- Canonical Correlations and Applications. (1993-1996, NSF)
- Eigenvalue Problems for Large Matrices: Parallel Algorithms and Inner-Outer Iterations. (1996-1999, NSF)
- Large-Scale Matrix Computation Issues in Information Retrieval and Data Mining. (1999-2002, NSF)
- Identifiying the Structural Building Blocks of the Protein Universe (2002-2004, NASA), PI: Liang, co-PI: Zha
- Collaborative Research: Sufficient Di mension Reduction for High Dimensional Data with Applications in Bioinformatics (2004-2007, NSF), PIs: Cook & Li, co-PIs: Zha & Chiaromonte
- Development of Quantitative Analysis Tools for Mapping Cellular Signaling Pathways. (2004-2006, Tobacco Formula Funded Health Research), PI: Dong, co-PIs: Zha & Antonetti
- Manifold Learning from Unorganized Hig h-dimensional Points. (2003-2006, NSF)
- Matrix Algorithms for Data Clustering . (2003-2006, NSF)
- CAMLET: A Combined Ab-initio Manif old Learning Toolbox for Nanostructure Simulations, (2004-2007, NSF), PI: Zha, co-PIs: Du, Li & Sofo
- Computational Methods for Nonlinear Dimension Reduction (2007-2010, NSF), PI: Zha, co-PI: Park
- Optimal Cross Parameterizations of Surfaces: Computational Methods and Scientific Applications (2007-2010, NSF), PI: Jiao, co-PI: Zha
- Robust Knowledge Acquisition from Social Media. (2009-2010, HP), PIs: Zha and Agichtein.
- User-Centered Multi-Modal Information Retrieval. (2009-2010, NSF China), PIs: Zha and Yang.
- Content Recommendation through Joint Matrix/Tensor Factorization, Yahoo! Faculty Research and Engagement Grant, 2010-2011.
- A Structured Learning Framework for Learning to Rank in Web Search. (2008-2011, Microsoft)
- When Social Meets Mobile: Geographical User Behavior Modeling and Recommendation, Yahoo! Faculty Research and Engagement Grant, 2011-2012.
- Evidence-Based Cost Effective Diagnosis for Pediatric Cardiac Disease: A Machine Learning and Data Mining Approach (2011-2012, Georgia Tech-Children's Hospital Healthcare of Atlanta Pilot Grant, PI: H. Zha, co-PIs: P. Frias, M. Braunstein, H. Park and A. Gray)
- Learning Evaluation Metrics for Information Retrieval (2010-2013, NSF).
- Interactive Generative Manifold Learning (2012-2013, ObjectVideo)
- Fast Algorithms on Imperfect, heterogeneous, distributed data for interactive analysis (2012-2014, DARPA), co-PI.
- Exploring Social and Behavioral Contexts for Information Retrieval (2011-2015, NSF).
- Cross-Domain and Multi-model User Group Behavior Modeling for Search and Recommendation (2011-2015, NSFC), PIs: H. Zha and X. Yang
- Collaborative Research: Robust Algorithms for Interpolation and Extrapolation in Manifold Learning (2013-2016, NSF)
- Social Behavior Driven Modeling and Optimization of Information Diffusion (2013-2016, NIH), PI: Le Song, co-PI: H. Zha

- IGERT-CIF21: Computation-Enabled Design and Manufacturing of High Performance Materials (2013-2018, NSF), PI: Richard Fujimot, co-PIs: H. Zha, S. Kalidindi, T. Blum and W. Newstetter
- TWC SBE: TTP Option: Medium: Collaborative: EPICA: Empowering People to Overcome Information Controls and Attacks (2014-2017, NSF), PI: Wenke Lee, co-PIs: H. Zha, H. Klein, N. Feamster
- Asynchronous Event Models for State-Topology Co-evolution of Temporal Networks. (2016-2018, NSF), PI: H. Zha, co-PI: L. Song
- Prediction, Optimization and Control for Information Propagation on Networks: A Differential Equation and Mass Transportation Based Approach. (2016-2019, NSF), PI: H. Zhou, co-PI: H. Zha
- SSDIM: Leveraging Point Processes and Mean Field Games Theory for Simulating Data on Interdependent Critical Infrastructures (2017-2019, NSF), PI: H. Zha, co-PI, X. Ye
- Topics in Temporal Marked Point Processes: Granger Causality, Imperfect Observations and Intervention. (2017-2020, NSF)