arXiv subjects

Bora Oztekin

Publications and source records attributed to Bora Oztekin.

6 recordsLinked to original sources

arXiv2022

Spherical Message Passing for 3D Graph Networks

We consider representation learning of 3D molecular graphs in which each atom is associated with a spatial position in 3D. This is an under-explored area of research, and a principled message passing framework is currently lacking. In this work, we conduct analyses in the spherical coordinate system (SCS) for the complete identification of 3D graph structures. Based on such observations, we propose the spherical message passing (SMP) as a novel and powerful scheme for 3D molecular learning. SMP dramatically reduces training complexity, enabling it to perform efficiently on large-scale molecules. In addition, SMP is capable of distinguishing almost all molecular structures, and the uncovered cases may not exist in practice. Based on meaningful physically-based representations of 3D information, we further propose the SphereNet for 3D molecular learning. Experimental results demonstrate that the use of meaningful 3D information in SphereNet leads to significant performance improvements in prediction tasks. Our results also demonstrate the advantages of SphereNet in terms of capability, efficiency, and scalability. Our code is publicly available as part of the DIG library (https://github.com/divelab/DIG).

cs.LG↗

arXiv2021

DIG: A Turnkey Library for Diving into Graph Deep Learning Research

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.

cs.LG↗

arXiv2021

GraphEBM: Molecular Graph Generation with Energy-Based Models

We note that most existing approaches for molecular graph generation fail to guarantee the intrinsic property of permutation invariance, resulting in unexpected bias in generative models. In this work, we propose GraphEBM to generate molecular graphs using energy-based models. In particular, we parameterize the energy function in a permutation invariant manner, thus making GraphEBM permutation invariant. We apply Langevin dynamics to train the energy function by approximately maximizing likelihood and generate samples with low energies. Furthermore, to generate molecules with a desirable property, we propose a simple yet effective strategy, which pushes down energies with flexible degrees according to the properties of corresponding molecules. Finally, we explore the use of GraphEBM for generating molecules with multiple objectives in a compositional manner. Comprehensive experimental results on random, goal-directed, and compositional generation tasks demonstrate the effectiveness of our proposed method.

cs.LG↗

arXiv2021

Unveiling Spatial Patterns of Disaster Impacts and Recovery Using Credit Card Transaction Variances

The objective of this study is to examine spatial patterns of impacts and recovery of communities based on variances in credit card transactions. Such variances could capture the collective effects of household impacts, disrupted accesses, and business closures, and thus provide an integrative measure for examining disaster impacts and community recovery in disasters. Existing studies depend mainly on survey and sociodemographic data for disaster impacts and recovery effort evaluations, although such data has limitations, including large data collection efforts and delayed timeliness results. In addition, there are very few studies have concentrated on spatial patterns and disparities of disaster impacts and short-term recovery of communities, although such investigation can enhance situational awareness during disasters and support the identification of disparate spatial patterns of disaster impacts and recovery in the impacted regions. This study examines credit card transaction data Harris County (Texas, USA) during Hurricane Harvey in 2017 to explore spatial patterns of disaster impacts and recovery during from the perspective of community residents and businesses at ZIP code and county scales, respectively, and to further investigate their spatial disparities across ZIP codes. The results indicate that individuals in ZIP codes with populations of higher income experienced more severe disaster impact and recovered more quickly than those located in lower-income ZIP codes for most business sectors. Our findings not only enhance the understanding of spatial patterns and disparities in disaster impacts and recovery for better community resilience assessment, but also could benefit emergency managers, city planners, and public officials in harnessing population activity data, using credit card transactions as a proxy for activity, to improve situational awareness and resource allocation.

cs.CY↗

arXiv2021

Unraveling the Dynamic Importance of County-level Features in Trajectory of COVID-19

The objective of this study was to investigate the importance of multiple county-level features in the trajectory of COVID-19. We examined feature importance across 2,787 counties in the United States using a data-driven machine learning model. We trained random forest models using 23 features representing six key influencing factors affecting pandemic spread: social demographics of counties, population activities, mobility within the counties, movement across counties, disease attributes, and social network structure. Also, we categorized counties into multiple groups according to their population densities, and we divided the trajectory of COVID-19 into three stages: the outbreak stage, the social distancing stage, and the reopening stage. The study aims to answer two research questions: (1) The extent to which the importance of heterogeneous features evolves in different stages; (2) The extent to which the importance of heterogeneous features varies across counties with different characteristics. We fitted a set of random forest models to determine weekly feature importance. The results showed that: (1) Social demographic features, such as gross domestic product, population density, and minority status maintained high-importance features throughout stages of COVID-19 across the 2787 studied counties; (2) Within-county mobility features had the highest importance in county clusters with higher population densities; (3) The feature reflecting the social network structure (Facebook, social connectedness index), had higher importance in the models for counties with higher population densities. The results show that the data-driven machine learning models could provide important insights to inform policymakers regarding feature importance for counties with various population densities and in different stages of a pandemic life cycle.

physics.soc-ph↗

arXiv2020

Effects of Population Co-location Reduction on Cross-county Transmission Risk of COVID-19 in the United States

The rapid spread of COVID-19 in the United States has imposed a major threat to public health, the real economy, and human well-being. With the absence of effective vaccines, the preventive actions of social distancing and travel reduction are recognized as essential non-pharmacologic approaches to control the spread of COVID-19. Prior studies demonstrated that human movement and mobility drove the spatiotemporal distribution of COVID-19 in China. Little is known, however, about the patterns and effects of co-location reduction on cross-county transmission risk of COVID-19. This study utilizes Facebook co-location data for all counties in the United States from March to early May 2020. The analysis examines the synchronicity and time lag between travel reduction and pandemic growth trajectory to evaluate the efficacy of social distancing in ceasing the population co-location probabilities, and subsequently the growth in weekly new cases. The results show that the mitigation effects of co-location reduction appear in the growth of weekly new cases with one week of delay. Furthermore, significant segregation is found among different county groups which are categorized based on numbers of cases. The results suggest that within-group co-location probabilities remain stable, and social distancing policies primarily resulted in reduced cross-group co-location probabilities (due to travel reduction from counties with large number of cases to counties with low numbers of cases). These findings could have important practical implications for local governments to inform their intervention measures for monitoring and reducing the spread of COVID-19, as well as for adoption in future pandemics. Public policy, economic forecasting, and epidemic modeling need to account for population co-location patterns in evaluating transmission risk of COVID-19 across counties.

physics.soc-ph↗