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1. A review of mathematical representations of biomolecular data

   https://doi.org/10.1039/c9cp06554g  

   Nguyen, Duc Duy; Cang, Zixuan; Wei, Guo-Wei (February 2020, Physical Chemistry Chemical Physics)

   Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein–ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc. 

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2. User Response Prediction in Online Advertising

   https://doi.org/10.1145/3446662  

   Gharibshah, Zhabiz; Zhu, Xingquan (June 2021, ACM Computing Surveys)

   null (Ed.)

   Online advertising, as a vast market, has gained significant attention in various platforms ranging from search engines, third-party websites, social media, and mobile apps. The prosperity of online campaigns is a challenge in online marketing and is usually evaluated by user response through different metrics, such as clicks on advertisement (ad) creatives, subscriptions to products, purchases of items, or explicit user feedback through online surveys. Recent years have witnessed a significant increase in the number of studies using computational approaches, including machine learning methods, for user response prediction. However, existing literature mainly focuses on algorithmic-driven designs to solve specific challenges, and no comprehensive review exists to answer many important questions. What are the parties involved in the online digital advertising eco-systems? What type of data are available for user response prediction? How do we predict user response in a reliable and/or transparent way? In this survey, we provide a comprehensive review of user response prediction in online advertising and related recommender applications. Our essential goal is to provide a thorough understanding of online advertising platforms, stakeholders, data availability, and typical ways of user response prediction. We propose a taxonomy to categorize state-of-the-art user response prediction methods, primarily focusing on the current progress of machine learning methods used in different online platforms. In addition, we also review applications of user response prediction, benchmark datasets, and open source codes in the field. 

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3. Advancing Fusion with Machine Learning Research Needs Workshop Report

   https://doi.org/10.1007/s10894-020-00258-1  

   Humphreys, David; Kupresanin, A.; Boyer, M. D.; Canik, J.; Chang, C. S.; Cyr, E. C.; Granetz, R.; Hittinger, J.; Kolemen, E.; Lawrence, E.; et al (August 2020, Journal of Fusion Energy)

   null (Ed.)

   Abstract Machine learning and artificial intelligence (ML/AI) methods have been used successfully in recent years to solve problems in many areas, including image recognition, unsupervised and supervised classification, game-playing, system identification and prediction, and autonomous vehicle control. Data-driven machine learning methods have also been applied to fusion energy research for over 2 decades, including significant advances in the areas of disruption prediction, surrogate model generation, and experimental planning. The advent of powerful and dedicated computers specialized for large-scale parallel computation, as well as advances in statistical inference algorithms, have greatly enhanced the capabilities of these computational approaches to extract scientific knowledge and bridge gaps between theoretical models and practical implementations. Large-scale commercial success of various ML/AI applications in recent years, including robotics, industrial processes, online image recognition, financial system prediction, and autonomous vehicles, have further demonstrated the potential for data-driven methods to produce dramatic transformations in many fields. These advances, along with the urgency of need to bridge key gaps in knowledge for design and operation of reactors such as ITER, have driven planned expansion of efforts in ML/AI within the US government and around the world. The Department of Energy (DOE) Office of Science programs in Fusion Energy Sciences (FES) and Advanced Scientific Computing Research (ASCR) have organized several activities to identify best strategies and approaches for applying ML/AI methods to fusion energy research. This paper describes the results of a joint FES/ASCR DOE-sponsored Research Needs Workshop on Advancing Fusion with Machine Learning, held April 30–May 2, 2019, in Gaithersburg, MD (full report available at https://science.osti.gov/-/media/fes/pdf/workshop-reports/FES_ASCR_Machine_Learning_Report.pdf ). The workshop drew on broad representation from both FES and ASCR scientific communities, and identified seven Priority Research Opportunities (PRO’s) with high potential for advancing fusion energy. In addition to the PRO topics themselves, the workshop identified research guidelines to maximize the effectiveness of ML/AI methods in fusion energy science, which include focusing on uncertainty quantification, methods for quantifying regions of validity of models and algorithms, and applying highly integrated teams of ML/AI mathematicians, computer scientists, and fusion energy scientists with domain expertise in the relevant areas. 

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4. Quantifying the economic impact of disasters on businesses using human mobility data: a Bayesian causal inference approach

   https://doi.org/10.1140/epjds/s13688-020-00255-6  

   Yabe, Takahiro; Zhang, Yunchang; Ukkusuri, Satish V. (December 2020, EPJ Data Science)

   null (Ed.)

   Abstract In recent years, extreme shocks, such as natural disasters, are increasing in both frequency and intensity, causing significant economic loss to many cities around the world. Quantifying the economic cost of local businesses after extreme shocks is important for post-disaster assessment and pre-disaster planning. Conventionally, surveys have been the primary source of data used to quantify damages inflicted on businesses by disasters. However, surveys often suffer from high cost and long time for implementation, spatio-temporal sparsity in observations, and limitations in scalability. Recently, large scale human mobility data (e.g. mobile phone GPS) have been used to observe and analyze human mobility patterns in an unprecedented spatio-temporal granularity and scale. In this work, we use location data collected from mobile phones to estimate and analyze the causal impact of hurricanes on business performance. To quantify the causal impact of the disaster, we use a Bayesian structural time series model to predict the counterfactual performances of affected businesses ( what if the disaster did not occur? ), which may use performances of other businesses outside the disaster areas as covariates. The method is tested to quantify the resilience of 635 businesses across 9 categories in Puerto Rico after Hurricane Maria. Furthermore, hierarchical Bayesian models are used to reveal the effect of business characteristics such as location and category on the long-term resilience of businesses. The study presents a novel and more efficient method to quantify business resilience, which could assist policy makers in disaster preparation and relief processes. 

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5. Physics-Guided, Physics-Informed, and Physics-Encoded Neural Networks and Operators in Scientific Computing: Fluid and Solid Mechanics

   https://doi.org/10.1115/1.4064449  

   Faroughi, Salah A; Pawar, Nikhil M; Fernandes, Célio; Raissi, Maziar; Das, Subasish; Kalantari, Nima K; Kourosh_Mahjour, Seyed (April 2024, Journal of Computing and Information Science in Engineering)

   Abstract Advancements in computing power have recently made it possible to utilize machine learning and deep learning to push scientific computing forward in a range of disciplines, such as fluid mechanics, solid mechanics, materials science, etc. The incorporation of neural networks is particularly crucial in this hybridization process. Due to their intrinsic architecture, conventional neural networks cannot be successfully trained and scoped when data are sparse, which is the case in many scientific and engineering domains. Nonetheless, neural networks provide a solid foundation to respect physics-driven or knowledge-based constraints during training. Generally speaking, there are three distinct neural network frameworks to enforce the underlying physics: (i) physics-guided neural networks (PgNNs), (ii) physics-informed neural networks (PiNNs), and (iii) physics-encoded neural networks (PeNNs). These methods provide distinct advantages for accelerating the numerical modeling of complex multiscale multiphysics phenomena. In addition, the recent developments in neural operators (NOs) add another dimension to these new simulation paradigms, especially when the real-time prediction of complex multiphysics systems is required. All these models also come with their own unique drawbacks and limitations that call for further fundamental research. This study aims to present a review of the four neural network frameworks (i.e., PgNNs, PiNNs, PeNNs, and NOs) used in scientific computing research. The state-of-the-art architectures and their applications are reviewed, limitations are discussed, and future research opportunities are presented in terms of improving algorithms, considering causalities, expanding applications, and coupling scientific and deep learning solvers. 

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