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Genetics in Medicine Open 2023年第1期1卷 100727-100727页

作者： Katrin Sangkuhl Ryan Whaley Mark Woon Karl Keat Li Gong Michelle Whirl-Carrillo Marylyn Ritchie Teri Klein Department of Biomedical Data Science Stanford University Stanford CA Genomics and Computational Biology PhD Program University of Pennsylvania Philadelphia PA Department of Genetics University of Pennsylvania Philadelphia PA

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A holistic exploration of the potentially recoverable redshift information of Stage IV galaxy surveys

arXiv

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arXiv 2024年

作者： Scott, Bryan R. Malz, Alex I. Sorba, Robert Northwestern University 1800 Sherman Ave 8th Floor EvanstonIL60201 United States LSST Discovery Alliance Data Science Fellowship Program United States McWilliams Center for Cosmology and Astrophysics Department of Physics Carnegie Mellon University United States Institute for Computational Astrophysics Saint Mary’s University 923 Robie Street HalifaxNSB3H 3C3 Canada

Extragalactic science and cosmology with Stage IV galaxy surveys will rely almost exclusively on redshift measurements derived solely from photometry, which are subject to systematic and statistical uncertainties with numerous analysis choices, such as that of an estimator and prior information and no universal solution. Single-survey photometric redshift estimates ought to be improved by combining data from multiple surveys, with common wisdom asserting that optical data benefits from additional infrared coverage but not from additional ultraviolet coverage. The degree of improvement for either case is not well-characterized and attempts to quantify it necessitate assumptions of a chosen estimator and its prior information. We apply an information theoretic metric of potentially recoverable redshift information to assess the impact of multi-survey photometry combinations without assuming an estimator nor priors in the context of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) in the optical, Roman and Euclid Surveys in the infrared, and Cosmological Advanced Survey Telescope for Optical-UV Research (CASTOR) in the ultraviolet. We conclude that the addition of UV photometry can benefit redshift determination of certain galaxy populations, but that gain is tempered by their decreased chance of meeting detection criteria at higher wavelengths. We explore the spectral energy distribution (SEDs) of galaxies whose potentially recoverable redshift information is most impacted by additional photometry to provide a basis for future evaluation of which science cases may motivate which combinations. The holistic assessment approach we develop here is generic and may be applied to quantify the impact of combining photometric datasets, changing experimental design choices, including observing strategy optimization, and evaluating systematics mitigation procedures. © 2024, CC BY.

关键词： Cosmology

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Temporal networks provide a unifying understanding of the evolution of cooperation

arXiv

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arXiv 2023年

作者： Li, Aming Meng, Yao Zhou, Lei Masuda, Naoki Wang, Long Center for Systems and Control College of Engineering Peking University Beijing100871 China Center for Multi-Agent Research Institute for Artificial Intelligence Peking University Beijing100871 China School of Automation Beijing Institute of Technology Beijing100081 China Department of Mathematics State University of New York at Buffalo BuffaloNY14260 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260 United States

Understanding the evolution of cooperation in structured populations represented by networks is a problem of long research interest, and a most fundamental and widespread property of social networks related to cooperation phenomena is that the node’s degree (i.e., number of edges connected to the node) is heterogeneously distributed. Previous results indicate that static heterogeneous (i.e., degree-heterogeneous) networks promote cooperation in stationarity compared to static regular (i.e., degree-homogeneous) networks if equilibrium dynamics starting from many cooperators and defectors is employed. However, the above conclusion reverses if we employ non-equilibrium stochastic processes to measure the fixation probability for cooperation, i.e., the probability that a single cooperator successfully invades a population. Here we resolve this conundrum by analyzing the fixation of cooperation on temporal (i.e., time-varying) networks. We theoretically prove and numerically confirm that on both synthetic and empirical networks, contrary to the case of static networks, temporal heterogeneous networks can promote cooperation more than temporal regular networks in terms of the fixation probability of cooperation. Given that the same conclusion is known for the equilibrium fraction of cooperators on temporal networks, the present results provide a unified understanding of the effect of temporal degree heterogeneity on promoting cooperation across two main analytical frameworks, i.e., equilibrium and non-equilibrium ones. Copyright © 2023, The Authors. All rights reserved.

关键词： Heterogeneous networks

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Detecting anomalous citation groups in journal networks

arXiv

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arXiv 2020年

作者： Kojaku, Sadamori Livan, Giacomo Masuda, Naoki Luddy School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Computer Science University College London LondonWC1E 6EA United Kingdom Systemic Risk Centre London School of Economics and Political Science LondonWC2A 2AE United Kingdom Department of Mathematics University at Buffalo State University of New York BuffaloNY United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-2900 United States Faculty of Science and Engineering Waseda University Tokyo169-8555 Japan

The ever-increasing competitiveness in the academic publishing market incentivizes journal editors to pursue higher impact factors. This translates into journals becoming more selective, and, ultimately, into higher publication standards. However, the fixation on higher impact factors leads some journals to artificially boost impact factors through the coordinated effort of a "citation cartel" of journals. "Citation cartel" behavior has become increasingly common in recent years, with several instances being reported. Here, we propose an algorithm—-named CIDRE—to detect anomalous groups of journals that exchange citations at excessively high rates when compared against a null model that accounts for scientific communities and journal size. CIDRE detects more than half of the journals suspended from Journal Citation Reports due to anomalous citation behavior in the year of suspension or in advance. Furthermore, CIDRE detects many new anomalous groups, where the impact factors of the member journals are lifted substantially higher by the citations from other member journals. We describe a number of such examples in detail and discuss the implications of our findings with regard to the current academic climate. Copyright © 2020, The Authors. All rights reserved.

关键词： Publishing

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Estimation of the main air pollutants from different biomasses under combustion atmospheres by artificial neural networks

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Chemosphere 2024年 352卷 141484页

作者： Monteiro, Thalyssa Oliveira Alves, Pedro Augusto Araújo da Silva de Almeida Nava Barradas Filho, Alex Oliveira Villa-Vélez, Harvey Alexander Cruz, Glauber Postgraduate Program in Mechanical Engineering (PPGMEC) Department of Mechanics and Materials Federal Institute of Education Science and Technology of Maranhão (IFMA) Maranhão São Luís Brazil Postgraduate Program in Computer Science and Computational Mathematics (PPG-CCMC) Department of Computer Science University of São Paulo (USP) São Carlos São Paulo Brazil Data Analysis and Artificial Intelligence Laboratory (DARTi) Department of Computational Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Department of Chemical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Processes and Thermal Systems Laboratory (LPSisTer) Department of Mechanical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO2, NOx, SOx, and other pollutants), affecting living organisms and requiring careful assessments. H... 详细信息

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO₂, NO_x, SO_x, and other pollutants), affecting living organisms and requiring careful assessments. However, obtaining such information experimentally for data evaluation is costly and time-consuming and its in situ obtaining for regional biomasses (e.g., those from Northeast Brazil (NEB) is still a major challenge. This paper reports on the application of artificial neural networks (ANNs) for the prediction of the main air pollutants (CO, CO₂, NO, and SO₂) produced during the direct biomass combustion (N₂/O₂:80/20%) with the use of ultimate analysis (carbon, hydrogen, nitrogen, sulfur, and oxygen). 116 worldwide biomasses were used as input data, which is a relevant alternative to overcome the lack of experimental resources in NEB and obtain such information. Cross-validation was conducted with k-fold to optimize the ANNs and performance was analyzed with the use of statistical errors for accuracy assessments. The results showed an acceptable statistical performance for all architectures of ANNs, with 0.001–12.41% MAPE, 0.001–5.82 mg Nm⁻³ MAE, and 0.03–52.30 mg Nm⁻³ RMSE, highlighting the high precision of the emissions studied. On average, the differences between predicted and real values for CO, CO₂, NO, and SO₂ emissions from NEB biomasses were approximately 0.01%, 10⁻⁶%, 0.14%, and 0.05%, respectively. Pearson coefficient provided consistent results of concentration of the ultimate analysis in relation to the emissions studied and effectiveness of the test set in the developed models. © 2024 Elsevier Ltd

关键词： Brazilian northeastern Environmental statistics Evaluation metrics Gaseous emissions Predictive models Thermoconversion

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Interpretable bias mitigation for textual data: Reducing gender bias in patient notes while maintaining classification performance

arXiv

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arXiv 2021年

作者： Minot, Joshua R. Cheney, Nicholas Maier, Marc Elbers, Danne C. Danforth, Christopher M. Dodds, Peter Sheridan Computational Story Lab University of Vermont BurlingtonVT05401 United States Vermont Complex Systems Center University of Vermont BurlingtonVT05401 United States Department of Computer Science University of Vermont BurlingtonVT05401 United States Neurobotics Lab University of Vermont BurlingtonVT05401 United States MassMutual Data Science AmherstMA01002 United States VA Cooperative Studies Program VA Boston Healthcare System BostonMA02130 United States Department of Mathematics and Statistics University of Vermont BurlingtonVT05401 United States

Medical systems in general, and patient treatment decisions and outcomes in particular, are affected by bias based on gender and other demographic elements. As language models are increasingly applied to medicine, there is a growing interest in building algorithmic fairness into processes impacting patient care. Much of the work addressing this question has focused on biases encoded in language models—statistical estimates of the relationships between concepts derived from distant reading of corpora. Building on this work, we investigate how word choices made by healthcare practitioners and language models interact with regards to bias. We identify and remove gendered language from two clinical-note datasets and describe a new debiasing procedure using BERT-based gender classifiers. We show minimal degradation in health condition classification tasks for low- to medium-levels of bias removal via data augmentation. Finally, we compare the bias semantically encoded in the language models with the bias empirically observed in health records. This work outlines an interpretable approach for using data augmentation to identify and reduce the potential for bias in natural language processing pipelines. Copyright © 2021, The Authors. All rights reserved.

关键词： Natural language processing systems

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Unsupervised extraction of phenotypes from cancer clinical notes for association studies

arXiv

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arXiv 2019年

作者： Stark, Stefan G. Hyland, Stephanie L. Pradier, Melanie F. Lehmann, Kjong-Van Wicki, Andreas Perez-Cruz, Fernando Vogt, Julia E. Rätsch, Gunnar Computational Biology Program Memorial Sloan Kettering Cancer Center New York United States Tri-Institutional Ph.D. Program in Computational Biology and Medicine Weill Cornell Medicine New York United States Department of Computer Science ETH Zürich Zürich Switzerland Medical Informatics Group University Hospital Zürich Zürich Switzerland Swiss Institute for Bioinformatics Zurich Switzerland Department of Biology ETH Zürich Zürich Switzerland Department of Signal Processing and Information Theory University Carlos III in Madrid Leganés Spain School of Engineering and Applied Sciences Harvard University CambridgeMA United States Department of Biomedicine University of Basel Basel Switzerland Tumorzentrum University Hospital Basel Basel Switzerland Swiss Data Science Center ETH Zürich and EPFL Lausanne Switzerland Department of Mathematics and Computer Science University of Basel Basel Switzerland

The recent adoption of Electronic Health Records (EHRs) by healthcare providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured text designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and utilize the clusters to represent information about the patient compactly. Additionally, we define the sentences on ontologic and natural language vocabularies to automatically detect pertinent combinations of concepts present in the corpus, even when an ontology is not available. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of .65 thousand documents with a total of .3.2 million sentences. After correcting for cancer type and other confounding factors, we identify a total of 340 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty and we report several known associations. We also propose 37 plausible, testable hypothesis for associations where the underlying biological mechanism does not appear to be known. These results illustrate that the automated discovery of clinical features

关键词： Diseases

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Wait, but Tylenol is Acetaminophen… Investigating and Improving Language Models' Ability to Resist Requests for Misinformation

arXiv

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arXiv 2024年

作者： Chen Gao, Mingye Sasse, Kuleen Hartvigsen, Tom Anthony, Brian Fan, Lizhou Aerts, Hugo Gallifant, Jack Bitterman, Danielle Program Mass General Brigham Harvard Medical School BostonMA United States Department of Radiation Oncology Brigham and Women’s Hospital Dana-Farber Cancer Institute BostonMA United States Computational Health Informatics Program Boston Children’s Hospital Harvard Medical School BostonMA United States Massachusetts Institute of Technology CambridgeMA United States Johns Hopkins University BaltimoreMD United States Department of Data Science University of Virginia CharlottesvilleVA United States Radiology and Nuclear Medicine GROW & CARIM Maastricht University Netherlands

Background: Large language models (LLMs) are trained to follow directions, but this introduces a vulnerability to blindly comply with user requests even if they generate wrong information. In medicine, this could accelerate the generation of misinformation that impacts human well-being. Objectives/Methods: We analyzed compliance to requests to generate misleading content about medications in settings where models know the request is illogical. We investigated whether in-context directions and instruction-tuning of LLMs to prioritize logical reasoning over compliance reduced misinformation risk. Results: While all frontier LLMs complied with misinformation requests, both prompt-based and parameter-based approaches can improve the detection of logic flaws in requests and prevent the dissemination of medical misinformation. Conclusion: Shifting LLMs to prioritize logic over compliance could reduce risks of exploitation for medical misinformation. © 2024, CC BY-NC-ND.

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Skater’s dilemma

arXiv

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arXiv 2020年

作者： Ichinose, Genki Miyagawa, Daiki Ito, Junji Masuda, Naoki Department of Mathematical and Systems Engineering Shizuoka University 3-5-1 Johoku Naka-ku Hamamatsu432-8561 Japan Skating Club Yamanashi Gakuin University 2-4-5 Sakaori Kofu Yamanashi400-8575 Japan Department of Mathematics University at Buffalo State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-5030 United States

In some athletic races, such as cycling and types of speed skating races, athletes have to complete a relatively long distance at a high speed in the presence of direct opponents. To win such a race, athletes are motivated to hide behind others to suppress energy consumption before a final moment of the race. This situation seems to produce a social dilemma: players want to hide behind others, whereas if a group of players attempts to do so, they may all lose to other players that overtake them. To support that speed skaters are involved in such a social dilemma, we analyzed video footage data for 14 mass start skating races to find that skaters that hid behind others to avoid air resistance for a long time before the final lap tended to win. Furthermore, the finish rank of the skaters in mass start races was independent of the record of the same skaters in time-trial races measured in the absence of direct opponents. The results suggest that how to strategically cope with a skater’s dilemma may be a key determinant for winning long-distance and high-speed races with direct *** Codes 91A80 Copyright © 2020, The Authors. All rights reserved.

关键词： Game theory

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Modeling temporal networks with bursty activity patterns of nodes and links

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Physical Review Research 2020年第2期2卷 023073-023073页

作者： Takayuki Hiraoka Naoki Masuda Aming Li Hang-Hyun Jo Department of Computer Science Aalto University Espoo 00076 Finland Asia Pacific Center for Theoretical Physics Pohang 37673 Republic of Korea Department of Mathematics University at Buffalo State University of New York Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New York 14260-5030 USA Department of Zoology University of Oxford Oxford OX1 3PS United Kingdom Department of Biochemistry University of Oxford Oxford OX1 3QU United Kingdom Department of Physics The Catholic University of Korea Bucheon 14662 Republic of Korea

The concept of temporal networks provides a framework to understand how the interaction between system components changes over time. In empirical communication data, we often detect non-Poissonian, so-called bursty behavior in the activity of nodes as well as in the interaction between nodes. However, such reconciliation between node burstiness and link burstiness cannot be explained if the interaction processes on different links are independent of each other. This is because the activity of a node is the superposition of the interaction processes on the links incident to the node, and the superposition of independent bursty point processes is not bursty in general. Here we introduce a temporal network model based on bursty node activation, and we show that it leads to heavy-tailed interevent time distributions for both node dynamics and link dynamics. Our analysis indicates that activation processes intrinsic to nodes give rise to dynamical correlations across links. Our framework offers a way to model competition and correlation between links, which is key to understanding dynamical processes in various systems.

关键词： Collective behavior in networks Dynamics of networks Scaling laws of complex systems Social systems Communication networks Multiple time scale dynamics Networks & random structures Social networks Evolving network models Network Models Non-Markovian processes Time series analysis

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