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Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes

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arXiv 2022年

作者： Zhang, Shuo Liu, Yang Xie, Lei Ph.D. Program in Computer Science The Graduate Center The City University of New York United States Department of Computer Science Hunter College The City University of New York United States Helen & Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University United States

Recent advances in applying Graph Neural Networks (GNNs) to molecular science have showcased the power of learning three-dimensional (3D) structure representations with GNNs. However, most existing GNNs suffer from the limitations of insufficient modeling of diverse interactions, computational expensive operations, and ignorance of vectorial values. Here, we tackle these limitations by proposing a novel GNN model, Physics-aware Multiplex Graph Neural Network (PaxNet), to efficiently and accurately learn the representations of 3D molecules for both small organic compounds and macromolecule complexes. PaxNet separates the modeling of local and non-local interactions inspired by molecular mechanics, and reduces the expensive angle-related computations. Besides scalar properties, PaxNet can also predict vectorial properties by learning an associated vector for each atom. To evaluate the performance of PaxNet, we compare it with state-of-the-art baselines in two tasks. On small molecule dataset for predicting quantum chemical properties, PaxNet reduces the prediction error by 15% and uses 73% less memory than the best baseline. On macromolecule dataset for predicting protein-ligand binding affinities, PaxNet outperforms the best baseline while reducing the memory consumption by 33% and the inference time by 85%. Thus, PaxNet provides a universal, robust and accurate method for large-scale machine learning of molecules. Our code is available at https://***/zetayue/Physics-aware-Multiplex-GNN. Copyright © 2022, The Authors. All rights reserved.

关键词： Macromolecules

Robust Prediction of Patient-Specific Clinical Response to Unseen Drugs From in vitro Screens Using Context-aware Deconfounding Autoencoder

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Research Square

Research Square 2021年

作者： He, Di Liu, Qiao Xie, Lei Program in Computer Science Graduate Center City University of New York New York City10016 United States Department of Computer Science Hunter College City University of New York New York City10065 United States

Accurate and robust prediction of patient-specific responses to drug treatments is critical for drug development and personalized medicine. However, patient data are often too scarce to train a generalized machine learning model. Although many methods have been developed to utilize cell line data, few of them can reliably predict individual patient clinical responses to new drugs due to data distribution shift and confounding factors. We develop a novel Context-aware Deconfounding Autoencoder (CODE-AE) that can extract common biological signals masked by context-specific patterns and confounding factors. Extensive studies demonstrate that CODE-AE effectively alleviates the out-of-distribution problem for the model generalization, significantly improves accuracy and robustness over state-of-the-art methods in both predicting patient-specific ex vivo and in vivo drug responses purely from in vitro screens and disentangling intrinsic biological signals from confounding factors. Using CODE-AE, we screened 50 drugs for 9,808 cancer patients and discovered novel personalized anti-cancer therapies and drug-response biomarkers. © 2021, CC BY.

关键词： Cell culture

Count time series modelling of Twitter data topic modelling: A case of Indonesia flood events

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AIP Conference Proceedings 2023年第1期2594卷

作者： A. A. Hidayat B Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Twitter data provide rich and powerful information to leverage the dynamics of public perception to establish situational awareness and disaster mitigation strategies during critical times. In this paper, we perform topic modeling via Latent Dirichlet Allocation to extract topics from a collection of tweets related to Indonesia flood events in February 2021 with the query: “banjir”. The extracted topics are used as one of the features to build a generalized linear count time series model with Negative Binomial distribution. We find seven major topics from the model in which tweets containing a topic about the government’s role in handling the situation dominate the conversation. Taking into account a simple intervention analysis, we demonstrate a statistically significant change in the users’ behavior before and after the severe Jakarta flood on 20 February 2021. Moreover, a metric evaluation demonstrates that a covariate that describes the turning point of the Jakarta flood event is convenient to build a more accurate count time series model of the tweets.

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Meteorological parameters for PV installations in Indonesia

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AIP Conference Proceedings 2024年第1期3026卷

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Reza Rahutomo Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Many countries are still dependent on fossil fuels as their primary energy supply. However, there is a growing concern about the sustainability and the environmental issue of fossil fuels. Therefore, it is important to utilize renewable resources as the energy supply, such as solar energy. As a country with a tropical climate, Indonesia has a great potential to use solar energy, due to the abundance of sunlight exposure. The present study aims to analyze several meteorological parameters for the installation of photovoltaic (PV) technology in Jakarta, Indonesia. The meteorological data provided by the Ministry of Environment and Forestry, Indonesia from 2008-2021 were used at three different locations in Jakarta. Data visualizations were used to show the difference between each variable in different locations. In addition, the statistical difference between the variables in the three locations was also examined using the Mann-Whitney U test. The test shows that all parameters are evenly distributed in the three locations except for a moderate difference in air temperature in the two locations. Furthermore, the monthly analysis of the parameters also indicates that the dry season, especially from August to September, would be the optimal time to utilize PV technology. Hence, this study would be useful to give preliminary insight regarding a site-specified assessment of PV plants in Jakarta based on local meteorological data.

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Generative AI-enabled Vehicular Networks: Fundamentals, Framework, and Case Study

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arXiv 2023年

作者： Zhang, Ruichen Xiong, Ke Du, Hongyang Niyato, Dusit Kang, Jiawen Shen, Xuemin Poor, H. Vincent The Engineering Research Center of Network Management Technology High Speed Railway of Ministry of Education School of Computer and Information Technology Beijing Jiaotong University Beijing100044 China The Collaborative Innovation Center of Railway Traffic Safety Beijing Jiaotong University Beijing100044 China The National Engineering Research Center of Advanced Network Technologies Beijing Jiaotong University Beijing100044 China The School of Computer Science and Engineering The Energy Research Institute @ NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore The School of Automation Guangdong University of Technology China The Department of Electrical and Computer Engineering University of Waterloo Canada The Department of Electrical and Computer Engineering Princeton University PrincetonNJ08544 United States

Recognizing the tremendous improvements that the integration of generative AI can bring to intelligent transportation systems, this article explores the integration of generative AI technologies in vehicular networks, focusing on their potential applications and challenges. Generative AI, with its capabilities of generating realistic data and facilitating advanced decision-making processes, enhances various applications when combined with vehicular networks, such as navigation optimization, traffic prediction, data generation, and evaluation. Despite these promising applications, the integration of generative AI with vehicular networks faces several challenges, such as real-time data processing and decision-making, adapting to dynamic and unpredictable environments, as well as privacy and security concerns. To address these challenges, we propose a multi-modality semantic-aware framework to enhance the service quality of generative AI. By leveraging multi-modal and semantic communication technologies, the framework enables the use of text and image data for creating multi-modal content, providing more reliable guidance to receiving vehicles and ultimately improving system usability and efficiency. To further improve the reliability and efficiency of information transmission and reconstruction within the framework, taking generative AI-enabled vehicle-to-vehicle (V2V) as a case study, a deep reinforcement learning (DRL)-based approach is proposed for resource allocation. Finally, we discuss potential research directions and anticipated advancements in the field of generative AI-enabled vehicular networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Reinforcement learning

CODE-AE: A coherent de-confounding autoencoder for predicting patient-specific drug response from cell line transcriptomics

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arXiv 2021年

作者： He, Di Xie, Lei PhD program in Computer Science Graduate Center City University of New York New York City10016 United States Department of Computer Science Hunter College City University of New York New York City10065 United States

Accurate and robust prediction of patient’s response to drug treatments is critical for developing precision medicine. However, it is often difficult to obtain a sufficient amount of coherent drug response data from patients directly for training a generalized machine learning model. Although the utilization of rich cell line data provides an alternative solution, it is challenging to transfer the knowledge obtained from cell lines to patients due to various confounding factors. Few existing transfer learning methods can reliably disentangle common intrinsic biological signals from confounding factors in the cell line and patient data. In this paper, we develop a Coherent Deconfounding Autoencoder (CODE-AE) that can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them. Extensive studies on multiple data sets demonstrate that CODE-AE significantly improves the accuracy and robustness over state-of-the-art methods in both predicting patient drug response and deconfounding biological signals. Thus, CODE-AE provides a useful framework to take advantage of in vitro omics data for developing generalized patient predictive models. The source code is available at https://***/XieResearchGroup/CODE-AE. © 2021, CC BY.

关键词： Learning systems

Robust prediction of personalized in vivo response to unseen drugs from in vitro screens using a novel context-aware deconfounding autoencoder

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Research Square

Research Square 2021年

作者： He, Di Liu, Qiao Xie, Lei PhD program in Computer Science Graduate Center City University of New York New York City10016 United States Department of Computer Science Hunter College City University of New York New York City10065 United States

Accurate and robust prediction of patient-specific responses to drug treatments is critical for drug development and personalized medicine. However, patient data are often too scarce to train a generalized machine learning model. Although many methods have been developed to utilize cell line data, few of them can reliably predict individual patient clinical responses to new drugs due to data distribution shift and confounding factors. We have developed a novel Context-aware Deconfounding Autoencoder (CODE-AE) that can extract intrinsic biological signals masked by context-specific patterns and confounding factors. Extensive comparative studies demonstrated that CODE-AE effectively alleviated the out-of-distribution problem for the model generalization, significantly improved accuracy and robustness over state-of-the-art methods in predicting patient-specific in vivo drug responses purely from in vitro screens. Using CODE-AE, we screened 59 drugs for 9,808 cancer patients. Our results are consistent with existing clinical observations, suggesting the potential of CODE-AE in developing personalized anti-cancer therapies and drug-response biomarkers. © 2021, CC BY.

关键词： Cell culture

AVTENet: Audio-Visual Transformer-based Ensemble Network Exploiting Multiple Experts for Video Deepfake Detection

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arXiv 2023年

作者： Hashmi, Ammarah Shahzad, Sahibzada Adil Lin, Chia-Wen Tsao, Yu Wang, Hsin-Min The Social Networks and Human-Centered Computing Program Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan The Institute of Information Systems and Applications National Tsing Hua University Hsinchu30013 Taiwan The Department of Computer Science National Chengchi University Taipei11605 Taiwan The Department of Electrical Engineering The Institute of Communications Engineering National Tsing Hua University Hsinchu300044 Taiwan The Research Center for Information Technology Innovation Academia Sinica Taipei11529 Taiwan The Institute of Information Science Academia Sinica Taipei11529 Taiwan

Forged content shared widely on social media platforms is a major social problem that requires increased regulation and poses new challenges to the research community. The recent proliferation of hyper-realistic deepfake videos has drawn attention to the threat of audio and visual forgeries. Most previous work on detecting AI-generated fake videos only utilizes visual modality or audio modality. While there are some methods in the literature that exploit audio and visual modalities to detect forged videos, they have not been comprehensively evaluated on multi-modal datasets of deepfake videos involving acoustic and visual manipulations. Moreover, these existing methods are mostly based on CNN and suffer from low detection accuracy. Inspired by the recent success of Transformer in various fields, to address the challenges posed by deepfake technology, in this paper, we propose an Audio-Visual Transformer-based Ensemble Network (AVTENet) framework that considers both acoustic manipulation and visual manipulation to achieve effective video forgery detection. Specifically, the proposed model integrates several purely transformer-based variants that capture video, audio, and audio-visual salient cues to reach a consensus in prediction. For evaluation, we use the recently released benchmark multi-modal audio-video FakeAVCeleb dataset. For a detailed analysis, we evaluate AVTENet, its variants, and several existing methods on multiple test sets of the FakeAVCeleb dataset. Experimental results show that our best model outperforms all existing methods and achieves state-of-the-art performance on Testset-I and Testset-II of the FakeAVCeleb dataset. © 2023, CC BY.

关键词： Statistical tests

Measurement of Water Diffusion Coefficient in Cross-Linked Gelatins Using the Terahertz Time-Domain Spectroscopy Technique

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Measurement of Water Diffusion Coefficient in Cross-Linked G...

Conference on Lasers and Electro-Optics (CLEO)

作者： D. Walden D. Chakraborty J. Cheng A. Straksys A. Stirke W. CMA Melo A. Jukna I. Komissarov Roman Sobolewski Department of Physics and Astronomy University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA Materials Science Graduate Program University of Rochester Rochester New York USA State Research Institute Center for Physical Sciences & Technology Vilnius Lithuania Department of Physics Vilnius Gediminas Technical University Vilnius Lithuania Department of Electrical and Computer Engineering University of Rochester Rochester New York USA

A novel method has been developed to evaluate the water diffusion dynamics in gelatin-based gels, based on transient terahertz time-domain spectroscopy measurements. Such gels are widely used models for human skin.

ISBN: (纸本)9798350369311

关键词： Spectroscopy Measurement by laser beam Lasers and electrooptics Laser modes Skin Time-domain analysis Transient analysis Electro-optical waveguides