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arXiv 2024年

作者： Luo, Xiaoliang Rechardt, Akilles Sun, Guangzhi Nejad, Kevin K. Yáñez, Felipe Yilmaz, Bati Lee, Kangjoo Cohen, Alexandra O. Borghesani, Valentina Pashkov, Anton Marinazzo, Daniele Nicholas, Jonathan Salatiello, Alessandro Sucholutsky, Ilia Minervini, Pasquale Razavi, Sepehr Rocca, Roberta Yusifov, Elkhan Okalova, Tereza Gu, Nianlong Ferianc, Martin Khona, Mikail Patil, Kaustubh R. Lee, Pui-Shee Mata, Rui Myers, Nicholas E. Bizley, Jennifer K. Musslick, Sebastian Bilgin, Isil Poyraz Niso, Guiomar Ales, Justin M. Gaebler, Michael Murty, N. Apurva Ratan Loued-Khenissi, Leyla Behler, Anna Hall, Chloe M. Dafflon, Jessica Bao, Sherry Dongqi Love, Bradley C. Department of Experimental Psychology University College London London United Kingdom Department of Engineering University of Cambridge Cambridge United Kingdom Department of Physiology Anatomy & Genetics University of Oxford Oxford United Kingdom Max Planck Institute for Neurobiology of Behavior – caesar Bonn Germany Bilkent University Ankara Turkey Department of Computer Science University of Bristol Bristol United Kingdom The Alan Turing Institute London United Kingdom Department of Psychiatry Yale University New Haven United States Psychology Emory University Atlanta United States Faculty of Psychology and Educational Sciences Université de Genève Genève Switzerland Neurosurgery Novosibirsk State Medical University Novosibirsk Russia Federal Center of Neurosurgery FSBI Novosibirsk Russia Department of Data Collection and Processing Systems Novosibirsk State Technical University Novosibirsk Russia Department of Data Analysis Ghent University Ghent Belgium Psychology New York University New York United States Department of Cognitive Neurology University of Tübingen Tübingen Germany Computer Science Princeton University Princeton United States ILCC University of Edinburgh Edinburgh United Kingdom Philosophy Psychology and Language Sciences The University of Edinburgh Edinburgh United Kingdom Department of Culture Cognition and Computation Aarhus University Aarhus Denmark Department of Molecular Life Sciences University of Zurich Zurich Switzerland Bioengineering University of Pennsylvania Philadelphia United States Linguistic Research Infrastructure University of Zurich Zurich Switzerland Electronic and Electrical Engineering University College London London United Kingdom Brain and Cognitive Sciences Massachusetts Institute of Technology CambridgeMA United States Institute of Neuroscience and Medicine INM-7: Brain and Behaviour Research Centre Jülich Jülich Germany Medical Faculty Institute of Systems Neuroscience Heinrich Hein

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors. © 2024, CC BY.

关键词： Prediction models

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Achieving trust-based and privacy-preserving customer selection in ubiquitous computing

arXiv

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arXiv 2019年

作者： Zhang, Chuan Zhu, Liehuang Xu, Chang Sharif, Kashif Liu, Ximeng Du, Xiaojiang Guizani, Mohsen Beijing Engineering Research Center of Massive Language Information Processing and Cloud Computing Application School of Computer Science and Technology Beijing Institute of Technology Beijing China School of Information Systems Singapore Management University College of Mathematics and Computer Science Fuzhou University Department of Computer and Information Sciences Temple University Philadelphia United States Department of Electrical and Computer Engineering University of Idaho MoscowID United States

The recent proliferation of smart devices has given rise to ubiquitous computing, an emerging computing paradigm which allows anytime & anywhere computing possible. In such a ubiquitous computing environment, customers release different computing or sensing tasks, and people, also known as data processors, participate in these tasks and get paid for providing their idle computing and communication resources. Thus, how to select an appropriate and reliable customer while not disclosing processors' privacy has become an interesting problem. In this article, we present a trust-based and privacy-preserving customer selection scheme in ubiquitous computing, called TPCS, to enable potential processors select the customers with good reputation. The basic concept of TPCS is that each data processor holds a trust value, and the reputation score of the customer is calculated based on processors' trust values and feedbacks via a truth discovery process. To preserve processors' privacy, pseudonyms and Paillier cryptosystem are applied to conceal each processor's real identity. In addition, three authentication protocols are designed to ensure that only the valid data processors (i.e., the processors registering in the system, holding the truthful trust values, and joining the computing tasks) can pass the authentication. A comprehensive security analysis is conducted to prove that our proposed TPCS scheme is secure and can defend against several sophisticated attacks. Moreover, extensive simulations are conducted to demonstrate the correctness and effectiveness of the proposed scheme. Copyright © 2019, The Authors. All rights reserved.

关键词： Ubiquitous computing

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Metrics Reloaded: Recommendations for image analysis validation

arXiv

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arXiv 2022年

作者： Maier-Hein, Lena Reinke, Annika Godau, Patrick Tizabi, Minu D. Buettner, Florian Christodoulou, Evangelia Glocker, Ben Isensee, Fabian Kleesiek, Jens Kozubek, Michal Reyes, Mauricio Riegler, Michael A. Wiesenfarth, Manuel Emre Kavur, A. Sudre, Carole H. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Rädsch, Tim Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Jorge Cardoso, M. Cheplygina, Veronika Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian Ginneken, Bram Van Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kofler, Florian Kopp-Schneider, Annette Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rajpoot, Nasir Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Smeden, Maarten Van Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben Van Varoquaux, Gaël Jäger, Paul F. Heidelberg Division of Intelligent Medical Systems and HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt-Marburg Germany Heidelberg Goethe University Frankfurt Germany Department of Medicine Goethe University Frankfurt Germany Department of Informatics Frankfurt Cancer Insititute Germany Department of Computing Imperial College London London United Kingdom Heidelberg Division of Medical Image Computing and HI Applied Computer Vision Lab Germany Institute for AI in Medicine University Medicine Essen Essen Germany Centre for Biomedical Image Analysis Faculty of Informatics Masaryk University Brno Czech Republic ARTORG Center for Biomedical Engineering Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Bern Switzerland Simula Metropolitan Center for Digital Engineering Oslo Norway UiT The Arctic University of Norway Romsø Norway Heidelberg Division of Biostatistics Germany Heidelberg Division of Intelligent Medical Systems Division of Medical Image Computing HI Applied Computer Vision Lab Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Heidelberg Division of Medical Image Computing Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. It was developed by a large international consortium in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint – a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases. © 2022, CC BY.

关键词： Semantic Segmentation

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OCTAVA: An open-source toolbox for quantitative analysis of optical coherence tomography angiography images

arXiv

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arXiv 2021年

作者： Untracht, Gavrielle R. Matos, Rolando Dikaios, Nikolaos Bapir, Mariam Durrani, Abdullah K. Butsabong, Teemapron Campagnolo, Paola Sampson, David D. Heiss, Christian Sampson, Danuta M. Optical+Biomedical Engineering Laboratory School of Electrical Electronic and Computer Engineering The University of Western Australia 35 Stirling Highway PerthWA6009 Australia Surrey Biophotonics Advanced Technology Institute School of Physics School of Biosciences and Medicine University of Surrey Surrey GuildfordGU2 7XH United Kingdom Department of Biochemical Sciences Department of Clinical and Experimental Medicine School of Biosciences and Medicine University of Surrey Surrey GuildfordGU2 7XH United Kingdom Mathematics Research Center Academy of Athens Athens106 79 Greece Surrey and Sussex Healthcare NHS Trust East Surrey Hospital Surrey RedhillRH1 5RH United Kingdom Surrey Biophotonics Centre for Vision Speech and Signal Processing School of Biosciences and Medicine The University of Surrey GuildfordGU2 7XH United Kingdom

Optical coherence tomography angiography (OCTA) performs non-invasive visualization and characterization of microvasculature in research and clinical applications mainly in ophthalmology and dermatology. A wide variety of instruments, imaging protocols, processing methods and metrics have been used to describe the microvasculature, such that comparing different study outcomes is currently not feasible. With the goal of contributing to standardization of OCTA data analysis, we report a user-friendly, open-source toolbox, OCTAVA (OCTA Vascular Analyzer), to automate the pre-processing, segmentation, and quantitative analysis of en face OCTA maximum intensity projection images in a standardized workflow. We present each analysis step, including optimization of filtering and choice of segmentation algorithm, and definition of metrics. We perform quantitative analysis of OCTA images from different commercial and non-commercial instruments and samples and show OCTAVA can accurately and reproducibly determine metrics for characterization of microvasculature. Wide adoption could enable studies and aggregation of data on a scale sufficient to develop reliable microvascular biomarkers for early detection, and to guide treatment, of microvascular disease. © 2021, CC BY-NC-SA.

关键词： Optical tomography

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Challenges of using text classifiers for causal inference

arXiv

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arXiv 2018年

作者： Wood-Doughty, Zach Shpitser, Ilya Dredze, Mark Department of Computer Science Center for Language and Speech Processing Malone Center for Engineering in Healthcare Johns Hopkins University BaltimoreMD21218 United States

Causal understanding is essential for many kinds of decision-making, but causal inference from observational data has typically only been applied to structured, low-dimensional datasets. While text classifiers produce low-dimensional outputs, their use in causal inference has not previously been studied. To facilitate causal analyses based on language data, we consider the role that text classifiers can play in causal inference through established modeling mechanisms from the causality literature on missing data and measurement error. We demonstrate how to conduct causal analyses using text classifiers on simulated and Yelp data, and discuss the opportunities and challenges of future work that uses text data in causal inference. Copyright © 2018, The Authors. All rights reserved.

关键词： Classification (of information)

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A GPU-based WFST decoder with exact lattice generation

arXiv

引用

arXiv 2018年

作者： Chen, Zhehuai Luitjens, Justin Xu, Hainan Wang, Yiming Povey, Daniel Khudanpur, Sanjeev SpeechLab Department of Computer Science and Engineering Shanghai Jiao Tong University NVIDIA United States Center for Language and Speech Processing Johns Hopkins University

We describe initial work on an extension of the Kaldi toolkit that supports weighted finite-state transducer (WFST) decoding on Graphics processing Units (GPUs). We implement token recombination as an atomic GPU operation in order to fully parallelize the Viterbi beam search, and propose a dynamic load balancing strategy for more efficient token passing scheduling among GPU threads. We also redesign the exact lattice generation and lattice pruning algorithms for better utilization of the GPUs. Experiments on the Switchboard corpus show that the proposed method achieves identical 1-best results and lattice quality in recognition and confidence measure tasks, while running 3 to 15 times faster than the single process Kaldi decoder. The above results are reported on different GPU architectures. Additionally we obtain a 46-fold speedup with sequence parallelism and multi-process service (MPS) in *** Codes 68T10 Copyright © 2018, The Authors. All rights reserved.

关键词： Graphics processing unit

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End-to-end monaural multi-speaker asr system without pretraining

arXiv

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arXiv 2018年

作者： Chang, Xuankai Qian, Yanmin Yu, Kai Watanabe, Shinji SpeechLab Department of Computer Science and Engineering Shanghai Jiao Tong University China Center for Language and Speech Processing Johns Hopkins University United States

Recently, end-to-end models have become a popular approach as an alternative to traditional hybrid models in automatic speech recognition (ASR). The multi-speaker speech separation and recognition task is a central task in cocktail party problem. In this paper, we present a state-of-the-art monaural multi-speaker end-to-end automatic speech recognition model. In contrast to previous studies on the monaural multi-speaker speech recognition, this end-to-end framework is trained to recognize multiple label sequences completely from scratch. The system only requires the speech mixture and corresponding label sequences, without needing any indeterminate supervisions obtained from non-mixture speech or corresponding labels/alignments. Moreover, we exploited using the individual attention module for each separated speaker and the scheduled sampling to further improve the performance. Finally, we evaluate the proposed model on the 2-speaker mixed speech generated from the WSJ corpus and the wsj0-2mix dataset, which is a speech separation and recognition benchmark. The experiments demonstrate that the proposed methods can improve the performance of the end-to-end model in separating the overlapping speech and recognizing the separated streams. From the results, the proposed model leads to ∼ 10.0% relative performance gains in terms of CER and WER respectively. Copyright © 2018, The Authors. All rights reserved.

关键词： speech

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A potential neurophysiological correlate of electric-acoustic pitch matching in adult cochlear implant users: Pilot data

引用

Cochlear Implants International 2018年第4期19卷 198-209页

作者： Tan, Chin-Tuan Martin, Brett A. Svirsky, Mario A. Department of Electrical and Computer Engineering School of Behavioral and Brain Science (Callier Center for Communication Disorders) University of Texas at Dallas Richardson TX United States Program in Speech-Language-Hearing Sciences and Program in Audiology Graduate Center City University of New York New York NY United States Department of Otolaryngology New York University New York NY United States

The overall goal of this study was to identify an objective physiological correlate of electric-acoustic pitch matching in unilaterally implanted cochlear implant (CI) participants with residual hearing in the non-implanted ear. electrical and acoustic stimuli were presented in a continuously alternating fashion across ears. The acoustic stimulus and the electrical stimulus were either matched or mismatched in pitch. Auditory evoked potentials were obtained from nine CI users. Results indicated that N1 latency was stimulus-dependent, decreasing when the acoustic frequency of the tone presented to the non-implanted ear was increased. More importantly, there was an additional decrease in N1 latency in the pitch-matched condition. These results indicate the potential utility of N1 latency as an index of pitch matching in CI users. © 2018 Informa UK Limited, trading as Taylor & Francis Group.

关键词： Auditory evoked potential Electric-acoustic pitch matching N1 latency

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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Database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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An improved dnn-based spectral feature mapping that removes noise and reverberation for robust automatic speech recognition

arXiv

引用

arXiv 2018年

作者： Escudero, Juan Pablo Novoa, José Mahu, Rodrigo Wuth, Jorge Huenupán, Fernando Stern, Richard Yoma, Néstor Becerra Electrical Engineering Department Speech Processing and Transmission Laboratory Universidad de Chile Santiago Chile Department of Electrical Engineering Universidad de la Frontera Temuco Chile Department of Electrical and Computer Engineering and Language Technologies Institute Carnegie Mellon University Pittsburgh United States

Reverberation and additive noise have detrimental effects on the performance of automatic speech recognition systems. In this paper we explore the ability of a DNN-based spectral feature mapping to remove the effects of reverberation and additive noise. Experiments with the CHiME-2 database show that this DNN can achieve an average reduction in WER of 4.5%, when compared to the baseline system, at SNRs equal to-6 dB,-3 dB, 0 dB and 3 dB, and just 0.8% at greater SNRs of 6 dB and 9 dB. These results suggest that this DNN is more effective in removing additive noise than reverberation. To improve the DNN performance, we combine it with the weighted prediction error (WPE) method that shows a complementary behavior. While this combination provided a reduction in WER of approximately 11% when compared with the baseline, the observed improvement is not as great as that obtained using WPE alone. However, modifications to the DNN training process were applied and an average reduction in WER equal to 18.3% was achieved when compared with the baseline system. Furthermore, the improved DNN combined with WPE achieves a reduction in WER of 7.9% when compared with WPE alone. Copyright © 2018, The Authors. All rights reserved.

关键词： speech enhancement

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