Publications
] , "Accurate and Scalable Techniques for the Complex/Pathway Membership Problem in Protein Networks", Adv. Bioinformatics, vol. 2009, pp. 787128:1–787128:9, 2009.
, "AI Decision Systems with Feedback Loop Active Learner", WSDM Crowd Science Workshop, 2023.
, "Answering Top-k Queries Over a Mixture of Attractive and Repulsive Dimensions", CoRR, vol. abs/1111.7165, 2011.
, "Answering Top-k Queries Over a Mixture of Attractive and Repulsive Dimensions", {PVLDB}, vol. 5, no. 3, pp. 169–180, 2011.
, "Application of Transformers in Cheminformatics", Journal of Chemical Information and Modeling, vol. 64, pp. 4392-4409, 05/2024.
, "Approximate Algorithms for Data-driven Influence Limitation", IEEE Transactions on Knowledge and Data Engineering (TKDE), 2020.
, "Approximate Algorithms for Data-Driven Influence Limitation", IEEE Trans. Knowl. Data Eng., vol. 34, pp. 2641–2652, 2022.
, "Base motif recognition and design of DNA templates for fluorescent silver clusters by machine learning", Advanced Materials, vol. 26, pp. 5839–5845, 2014.
, "Behavior Query Discovery in System-Generated Temporal Graphs", {PVLDB}, vol. 9, pp. 240–251, 2015.
, "Bisque: a platform for bioimage analysis and management", Bioinformatics, vol. 26, no. 4, pp. 544–552, 2010.
, "Bisque: Advances in Bioimage Databases", {IEEE} Data Eng. Bull., vol. 35, no. 3, pp. 56–64, 2012.
, "Browsing and placement of multi-resolution images on parallel disks", Multimedia Syst., vol. 8, no. 6, pp. 459–469, 2003.
, "Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43307–319 Aggregation", ACS Chemical Neuroscience, vol. 14, pp. 4395–4408, 2023.
, "Computationally designed small molecules disassemble both soluble oligomers and protofibrils of amyloid β-protein responsible for Alzheimer’s disease", ACS Chemical Neuroscience, vol. 14, pp. 2717–2726, 2023.
, "Decision Tree Based Information Integration for Automated Protein Classification", J. Bioinformatics and Computational Biology, vol. 3, no. 3, pp. 717–742, 2005.
, "Discovery of LRRK2 inhibitors using sequential in silico joint pharmacophore space (JPS) and ensemble docking", Bioorganic & medicinal chemistry letters, vol. 25, pp. 2713–2719, 2015.
, "A Distributed Database for BioMolecular Images", {SIGMOD} Record, vol. 33, no. 2, pp. 65–71, 2004.
, "Dynamic Query-Based Debugging of Object-Oriented Programs", Autom. Softw. Eng., vol. 10, no. 1, pp. 39–74, 2003.
, "Efficient and Robust Detection of Duplicate Videos in a Large Database", {IEEE} Trans. Circuits Syst. Video Techn., vol. 20, no. 6, pp. 870–885, 2010.
, "Estimating localized complexity of white-matter wiring with GANs", Medical Imaging meets NeurIPS, 2019.
, "Expertise and confidence explain how social influence evolves along intellective tasks", CoRR, vol. abs/2011.07168, 2020.
, "Faster Similarity Search for Multimedia Data Via Query Transformations", Int. J. Image Graphics, vol. 3, no. 1, pp. 3–30, 2003.
, "Feature-based Individual Fairness in k-Clustering", International Conference on Autonomous Agents and Multiagent Systems (AAMAS Extended Abstract), 2023.
, "Finding Significant Subregions in Large Image Databases", CoRR, vol. abs/0906.3585, 2009.
, "Finding top-k similar pairs of objects annotated with terms from an ontology", CoRR, vol. abs/1001.2625, 2010.
, "A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics", {BMC} Bioinformatics, vol. 9, 2008.
, "GPOP: Scalable Group-level Popularity Prediction for Online Content in Social Networks", Proceedings of the 26th International Conference on World Wide Web, 2017.
, "Graph Neural Diffusion Networks for Semi-supervised Learning", CoRR, vol. abs/2201.09698, 2022.
, "Incorporating Heterophily into Graph Neural Networks for Graph Classification", CoRR, vol. abs/2203.07678, 2022.
, "Incorporating User's Preference into Attributed Graph Clustering", IEEE Trans. Knowl. Data Eng., vol. 33, pp. 3716–3728, 2021.
, "Index-based Similarity Search for Protein Structure Databases", J. Bioinformatics and Computational Biology, vol. 2, no. 1, pp. 99–126, 2004.
, "Indexing the Earth Mover's Distance Using Normal Distributions", CoRR, vol. abs/1111.7168, 2011.
, "Indexing the Earth Mover's Distance Using Normal Distributions", {PVLDB}, vol. 5, no. 3, pp. 205–216, 2011.
, "Inferring causal molecular networks: empirical assessment through a community-based effort", Nature methods, vol. 13, pp. 310–318, 2016.
, "Inferring the Underlying Structure of Information Cascades", CoRR, vol. abs/1210.3587, 2012.
, "Inhibiting and remodeling toxic amyloid-beta oligomer formation using a computationally designed drug molecule that targets Alzheimer’s disease", Journal of The American Society for Mass Spectrometry, vol. 30, pp. 85–93, 2018.
, "Integrating multi-attribute similarity networks for robust representation of the protein space", Bioinformatics, vol. 22, no. 13, pp. 1585–1592, 2006.
, "A Latent Parameter Node-Centric Model for Spatial Networks", CoRR, vol. abs/1210.4246, 2012.
, "Learning about learning: Mining human brain sub-network biomarkers from fMRI data", PLoS one, vol. 12, pp. e0184344, 2017.
, "Learning Deep Graph Representations via Convolutional Neural Networks", IEEE Trans. Knowl. Data Eng., vol. 34, pp. 2268–2279, 2022.
, "Learning Neural Contracting Dynamics: Extended Linearization and Global Guarantees", CoRR, vol. abs/2402.08090, 2024.
, "Making a Small World Smaller: Path Optimization in Networks", IEEE Transactions on Knowledge and Data Engineering (TKDE), 2018.
, "Mining Statistically Significant Molecular Substructures for Efficient Molecular Classification", Journal of Chemical Information and Modeling, vol. 49, no. 11, pp. 2537–2550, 2009.
, "Modeling Human-AI Team Decision Making", CoRR, vol. abs/2201.02759, 2022.
, "Modeling individual topic-specific behavior and influence backbone networks in social media", Social Netw. Analys. Mining, vol. 4, no. 1, pp. 204, 2014.
, "Modulating ALS-Related Amyloidogenic TDP-43307–319 Oligomeric Aggregates with Computationally Derived Therapeutic Molecules", Biochemistry, vol. 59, pp. 499–508, 2019.
, "Molecular Function Prediction Using Neighborhood Features", {IEEE/ACM} Trans. Comput. Biology Bioinform., vol. 7, no. 2, pp. 208–217, 2010.
, "Nearest Keyword Set Search in Multi-dimensional Datasets", CoRR, vol. abs/1409.3867, 2014.
, "Nearest Keyword Set Search in Multi-Dimensional Datasets", {IEEE} Trans. Knowl. Data Eng., vol. 28, pp. 741–755, 2016.
, "Novel Method for Pharmacophore Analysis by Examining the Joint Pharmacophore Space", Journal of Chemical Information and Modeling, vol. 51, no. 5, pp. 1106–1121, 2011.
, "Optimization Techniques for Reactive Network Monitoring", {IEEE} Trans. Knowl. Data Eng., vol. 21, no. 9, pp. 1343–1357, 2009.
, "Optimizing Similarity Search for Arbitrary Length Time Series Queries", {IEEE} Trans. Knowl. Data Eng., vol. 16, no. 4, pp. 418–433, 2004.
, "Outlier Detection from Network Data with Subnetwork Interpretation", IEEE International Conference Data Mining (ICDM), 2016.
, "Polar Opinion Dynamics in Social Networks", IEEE Transactions on Automatic Control (TAC), 2017.
, "Predicting genetic interactions with random walks on biological networks", {BMC} Bioinformatics, vol. 10, 2009.
, "Predictive models for human–AI nexus in group decision making", Annals of the New York Academy of Sciences, vol. 1514, pp. 70–81, 2022.
, "Profile Based Sub-Image Search in Image Databases", CoRR, vol. abs/1010.1496, 2010.
, "Progressive Searching of Biological Sequences", {IEEE} Data Eng. Bull., vol. 27, no. 3, pp. 32–39, 2004.
, "Quantifying spatial relationships from whole retinal images", Bioinformatics, vol. 29, no. 7, pp. 940–946, 2013.
, "Querying and Mining Biological Databases", {OMICS}, vol. 7, no. 1, pp. 7–8, 2003.
, "RRW: repeated random walks on genome-scale protein networks for local cluster discovery", {BMC} Bioinformatics, vol. 10, pp. 283, 2009.
, "Scalable Discovery of Best Clusters on Large Graphs", {PVLDB}, vol. 3, no. 1, pp. 693–702, 2010.
, "Sign prediction in social networks based on users reputation and optimism", Social Network Analysis and Mining, vol. 6, pp. 91, 2016.
, "The Social Media Genome: Modeling Individual Topic-Specific Behavior in Social Media", CoRR, vol. abs/1307.0309, 2013.
, "Spatial coherence of oriented white matter microstructure: Applications to white matter regions associated with genetic similarity", NeuroImage, 2018.
, "Speeding up whole-genome alignment by indexing frequency vectors", Bioinformatics, vol. 20, no. 13, pp. 2122–2134, 2004.
, "Static and Dynamic Structural Correlations in Graphs", {IEEE} Trans. Knowl. Data Eng., vol. 25, no. 9, pp. 2147–2160, 2013.
, "Subnetwork Mining with Spatial and Temporal Smoothness", SIAM international conference on data mining (SDM), 2017.
, "Through the Grapevine: A Comparison of News in Microblogs and Traditional Media", Trends in Social Network Analysis: Information Propagation, User Behavior Modeling, Forecasting, and Vulnerability Assessment, pp. 135–168, 2017.
, "Tree++: Truncated Tree Based Graph Kernels", IEEE Trans. Knowl. Data Eng., vol. 33, pp. 1778–1789, 2021.
, "Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets", {BMC} Bioinformatics, vol. 12, pp. 7, 2011.
, "Dynamics of Collective Performance in Collaboration Networks", XXXVI International Sunbelt Conference, Newport Beach, California, US, International Network for Social Network Analysis (INSNA), 2016.