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Center for Artificial Intelligence and Modeling: Publications

Chen, Y., Huerta, E. A., Duarte, J., Harris, P., Katz, D. S., Neubauer, M. S., Diaz, D., Mokhtar, F., Kansal, R., Park, S. E., Kindratenko, V. V., Zhao, Z., & Rusack, R. (2022). A FAIR and AI-ready Higgs boson decay dataset. Scientific Data, 9(1), [31].

Long, A. A., Wright, W. J., Gu, X., Thackray, A., Nakib, M., Uhl, J. T., & Dahmen, K. A. (2022). Experimental evidence that shear bands in metallic glasses nucleate like cracks. Scientific reports, 12(1), [18499].

Brown, M. D., Shinn, L. M., Reeser, G., Browning, M., Schwingel, A., Khan, N. A., & Holscher, H. D. (2022). Fecal and soil microbiota composition of gardening and non-gardening families. Scientific reports, 12(1), [1595].

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Fredrickson, R. L., Wang, T., Wong, G. N., Uelmen, J., Maslov, S., Weiner, Z. J., Tkachenko, A. V., Zhang, H., Liu, Z., Ibrahim, A., Patel, S. J., Paul, J. M., Vance, N. P., Gulick, J. G., ... Burke, M. D. (2022). Mitigation of SARS-CoV-2 transmission at a large public university. Nature communications, 13(1), [3207].

Sashittal, P., Zaccaria, S., & El-Kebir, M. (2022). Parsimonious Clone Tree Integration in cancer. Algorithms for Molecular Biology, 17(1), [3].

Pan, C., Tabatabaei, S. K., Tabatabaei Yazdi, S. M. H., Hernandez, A. G., Schroeder, C. M., & Milenkovic, O. (2022). Rewritable two-dimensional DNA-based data storage with machine learning reconstruction. Nature communications, 13(1), [2984].

Khandelwal, A., Athreya, N., Tu, M. Q., Janavicius, L. L., Yang, Z., Milenkovic, O., Leburton, J. P., Schroeder, C. M., & Li, X. (2022). Self-assembled microtubular electrodes for on-chip low-voltage electrophoretic manipulation of charged particles and macromolecules. Microsystems and Nanoengineering, 8(1), [27].

Bosch, N., Chan, A. S., Davis, J. L., Gutiérrez, R., He, J. R., Karahalios, K. G., Koyejo, O. O., Loui, M. C., Mendenhall, R., Tong, H., Varshney, L. R., & Wang, Y. (2022). Artificial Intelligence and Social Responsibility: The Roles of the University.

Tsai, K., Koyejo, O., & Kolar, M. (2022). Joint Gaussian graphical model estimation: A survey. Wiley Interdisciplinary Reviews: Computational Statistics, 14(6), [e1582].

Xiong, J., Yang, A., Raginsky, M., & Rosenbaum, E. (2022). Neural Ordinary Differential Equation Models of Circuits: Capabilities and Pitfalls. IEEE Transactions on Microwave Theory and Techniques, 70(11), 4869-4884.

Smith, R., Varshney, L. R., Nagayama, S., Kazama, M., Kitagawa, T., Managi, S., & Ishikawa, Y. (2022). A computational neuroscience perspective on subjective wellbeing within the active inference framework. International Journal of Wellbeing, 12(4), 102-131.

Berger, B., Tian, D., Li, W. V., El-Kebir, M., Tomescu, A. I., Singh, R., Beerenwinkel, N., Li, Y., Boucher, C., & Bar-Joseph, Z. (2022). What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems, 13(10), 781-785.

O’Shaughnessy, M. R., Schiff, D. S., Varshney, L. R., Rozell, C. J., & Davenport, M. A. (2022). What governs attitudes toward artificial intelligence adoption and governance? Science and Public Policy, [scac056].

Lalani, Z., Chu, G., Hsu, S., Kagawa, S., Xiang, M., Zaccaria, S., & El-Kebir, M. (2022). CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLoS computational biology, 18(10), e1010614.

Greenberg, G., & Shomorony, I. (2022). Improving bacterial genome assembly using a test of strand orientation. Bioinformatics (Oxford, England), 38(2), ii34-ii41.

Liu, X., & Milenkovic, O. (2022). Finding the second-best candidate under the Mallows model. Theoretical Computer Science, 929, 39-68.

Holthaus, T. A., Kashi, M., Cannavale, C. N., Edwards, C. G., Aguiñaga, S., Walk, A. D. M., Burd, N. A., Holscher, H. D., & Khan, N. A. (2022). MIND Dietary Pattern Adherence Is Selectively Associated with Cognitive Processing Speed in Middle-Aged Adults. The Journal of nutrition, [nxac203].

Nijholt, E., & Deville, L. (2022). Dynamical systems defined on simplicial complexes: Symmetries, conjugacies, and invariant subspaces. Chaos, 32(9), [093131].

Abdelmeguid, M., & Elbanna, A. (2022). Sequences of seismic and aseismic slip on bimaterial faults show dominant rupture asymmetry and potential for elevated seismic hazard. Earth and Planetary Science Letters, 593, [117648].

Amlani, F., Bhat, H. S., Simons, W. J. F., Schubnel, A., Vigny, C., Rosakis, A. J., Efendi, J., Elbanna, A. E., Dubernet, P., & Abidin, H. Z. (2022). Supershear shock front contribution to the tsunami from the 2018 Mw7.5 Palu, Indonesia earthquake. Geophysical Journal International, 230(3), 2089-2097.

Salners, T., Curry, J. F., Hinkle, A. R., Babuska, T. F., Argibay, N., DelRio, F. W., Chandross, M., & Dahmen, K. (2022). Linking Friction Scales from Nano to Macro via Avalanches. Tribology Letters, 70(3), [82].

Mysonhimer, A. R., & Holscher, H. D. (2022). Gastrointestinal Effects and Tolerance of Nondigestible Carbohydrate Consumption. Advances in Nutrition, [nmac094].

Holscher, H. D., Chumpitazi, B. P., Dahl, W. J., Fahey, G. C., Liska, D. J., Slavin, J. L., & Verbeke, K. (2022). Perspective: Assessing Tolerance to Nondigestible Carbohydrate Consumption. Advances in Nutrition, [nmac091].

McMath, A. L., Iwinski, S., Shen, S., Bost, K. F., Donovan, S. M., & Khan, N. A. (2022). Adherence to screen time and physical activity guidelines is associated with executive function in US toddlers participating in the STRONG Kids 2 birth cohort study. The Journal of Pediatrics.

Chien, E., Tabaghi, P., & Milenkovic, O. (2022). HyperAid: Denoising in Hyperbolic Spaces for Tree-fitting and Hierarchical Clustering. In KDD 2022 - Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 201-211). (Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining). Association for Computing Machinery.

Liechty, J. M., Keck, A. S., Sloane, S., Donovan, S. M., & Fiese, B. H. (2022). Assessing Transdisciplinary Scholarly Development: A Longitudinal Mixed Method Graduate Program Evaluation. Innovative Higher Education, 47(4), 661-681.

Wang, X., Shih, H. Y., & Goldenfeld, N. (2022). Stochastic Model for Quasi-One-Dimensional Transitional Turbulence with Streamwise Shear Interactions. Physical review letters, 129(3), [034501].

Zhang, C., Sashittal, P., Xiang, M., Zhang, Y., Kazi, A., & El-Kebir, M. (2022). Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Molecular biology and evolution, 39(7), [msac133].

Das, P., & Varshney, L. R. (2022). Explaining Artificial Intelligence Generation and Creativity: Human interpretability for novel ideas and artifacts. IEEE Signal Processing Magazine, 39(4), 85-95.

Naik, A., Varshney, L. R., Hassaneen, W., & Arnold, P. M. (2022). Letter: Development of Machine Learning-Based Models to Predict Treatment Response to Spinal Cord Stimulation. Neurosurgery, 91(1), e30.

Ishaq, S. L., Wissel, E. F., Wolf, P. G., Grieneisen, L., Eggleston, E. M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J., Weatherford Darling, K., Pearson, A. L., Wertheim, F. S., Johnson, A. J., Hodges, L., Young, S. K., Nielsen, C. C., Kozyrskyj, A. L., MacRae, J. D., Myers, E. M., ... Hosler, S. (2022). Designing the Microbes and Social Equity Symposium: A Novel Interdisciplinary Virtual Research Conference Based on Achieving Group-Directed Outputs. Challenges, 13(2).

Xie, C., Koyejo, O., & Gupta, I. (2022). ZenoPS: A Distributed Learning System Integrating Communication Efficiency and Security. Algorithms, 15(7), [233].

Ge, X., Goodwin, R. T., Yu, H., Romero, P., Abdelrahman, O., Sudhalkar, A., Kusuma, J., Cialdella, R., Garg, N., & Varshney, L. R. (2022). Accelerated Design and Deployment of Low-Carbon Concrete for Data Centers. In Proceedings of the 4th ACM SIGCAS/SIGCHI Conference on Computing and Sustainable Societies, COMPASS 2022 (pp. 340-352). (ACM International Conference Proceeding Series; Vol. Par F180472). Association for Computing Machinery.

Jankelow, A. M., Lee, H., Wang, W., Hoang, T. H., Bacon, A., Sun, F., Chae, S., Kindratenko, V., Koprowski, K., Stavins, R. A., Ceriani, D. D., Engelder, Z. W., King, W. P., Do, M. N., Bashir, R., Valera, E., & Cunningham, B. T. (2022). Smartphone clip-on instrument and microfluidic processor for rapid sample-to-answer detection of Zika virus in whole blood using spatial RT-LAMP. Analyst, 147(17), 3838-3853.

Abolfathi, M., Shomorony, I., Vahid, A., & Jafarian, J. H. (2022). A Game-Theoretically Optimal Defense Paradigm against Traffic Analysis Attacks using Multipath Routing and Deception. In SACMAT 2022 - Proceedings of the 27th ACM Symposium on Access Control Models and Technologies (pp. 67-78). (Proceedings of ACM Symposium on Access Control Models and Technologies, SACMAT). Association for Computing Machinery.

Bandak, D., Goldenfeld, N., Mailybaev, A. A., & Eyink, G. (2022). Dissipation-range fluid turbulence and thermal noise. Physical Review E, 105(6), [065113].

Davis, E. C., Wang, M., & Donovan, S. M. (2022). Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum. Microorganisms, 10(6).

Xu, A., & Raginsky, M. (2022). Minimum Excess Risk in Bayesian Learning. IEEE Transactions on Information Theory.

Bode, L., & Donovan, S. M. (2022). Fructooligosaccharides are not the same as Fucosylated Human Milk Oligosaccharides. Advances in Nutrition, 13(3), 972-973.

Goyal, M., Serrano, G., Argemi, J., Shomorony, I., Hernaez, M., & Ochoa, I. (2022). JIND: Joint integration and discrimination for automated single-cell annotation. Bioinformatics, 38(9), 2488-2495.

Bhimaraju, A., Chatterjee, A., & Varshney, L. (2022). Expected Extinction Times of Epidemics with State-dependent Infectiousness. IEEE Transactions on Network Science and Engineering, 9(3), 1104-1116.

Kara, A. D., Raginsky, M., & Yüksel, S. (2022). Robustness to incorrect models and data-driven learning in average-cost optimal stochastic control. Automatica, 139, [110179].

Mia, M. S., Abdelmeguid, M., & Elbanna, A. E. (2022). Spatio-Temporal Clustering of Seismicity Enabled by Off-Fault Plasticity. Geophysical Research Letters, 49(8), [e2021GL097601].

Sutkus, L. T., Joung, S., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Donovan, S. M., & Dilger, R. N. (2022). Influence of 2′-Fucosyllactose and Bifidobacterium longum Subspecies infantis Supplementation on Cognitive and Structural Brain Development in Young Pigs. Frontiers in Neuroscience, 16, [860368].

Spencer, T. E., Wells, K. D., Lee, K., Telugu, B. P., Hansen, P. J., Bartol, F. F., Blomberg, L., Schook, L. B., Dawson, H., Lunney, J. K., Driver, J. P., Davis, T. A., Donovan, S. M., Dilger, R. N., Saif, L. J., Moeser, A., McGill, J. L., Smith, G., & Ireland, J. J. (2022). Future of biomedical, agricultural, and biological systems research using domesticated animals. Biology of reproduction, 106(4), 629-638.

Song, Z., Koyejo, O., & Zhang, J. (2022). Toward a Controllable Disentanglement Network. IEEE Transactions on Cybernetics, 52(4), 2491-2504.

Oh, C., Sashittal, P., Zhou, A., Wang, L., El-Kebir, M., & Nguyen, T. H. (2022). Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Applied and environmental microbiology, 88(7), [e0228921].

Traniello, I. M., Hamilton, A. R., Gernat, T., Cash-Ahmed, A. C., Harwood, G. P., Ray, A. M., Glavin, A., Torres, J., Goldenfeld, N., & Robinson, G. E. (2022). Context-dependent influence of threat on honey bee social network dynamics and brain gene expression. The Journal of experimental biology, 225(6).

Tabatabaei, S. K., Pham, B., Pan, C., Liu, J., Chandak, S., Shorkey, S. A., Hernandez, A. G., Aksimentiev, A., Chen, M., Schroeder, C. M., & Milenkovic, O. (2022). Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing. Nano letters, 22(5), 1905-1914.

Ellis, J. L., Wang, M., Fu, X., Fields, C. J., Donovan, S. M., & Booth, S. L. (2022). Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis. Current Developments in Nutrition, 6(3), [nzac019].

Moreno, L. A., Meyer, R., Donovan, S. M., Goulet, O., Haines, J., Kok, F. J., & Van't Veer, P. (2022). Perspective: Striking a Balance between Planetary and Human Health-Is There a Path Forward? Advances in Nutrition, 13(2), 355-375.

Hughes, R. L., Alvarado, D. A., Swanson, K. S., & Holscher, H. D. (2022). The Prebiotic Potential of Inulin-Type Fructans: A Systematic Review. Advances in Nutrition, 13(2), 492-529.

Lee, N. M., Varshney, L. R., Michelson, H. C., Goldsmith, P., & Davis, A. (2022). Digital trust substitution technologies to support smallholder livelihoods in Sub-Saharan Africa. Global Food Security, 32, [100604].

Shen, H., Huerta, E. A., O'Shea, E., Kumar, P., & Zhao, Z. (2022). Statistically-informed deep learning for gravitational wave parameter estimation. Machine Learning: Science and Technology, 3(1), [015007].

Shomorony, I., & Heckel, R. (2022). Information-Theoretic Foundations of DNA Data Storage. Foundations and Trends in Communications and Information Theory, 19(1), 1-106.

Lundquist, A., McBride, B. A., Donovan, S. M., & Wszalek, M. (2022). Father support for breastfeeding mothers who plan to utilize childcare: A qualitative look at Mothers’ perspectives. Appetite, 169, [105854].

Kern, J., Dupraz, E., Aïssa-El-Bey, A., Varshney, L. R., & Leduc-Primeau, F. (2022). Optimizing the Energy Efficiency of Unreliable Memories for Quantized Kalman Filtering. Sensors, 22(3), [853].

Lehman, S. Y., Christman, L. E., Jacobs, D. T., Johnson, N. S. D. E. F., Palchoudhuri, P., Tieman, C. E., Vajpeyi, A., Wainwright, E. R., Walker, J. E., Wilson, I. S., LeBlanc, M., McFaul, L. W., Uhl, J. T., & Dahmen, K. A. (2022). Universal aspects of cohesion. Granular Matter, 24(1), [35].

Xia, F., Allen, J., Balaprakash, P., Brettin, T., Garcia-Cardona, C., Clyde, A., Cohn, J., Doroshow, J., Duan, X., Dubinkina, V., Evrard, Y., Fan, Y. J., Gans, J., He, S., Lu, P., Maslov, S., Partin, A., Shukla, M., Stahlberg, E., ... Stevens, R. (2022). A cross-study analysis of drug response prediction in cancer cell lines. Briefings in bioinformatics, 23(1), [bbab356].

El-Kebir, M., Morris, Q., Oesper, L., & Sahinalp, S. C. (2022). Emerging Topics in Cancer Evolution. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27, 397-401.

Daniels, V. C., Monaco, M. H., Wang, M., Hirvonen, J., Jensen, H. M., Ouwehand, A. C., Mukherjea, R., Dilger, R. N., & Donovan, S. M. (2022). Evaluation of 2’-fucosyllactose and bifidobacterium longum subspecies infantis on growth, organ weights, and intestinal development of piglets. Nutrients, 14(1), [199].

Liu, J. M., Solem, C., Lu, T., & Jensen, P. R. (2022). Harnessing lactic acid bacteria in synthetic microbial consortia. Trends in Biotechnology, 40(1), 8-11.

Levick, K., Heckel, R., & Shomorony, I. (2022). Achieving the Capacity of a DNA Storage Channel with Linear Coding Schemes. In 2022 56th Annual Conference on Information Sciences and Systems, CISS 2022 (pp. 218-223). (2022 56th Annual Conference on Information Sciences and Systems, CISS 2022). Institute of Electrical and Electronics Engineers Inc..

Xie, Y., Wang, D., Chen, P. Y., Xiong, J., Liu, S., & Koyejo, S. (2022). A Word is Worth A Thousand Dollars: Adversarial Attack on Tweets Fools Stock Prediction. In NAACL 2022 - 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Proceedings of the Conference (pp. 587-599). (NAACL 2022 - 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Proceedings of the Conference). Association for Computational Linguistics (ACL).

Pan, C., Gabrys, R., Liu, X., Colbourn, C., & Milenkovic, O. (2022). Balanced and Swap-Robust Trades for Dynamical Distributed Storage. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 2385-2390). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc..

Ravi, A. N., Vahid, A., & Shomorony, I. (2022). Capacity of the Shotgun Sequencing Channel. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 210-215). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc..

Cannavale, C. N., Mysonhimer, A. R., Bailey, M. A., Cohen, N. J., Holscher, H. D., & Khan, N. A. (Accepted/In press). Consumption of a fermented dairy beverage improves hippocampal-dependent relational memory in a randomized, controlled cross-over trial. Nutritional Neuroscience.

Zhang, C., Sashittal, P., & El-Kebir, M. (2022). CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. In I. Pe’er (Ed.), Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings (pp. 360-362). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13278 LNBI). Springer.

Pyrros, A., Chen, A., Rodríguez-Fernández, J. M., Borstelmann, S. M., Cole, P. A., Horowitz, J., Chung, J., Nikolaidis, P., Boddipalli, V., Siddiqui, N., Willis, M., Flanders, A. E., & Koyejo, S. (Accepted/In press). Deep Learning–Based Digitally Reconstructed Tomography of the Chest in the Evaluation of Solitary Pulmonary Nodules: A Feasibility Study. Academic Radiology.

Edwards, C. G., Walk, A. M., Thompson, S. V., Reeser, G. E., Dilger, R. N., Erdman, J. W., Burd, N. A., Holscher, H. D., & Khan, N. A. (2022). Dietary lutein plus zeaxanthin and choline intake is interactively associated with cognitive flexibility in middle-adulthood in adults with overweight and obesity. Nutritional Neuroscience, 25(7), 1437-1452.

Tucker, N., Sutton, B. P., Duncan, C., Lu, C., Koyejo, S., Tsung, A. J., Maksimovic, J., Ralph, T., Pieta, S. M., & Bramlet, M. T. (2022). Fully Automated Conversion Of Glioma Clinical MRI Scans Into A 3D Virtual Reality Model For Presurgical Planning. In C. R. Martin, N. Emami, M. J. Blas, & R. Rezaee (Eds.), Proceedings of the 2022 Annual Modeling and Simulation Conference, ANNSIM 2022 (pp. 392-403). (Proceedings of the 2022 Annual Modeling and Simulation Conference, ANNSIM 2022). Institute of Electrical and Electronics Engineers Inc..

Mazooji, K., Kannan, S., Noble, W. S., & Shomorony, I. (2022). Fundamental Limits of Multi-Sample Flow Graph Decomposition. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 2403-2408). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc..

Hawthorne, K. M., Castle, J., & Donovan, S. M. (2022). Meat Helps Make Every Bite Count An Ideal First Food for Infants. Nutrition Today, 57(1), 8-13.

Markowitz, S., Snyder, C., Eldar, Y. C., & Do, M. N. (2022). Multimodal Unrolled Robust PCA for Background Foreground Separation. IEEE Transactions on Image Processing, 31, 3553-3564.

Saldi, N., Başar, T., & Raginsky, M. (Accepted/In press). Partially Observed Discrete-Time Risk-Sensitive Mean Field Games. Dynamic Games and Applications.

Bhimaraju, A., & Varshney, L. R. (2022). Scheduling Group Tests over Time. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 886-891). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc..

Marla, L., Varshney, L. R., Shah, D., Prakash, N. A., & Gale, M. E. (2022). Short and Wide Network Paths. IEEE Transactions on Network Science and Engineering, 9(2), 524-537.

Rana, V., Chien, E., Peng, J., & Milenkovic, O. (Accepted/In press). Small-sample estimation of the mutational support and distribution of SARS-CoV-2. IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Golm, R., Nahvi, M., Gabrys, R., & Milenkovic, O. (2022). The Gapped k-Deck Problem. In 2022 IEEE International Symposium on Information Theory, ISIT 2022 (pp. 49-54). (IEEE International Symposium on Information Theory - Proceedings; Vol. 2022-June). Institute of Electrical and Electronics Engineers Inc..

DeVille, L. (2022). The generalized distance spectrum of a graph and applications. Linear and Multilinear Algebra, 70(13), 2425-2458.