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Large language models surpass human experts in predicting neuroscience results

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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

Challenges of using text classifiers for causal inference

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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)

speech enhancement via deep spectrum image translation network

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arXiv 2019年

作者： Kashani, Hamidreza Baradaran Goodarzi, Mohammad Mohsen Jodeiri, Ata Rezaei, Iman Sarraf Electrical Engineering Faculty Amirkabir University of Technology Tehran Iran Department of Electrical and Computer Engineering Buein Zahra Technical University Qazvin Iran School of Electrical & Computer Engineering College of Engineering University of Tehran Tehran Iran Speech and Language Processing Group Research Center for Development of Advanced Technologies Tehran Iran

Quality and intelligibility of speech signals are degraded under additive background noise which is a critical problem for hearing aid and cochlear implant users. Motivated to address this problem, we propose a novel speech enhancement approach using a deep spectrum image translation network. To this end, we suggest a new architecture, called VGG19-UNet, where a deep fully convolutional network known as VGG19 is embedded at the encoder part of an image-to-image translation network, i.e. U-Net. Moreover, we propose a perceptually-modified version of the spectrum image that is represented in Mel frequency and power-law non-linearity amplitude domains, representing good approximations of human auditory perception model. By conducting experiments on a real challenge in speech enhancement, i.e. unseen noise environments, we show that the proposed approach outperforms other enhancement methods in terms of both quality and intelligibility measures, represented by PESQ and ESTOI, respectively. Copyright © 2019, The Authors. All rights reserved.

关键词： Audition

speech Enhancement via Deep Spectrum Image Translation Network

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Speech Enhancement via Deep Spectrum Image Translation Netwo...

Iranian Conference of Biomedical Engineering (ICBME)

作者： Hamidreza Baradaran Kashani Ata Jodeiri Mohammad Mohsen Goodarzi Iman Sarraf Rezaei Electrical Engineering Faculty Amirkabir University of Technology Tehran Iran School of Electrical & Computer Engineering College of Engineering University of Tehran Tehran Iran Department of Electrical and Computer Engineering Buein Zahra Technical University Qazvin Iran Research Center for Development of Advanced Technologies Speech and Language Processing Group Tehran Iran

ISBN: (数字)9781728156637

ISBN: (纸本)9781728156644

Quality and intelligibility of speech signals are degraded under additive background noise which is a critical problem for hearing aid and cochlear implant users. Motivated to address this problem, we propose a novel speech enhancement approach using a deep spectrum image translation network. To this end, we suggest a new architecture, called VGG19-UNet, where a deep fully convolutional network known as VGG19 is embedded at the encoder part of an image-to-image translation network, i.e. U-Net. Moreover, we propose a perceptuallymodified version of the spectrum image that is represented in Mel frequency and power-law non-linearity amplitude domains, representing good approximations of human auditory perception model. By conducting experiments on a real challenge in speech enhancement, i.e. unseen noise environments, we show that the proposed approach outperforms other enhancement methods in terms of both quality and intelligibility measures, represented by PESQ and ESTOI, respectively.

关键词： speech enhancement Noise measurement Feature extraction Training computer architecture Convolution Frequency-domain analysis

Metrics Reloaded: Recommendations for image analysis validation

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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

AIROGS: ARTIFICIAL INTELLIGENCE FOR ROBUST GLAUCOMA SCREENING CHALLENGE

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arXiv 2023年

作者： De Vente, Coen Vermeer, Koenraad A. Jaccard, Nicolas Wang, He Sun, Hongyi Khader, Firas Truhn, Daniel Aimyshev, Temirgali Zhanibekuly, Yerkebulan Le, Tien-Dung Galdran, Adrian Ballester, Miguel Ángel González Carneiro, Gustavo Devika, R.G. Hrishikesh, P.S. Puthussery, Densen Liu, Hong Yang, Zekang Kondo, Satoshi Kasai, Satoshi Wang, Edward Durvasula, Ashritha Heras, Jónathan Zapata, Miguel Ángel Araújo, Teresa Aresta, Guilherme Bogunović, Hrvoje Arikan, Mustafa Lee, Yeong Chan Cho, Hyun Bin Choi, Yoon Ho Qayyum, Abdul Razzak, Imran Van Ginneken, Bram Lemij, Hans G. Sánchez, Clara I. Group Informatics Institute Universiteit Van Amsterdam Noord-Holland Amsterdam Netherlands The Department of Biomedical Engineering and Physics Amsterdam Umc Locatie Amc Noord-Holland Amsterdam Netherlands Department of Radiology and Nuclear Medicine Radboudumc Gelderland Nijmegen Netherlands The Rotterdam Ophthalmic Institute Rotterdam Eye Hospital Rotterdam Netherlands Project Orbis International Inc. New York United States The Peking Union Medical College Hospital Beijing China The Xuanwu Hospital Capital Medical University Beijing100053 China The Tsinghua University Beijing China The Department of Diagnostic and Interventional Radiology University Hospital Aachen Aachen Germany Cmc Technologies Llp Nur-Sultan Kazakhstan Kbc Belgium Universitat Pompeu Fabra Barcelona Spain The Australian Institute for Machine Learning Aiml University of Adelaide Australia Icrea Barcelona Spain The Centre for Vision Speech and Signal Processing University of Surrey United Kingdom The College of Engineering Trivandrum India Founding Minds Software India The Institute of Computing Technology Chinese Academy of Sciences China The Muroran Institute of Technology Japan The Niigata University of Health and Welfare Japan The Schulich School of Medicine and Dentistry University of Western Ontario London Canada The Department of Mathematics and Computer Science University of la Rioja Spain Hospital Vall Hebron Passeig Roser 126 Sant Cugat del Vallès Barcelona08195 Spain UPRetina Barcelona Spain The Christian Doppler Laboratory for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria The Institute of Ophthalmology University College London London United Kingdom The Research Institute for Future Medicine Samsung Medical Center Seoul Korea Republic of Sungkyunkwan University Samsung Medical Center Seoul Korea Republic of The Department of Artificial Intelligence and Informatics Mayo Clinic Jacks

The early detection of glaucoma is essential in preventing visual impairment. Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible. While AI models for glaucoma screening from CFPs have shown promising results in laboratory settings, their performance decreases significantly in realworld scenarios due to the presence of out-of-distribution and low-quality images. To address this issue, we propose the Artificial Intelligence for Robust Glaucoma Screening (AIROGS) challenge. This challenge includes a large dataset of around 113,000 images from about 60,000 patients and 500 different screening centers, and encourages the development of algorithms that are robust to ungradable and unexpected input data. We evaluated solutions from 14 teams in this paper, and found that the best teams performed similarly to a set of 20 expert ophthalmologists and optometrists. The highest-scoring team achieved an area under the receiver operating characteristic curve of 0.99 (95% CI: 0.98-0.99) for detecting ungradable images on-the-fly. Additionally, many of the algorithms showed robust performance when tested on three other publicly available datasets. These results demonstrate the feasibility of robust AI-enabled glaucoma screening. Copyright © 2023, The Authors. All rights reserved.

关键词： Diagnosis

SDN controllers: Benchmarking & performance evaluation

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arXiv 2019年

作者： Zhu, Liehuang Karim, Md Monjurul Sharif, Kashif Li, Fan Du, Xiaojiang Guizani, Mohsen Beijing Engineering Research Center for Massive Language Information Processing & Cloud Computing Application School of Computer Science and Technology Beijing Institute of Technology Beijing China Department of Computer and Information Sciences Temple University Philadelphia United States Department of Electrical and Computer Engineering University of Idaho MoscowID United States

Software Defined Networks offer flexible and intelligent network operations by splitting a traditional network into a centralized control plane and a programmable data plane. The intelligent control plane is responsible for providing flow paths to switches and optimizes network performance. The controller in the control plane is the fundamental element used for all operations of data plane management. Hence, the performance and capabilities of the controller itself are extremely important. Furthermore, the tools used to benchmark their performance must be accurate and effective in measuring different evaluation parameters. There are dozens of controller proposals available in existing literature. However, there is no quantitative comparative analysis for them. In this article, we present a comprehensive qualitative comparison of different SDN controllers, along with a quantitative analysis of their performance in different network scenarios. More specifically, we categorize and classify 34 controllers based on their capabilities, and present a qualitative comparison of their properties. We also discuss in-depth capabilities of benchmarking tools used for SDN controllers, along with best practices for quantitative controller evaluation. This work uses three benchmarking tools to compare nine controllers against multiple criteria. Finally, we discuss detailed research findings on the performance, benchmarking criteria, and evaluation testbeds for SDN controllers. Copyright © 2019, The Authors. All rights reserved.

关键词： Benchmarking

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

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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

A GPU-based WFST decoder with exact lattice generation

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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