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Title: Prediction and prevention of pandemics via graphical model inference and convex programming
Abstract Hard-to-predict bursts of COVID-19 pandemic revealed significance of statistical modeling which would resolve spatio-temporal correlations over geographical areas, for example spread of the infection over a city with census tract granularity. In this manuscript, we provide algorithmic answers to the following two inter-related public health challenges of immense social impact which have not been adequately addressed (1) Inference Challenge assuming that there are N census blocks (nodes) in the city, and given an initial infection at any set of nodes, e.g. any N of possible single node infections, any $$N(N-1)/2$$ N ( N - 1 ) / 2 of possible two node infections, etc, what is the probability for a subset of census blocks to become infected by the time the spread of the infection burst is stabilized? (2) Prevention Challenge What is the minimal control action one can take to minimize the infected part of the stabilized state footprint? To answer the challenges, we build a Graphical Model of pandemic of the attractive Ising (pair-wise, binary) type, where each node represents a census tract and each edge factor represents the strength of the pairwise interaction between a pair of nodes, e.g. representing the inter-node travel, road closure and related, and each local bias/field represents the community level of immunization, acceptance of the social distance and mask wearing practice, etc. Resolving the Inference Challenge requires finding the Maximum-A-Posteriory (MAP), i.e. most probable, state of the Ising Model constrained to the set of initially infected nodes. (An infected node is in the $$+ \, 1$$ + 1 state and a node which remained safe is in the $$- \, 1$$ - 1 state.) We show that almost all attractive Ising Models on dense graphs result in either of the two possibilities (modes) for the MAP state: either all nodes which were not infected initially became infected, or all the initially uninfected nodes remain uninfected (susceptible). This bi-modal solution of the Inference Challenge allows us to re-state the Prevention Challenge as the following tractable convex programming : for the bare Ising Model with pair-wise and bias factors representing the system without prevention measures, such that the MAP state is fully infected for at least one of the initial infection patterns, find the closest, for example in $$l_1$$ l 1 , $$l_2$$ l 2 or any other convexity-preserving norm, therefore prevention-optimal, set of factors resulting in all the MAP states of the Ising model, with the optimal prevention measures applied, to become safe. We have illustrated efficiency of the scheme on a quasi-realistic model of Seattle. Our experiments have also revealed useful features, such as sparsity of the prevention solution in the case of the $$l_1$$ l 1 norm, and also somehow unexpected features, such as localization of the sparse prevention solution at pair-wise links which are NOT these which are most utilized/traveled.  more » « less
Award ID(s):
2027072
NSF-PAR ID:
10332258
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
Scientific Reports
Volume:
12
Issue:
1
ISSN:
2045-2322
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 
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