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Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers Machine learning Random Forest

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The sleep loss insult of spring daylight savings in the US is absorbed by Twitter users within 48 hours

arXiv

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arXiv 2020年

作者： Linnell, Kelsey Alshaabi, Thayer McAndrew, Thomas Lim, Jeanie Dodds, Peter Sheridan Danforth, Christopher M. Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems & Data Science University of Vermont Department of Mathematics & Statistics University of Vermont Department of Biostatistics & Epidemiology School of Public Health & Health Sciences University of Massachusetts at Amherst MassMutual Data Science

Sleep loss has been linked to heart disease, diabetes, cancer, and an increase in accidents, all of which are among the leading causes of death in the United States. Population-scale sleep studies have the potential to advance public health by helping to identify at-risk populations, changes in collective sleep patterns, and to inform policy change. Prior research suggests other kinds of health indicators such as depression and obesity can be estimated using social media activity. However, the inability to effectively measure collective sleep with publicly available data has limited large-scale academic studies. Here, we investigate the passive estimation of sleep loss through a proxy analysis of Twitter activity profiles. We use "Spring Forward" events, which occur at the beginning of Daylight Savings Time in the United States, as a natural experimental condition to estimate spatial differences in sleep loss across the United States. On average, peak Twitter activity occurs roughly 45 minutes later on the Sunday following Spring Forward. By Monday morning however, activity curves are realigned with the week before, suggesting that at least on Twitter, the lost hour of early Sunday morning has been quickly absorbed. Copyright © 2020, The Authors. All rights reserved.

关键词： Sleep research

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Nuclear Neural Networks: Emulating Late Burning Stages in Core Collapse Supernova Progenitors

arXiv

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arXiv 2025年

作者： Grichener, Aldana Renzo, Mathieu Kerzendorf, Wolfgang E. Farmer, Rob de Mink, Selma E. Bellinger, Earl Patrick Chan, Chi-Kwan Chen, Nutan Farag, Ebraheem Justham, Stephen Steward Steward Observatory Department of Astronomy University of Arizona 933 North Cherry Avenue TucsonAZ85721 United States Max Planck Institute for Astrophysics Karl-Schwarzschild-Str. 1 Garching85748 Germany Department of Physics Technion Haifa3200003 Israel Department of Computational Mathematics Science and Engineering Michigan State University East LansingMI48824 United States Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Ludwig-Maximilians-Universitat Munchen Geschwister-Scholl-Platz 1 Munchen80539 Germany Department of Astronomy Yale University New HavenCT06511 United States Steward Observatory Department of Astronomy University of Arizona 933 North Cherry Avenue TucsonAZ85721 United States Data Science Institute University of Arizona 1230 N. Cherry Avenue TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 North Santa Rita TucsonAZ85721 United States Machine Learning Research Lab Volkswagen AG Munich38440 Germany

One of the main challenges in modeling massive stars to the onset of core collapse is the computational bottleneck of nucleosynthesis during advanced burning stages. The number of isotopes formed requires solving a large set of fully-coupled stiff ordinary differential equations (ODEs), making the simulations computationally intensive and prone to numerical instability. To overcome this barrier, we design a nuclear neural network (NNN) framework with multiple hidden layers to emulate nucleosynthesis calculations and conduct a proof-of-concept to evaluate its performance. The NNN takes the temperature, density and composition of a burning region as input and predicts the resulting isotopic abundances along with the energy generation and loss rates. We generate training sets for initial conditions corresponding to oxygen core depletion and beyond using large nuclear reaction networks, and compare the predictions of the NNNs to results from a commonly used small net. We find that the NNNs improve the accuracy of the electron fraction by 280 − 660 % and the nuclear energy generation by 250 − 750 %, consistently outperforming the small network across all timesteps. They also achieve significantly better predictions of neutrino losses on relatively short timescales, with improvements ranging from 100 − 106 %. While further work is needed to enhance their accuracy and applicability to different stellar conditions, integrating NNN trained models into stellar evolution codes is promising for facilitating large-scale generation of core-collapse supernova (CCSN) progenitors with higher physical fidelity. © 2025, CC BY.

关键词： Nucleosynthesis

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Divergent modes of online collective attention to the COVID-19 pandemic are associated with future caseload variance

arXiv

引用

arXiv 2020年

作者： Dewhurst, David Rushing Alshaabi, Thayer Arnold, Michael V. Minot, Joshua R. Danforth, Christopher M. Dodds, Peter Sheridan Vermont Complex Systems Center Computational Story Lab University of Vermont BurlingtonVT05405 MassMutual Data Science BostonMA02110 Department of Mathematics and Statistics University of Vermont BurlingtonVT05405

Using a random 10% sample of tweets authored from 2019-09-01 through 2020-04-30, we analyze the dynamic behavior of words (1-grams) used on Twitter to describe the ongoing COVID-19 pandemic. Across 24 languages, we find two distinct dynamic regimes: One characterizing the rise and subsequent collapse in collective attention to the initial Coronavirus outbreak in late January, and a second that represents March COVID-19-related discourse. Aggregating countries by dominant language use, we find that volatility in the first dynamic regime is associated with future volatility in new cases of COVID-19 roughly three weeks (average 22.49 ± 3.26 days) later. Our results suggest that surveillance of change in usage of epidemiology-related words on social media may be useful in forecasting later change in disease case numbers, but we emphasize that our current findings are not causal or necessarily predictive. Copyright © 2020, The Authors. All rights reserved.

关键词： Coronavirus

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Sentiment and structure in word co-occurrence networks on Twitter

arXiv

引用

arXiv 2021年

作者： Fudolig, Mikaela Irene Alshaabi, Thayer Arnold, Michael V. Danforth, Christopher M. Dodds, Peter Sheridan Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Core University of Vermont BurlingtonVT United States Advanced Bioimaging Center UC Berkeley BerkeleyCA United States Department of Mathematics & Statistics University of Vermont BurlingtonVT United States Department of Computer Science University of Vermont BurlingtonVT United States

We explore the relationship between context and happiness scores in political tweets using word co-occurrence networks, where nodes in the network are the words, and the weight of an edge is the number of tweets in the corpus for which the two connected words co-occur. In particular, we consider tweets with hashtags #imwithher and #crookedhillary, both relating to Hillary Clinton’s presidential bid in 2016. We then analyze the network properties in conjunction with the word scores by comparing with null models to separate the effects of the network structure and the score distribution. Neutral words are found to be dominant and most words, regardless of polarity, tend to co-occur with neutral words. We do not observe any score homophily among positive and negative words. However, when we perform network backboning, community detection results in word groupings with meaningful narratives, and the happiness scores of the words in each group correspond to its respective theme. Thus, although we observe no clear relationship between happiness scores and co-occurrence at the node or edge level, a community-centric approach can isolate themes of competing sentiments in a corpus. © 2021, CC BY.

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computational Paremiology: Charting the temporal, ecological dynamics of proverb use in books, news articles, and tweets

arXiv

引用

arXiv 2021年

作者： Davis, Ethan Danforth, Christopher M. Mieder, Wolfgang Dodds, Peter Sheridan Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Core University of Vermont BurlingtonVT05401 United States Department of Mathematics and Statistics University of Vermont BurlingtonVT05401 United States Department of German and Russian University of Vermont BurlingtonVT05401 United States Department of Computer Science University of Vermont BurlingtonVT05401 United States

Proverbs are an essential component of language and culture, and though much attention has been paid to their history and currency, there has been comparatively little quantitative work on changes in the frequency with which they are used over time. With wider availability of large corpora reflecting many diverse genres of documents, it is now possible to take a broad and dynamic view of the importance of the proverb. Here, we measure temporal changes in the relevance of proverbs within three corpora, differing in kind, scale, and time frame: Millions of books over centuries;hundreds of millions of news articles over twenty years;and billions of tweets over a decade. We find that proverbs present heavy-tailed frequency-of-usage rank distributions in each venue;exhibit trends reflecting the cultural dynamics of the eras covered;and have evolved into contemporary forms on social media. Copyright © 2021, The Authors. All rights reserved.

关键词： History

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14 Examples of How LLMs Can Transform Materials science and Chemistry: A Reflection on a Large Language Model Hackathon

arXiv

引用

arXiv 2023年

作者： Jablonka, Kevin Maik Ai, Qianxiang Al-Feghali, Alexander Badhwar, Shruti Bocarsly, Joshua D. Bran, Andres M. Bringuier, Stefan Brinson, L. Catherine Choudhary, Kamal Circi, Defne Cox, Sam de Jong, Wibe A. Evans, Matthew L. Gastellu, Nicolas Genzling, Jerome Gil, María Victoria Gupta, Ankur K. Hong, Zhi Imran, Alishba Kruschwitz, Sabine labarre, Anne Lála, Jakub Liu, Tao Ma, Steven Majumdar, Sauradeep Merz, Garrett W. Moitessier, Nicolas Moubarak, Elias Mouriño, Beatriz Pelkie, Brenden Pieler, Michael Ramos, Mayk Caldas Ranković, Bojana Rodriques, Samuel G. Sanders, Jacob N. Schwaller, Philippe Schwarting, Marcus Shi, Jiale Smit, Berend Smith, Ben E. Van Herck, Joren Völker, Christoph Ward, Logan Warren, Sean Weiser, Benjamin Zhang, Sylvester Zhang, Xiaoqi Zia, Ghezal Ahmad Scourtas, Aristana Schmidt, K.J. Foster, Ian White, Andrew D. Blaiszik, Ben Sion Valais Switzerland Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Department of Chemistry McGill University MontrealQC Canada Reincarnate Inc. United States Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CambridgeCB2 1EW United Kingdom Lausanne Switzerland Lausanne Switzerland San Diego CA United States Mechanical Engineering and Materials Science Duke University United States Material Measurement Laboratory National Institute of Standards and Technology MD20899 United States Department of Chemical Engineering University of Rochester United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States UCLouvain Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Matgenix SRL 185 Rue Armand Bury Gozée 6534 Belgium CSIC Francisco Pintado Fe 26 Oviedo33011 Spain Department of Computer Science University of Chicago ChicagoIL60637 United States Computer Science University of California Berkeley BerkeleyCA94704 United States Bundesanstalt für Materialforschung und -Prüfung Unter den Eichen 87 Berlin12205 Germany Francis Crick Institute 1 Midland Rd LondonNW1 1AT United Kingdom American Family Insurance Data Science Institute University of Wisconsin-Madison MadisonWI53706 United States Department of Chemical Engineering University of Washington SeattleWA98105 United States *** Stability.AI United Kingdom Department of Chemistry and Biochemistry University of California Los AngelesCA90095 United States Department of Computer Science University of Chicago ChicagoIL60490 United States Data Science and Learning Division Argonne National Lab United States Globus University of Chicago Data Science and Learning Division Argonne National Lab United States Department of Computer Science University of Chicago Data Science and Learning Division Argonne National Lab United

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines. © 2023, CC BY.

关键词： computational linguistics

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Weisfeiler and Leman go Machine Learning: The Story so far

arXiv

引用

arXiv 2021年

作者： Morris, Christopher Lipman, Yaron Maron, Haggai Rieck, Bastian Kriege, Nils M. Grohe, Martin Fey, Matthias Borgwardt, Karsten Department of Computer Science RWTH Aachen University Aachen Germany Meta AI Research Department of Computer Science and Applied Mathematics Weizmann Institute of Science Rehovot Israel NVIDIA Research Tel Aviv Israel AIDOS Lab Institute of AI for Health Helmholtz Zentrum München and Technical University of Munich Munich Germany Faculty of Computer Science University of Vienna Vienna Austria Research Network Data Science University of Vienna Vienna Austria Kumo.AI Mountain ViewCA United States Machine Learning & Computational Biology Lab Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland

In recent years, algorithms and neural architectures based on the Weisfeiler–Leman algorithm, a well-known heuristic for the graph isomorphism problem, have emerged as a powerful tool for machine learning with graphs and relational data. Here, we give a comprehensive overview of the algorithm’s use in a machine-learning setting, focusing on the supervised regime. We discuss the theoretical background, show how to use it for supervised graph and node representation learning, discuss recent extensions, and outline the algorithm’s connection to (permutation-)equivariant neural architectures. Moreover, we give an overview of current applications and future directions to stimulate further research. Copyright © 2021, The Authors. All rights reserved.

关键词： Machine learning

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The incel lexicon: Deciphering the emergent cryptolect of a global misogynistic community

arXiv

引用

arXiv 2021年

作者： Gothard, Kelly Dewhurst, David Rushing Minot, Joshua R. Adams, Jane Lydia Danforth, Christopher M. Dodds, Peter Sheridan Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Core The University of Vermont BurlingtonVT05401 United States Charles River Analytics 625 Mount Auburn Street CambridgeMA02138 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05401 United States Department of Computer Science University of Vermont BurlingtonVT05401 United States

Evolving out of a gender-neutral framing of an involuntary celibate identity, the concept of 'incels' has come to refer to an online community of men who bear antipathy towards themselves, women, and society-at-large for their perceived inability to find and maintain sexual relationships. By exploring incel language use on Reddit, a global online message board, we contextualize the incel community's online expressions of misogyny and real-world acts of violence perpetrated against women. After assembling around three million comments from incel-themed Reddit channels, we analyze the temporal dynamics of a data driven rank ordering of the glossary of phrases belonging to an emergent incel lexicon. Our study reveals the generation and normalization of an extensive coded misogynist vocabulary in service of the group's identity. Copyright © 2021, The Authors. All rights reserved.

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computational timeline reconstruction of the stories surrounding Trump: Story turbulence, narrative control, and collective chronopathy

arXiv

引用

arXiv 2020年

作者： Dodds, Peter Sheridan Minot, Joshua R. Arnold, Michael V. Alshaabi, Thayer Adams, Jane Lydia Reagan, Andrew J. Danforth, Christopher M. Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Core University of Vermont BurlingtonVT05401 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05401 United States MassMutual Data Science BostonMA02110 United States

Measuring the specific kind, temporal ordering, diversity, and turnover rate of stories surrounding any given subject is essential to developing a complete reckoning of that subject’s historical impact. Here, we use Twitter as a distributed news and opinion aggregation source to identify and track the dynamics of the dominant day-scale stories around Donald Trump, the 45th President of the United States. Working with a data set comprising around 20 billion 1-grams, we first compare each day’s 1-gram and 2-gram usage frequencies to those of a year before, to create day- and week-scale timelines for Trump stories for 2016–2021. We measure Trump’s narrative control, the extent to which stories have been about Trump or put forward by Trump. We then quantify story turbulence and collective chronopathy—the rate at which a population’s stories for a subject seem to change over time. We show that 2017 was the most turbulent overall year for Trump. In 2020, story generation slowed dramatically during the first two major waves of the COVID-19 pandemic, with rapid turnover returning first with the Black Lives Matter protests following George Floyd’s murder and then later by events leading up to and following the 2020 US presidential election, including the storming of the US Capitol six days into 2021. Trump story turnover for 2 months during the COVID-19 pandemic was on par with that of 3 days in September 2017. Our methods may be applied to any well-discussed phenomenon, and have potential to enable the computational aspects of journalism, history, and biography. Copyright © 2020, The Authors. All rights reserved.

关键词： COVID-19

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