotional Word Vectors

LSTM-based Text Emotion Recognition Using Semantic and Emoti...

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Asian Conference on Affective computing and Intelligent Interaction (ACII Asia)

作者： Ming-Hsiang Su Chung-Hsien Wu Kun-Yi Huang Qian-Bei Hong Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Tainan Taiwan

ISBN: (纸本)9781538653128

This study proposes a long-short term memory (LSTM)-based approach to text emotion recognition based on semantic word vector and emotional word vector of the input text. For each word in an input text, the semantic word vector is extracted from the word 2vec model. Besides, each lexical word is projected to all the emotional words defined in an affective lexicon to derive an emotional word vector. An autoencoder is then adopted to obtain the bottleneck features from the emotional word vector for dimensionality reduction. The autoencoder bottleneck features are then concatenated with the features in the semantic word vector to form the final textual features for emotion recognition. Finally, given the textual feature sequence of the entire sentence, the LSTM is used for emotion recognition by modeling the contextual emotion evolution of the input text. For evaluation, the NLPCC-MHMC-TE database containing seven emotion categories: anger, boredom, disgust, anxiety, happiness, sadness, and surprise was constructed and used. Five-fold cross-validation was employed to evaluate the performance of the proposed method. Experimental results show that the proposed LSTM-based method achieved a recognition accuracy of 70.66%, improving 5.33% compared with the CNN-based method. Besides, the proposed method based on integration of the semantic word vector and emotional word vector of the input text outperformed that using the individual feature vector.

关键词： Emotion recognition Databases Logic gates Feature extraction Semantics Speech recognition Computer science

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Syncgan: Synchronize the Latent Spaces of Cross-Modal Generative Adversarial Networks

Syncgan: Synchronize the Latent Spaces of Cross-Modal Genera...

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IEEE International Conference on Multimedia and Expo (ICME)

作者： Wen-Cheng Chen Chien-Wen Chen Min-Chun Hu Dept. of Computer Science and Information Engineering National Cheng Kung University Taiwan Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Taiwan

Generative adversarial network (GAN) has achieved impressive success on cross-domain generation, but it faces difficulty in cross-modal generation due to the lack of a common distribution between heterogeneous data. Most existing methods of conditional based cross-modal GANs adopt the strategy of one-directional transfer and have achieved preliminary success on text-to-image transfer. Instead of learning the transfer between different modalities, we aim to learn a synchronous latent space representing the cross-modal common concept. A novel network component named synchronizer is proposed in this work to judge whether the paired data is synchronous/corresponding or not, which can constrain the latent space of generators in the GANs. Our GAN model, named as SyncGAN, can successfully generate synchronous data (e.g., a pair of image and sound) from identical random noise. For transforming data from one modality to another, we recover the latent code by inverting the mappings of a generator and use it to generate data of different modality. In addition, the proposed model can achieve semi-supervised learning, which makes our model more flexible for practical applications.

关键词： Synchronization Gallium nitride Generators Data models Training Generative adversarial networks Training data

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AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

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Immunoinformatics (Amsterdam, Netherlands) 2023年 10卷 100025页

作者： William D Lees Scott Christley Ayelet Peres Justin T Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G Cowell Gur Yaari Martin Corcoran Gunilla B Karlsson Hedestam Mats Ohlin Andrew M Collins Corey T Watson Christian E Busse Institute of Structural and Molecular Biology Birkbeck College London England. Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal. Peter O'Donnell Jr. School of Public Health UT Southwestern Medical Center Dallas TX USA. Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel. Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville KY USA. Department of Biological Sciences Simon Fraser University Burnaby BC Canada. Fred Hutchinson Cancer Research Center Seattle WA USA. Peter O'Donnell Jr. School of Public Health Department of Immunology School of Biomedical Sciences UT Southwestern Medical Center Dallas TX USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Swede. Department of Immunotechnology and SciLifeLab Lund University Lund Sweden. School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia. Division of B Cell Immunology German Cancer Research Center Heidelberg Germany.

Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.

关键词： AIRR-seq Immune receptor Immune receptor germline Immune receptor repertoire Rep-seq

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