*Chronologically ordered by month starting with January – December


1. A neural network to predict the knee adduction moment in patients with osteoarthritis using anatomical landmarks obtainable from 2D video analysis. M.A. Boswell, S.D. Uhlrich, Ł. Kidziński, K. Thomas, J.A. Kolesar, G.E. Gold, G.S. Beaupre, S.L. Delp. Osteoarthritis and Cartilage. PMCID: Pending

2. Muscle coordination retraining inspired by musculoskeletal simulations: a study on reducing knee loading. Uhlrich, S.D., Jackson, R.W., Seth, A., Kolesar, J.A., Delp, S.L. bioRxiv. PMCID: Pending

3. Assessment of Extractability and Accuracy of Electronic Health Record Data for Joint Implant Registries. Giori, N.J., Radin, J., Callahan, A., Fries, J.A., Halilaj, E., Ré, C., Delp, S.L., Shah, N.H., Harris, A.H.S. JAMA Netw Open. PMID: 33720372 PMCID: Pending

4. Wearable sensors enable personalized predictions of clinical laboratory measurements. Dunn, J., Kidzinski, L., Runge, R., Witt, D., Hicks, J. L., Schussler-Fiorenza Rose, S. M., Li, X., Bahmani, A., Delp, S. L., Hastie, T., Snyder, M. P. Nature medicine. PMID: 34031607 PMCID: Pending


1. Hidden stratification causes clinically meaningful failures in machine learning for medical imaging. Oakden-Rayner, L., Dunnmon, J., Carneiro, G., Re, C. Assocation for Computing Machinery, 151-159. PMC7665161

2. Personal Omics for Precision Health. Kellogg, R.A., Dunn, J., Snyder, M.P. Circulation Research, 122(9):1169-1171. PMID: 29700064 PMCID: N/A

3. Cross-Modal Data Programming Enables Rapid Medical Machine Learning. Dunnmon, J.A., Ratner. A.J., Saab, K., Khandwala, N., Markert, M., Sagreiya, H., Goldman, R., Lee-Messer, C., Lungren, M.P., Rubin, D.L., Ré, C. Patterns, 1(2): 2666-3899. PMID: 32776018 PMCID: PMC7413132

4. Pre-operative gastrocnemius lengths in gait predict outcomes following gastrocnemius lengthening surgery in children with cerebral palsy. Rajagopal, A., Kidziński, Ł., McGlaughlin, A.S., Hicks, J.L., Delp, S.L., et al. PLOS ONE 15(6): e0233706. PMID: 32502157 PMCID: PMC7274436

5. Deep neural networks enable quantitative movement analysis using single-camera videos. Kidziński, L., Yang, B., Hicks, J.L., Rajagopal, A., Delp, S.L., Schwartz, M. Nature Communications. 11:4054. PMCID: PMC7426855

6. On the Generalization Effects of Linear Transformations in Data Augmentation. Wu, S., Zhang, H.R., Valiant, G., Ré, C. International Conference on Machine learning (ICML) 2020. 

7. Fast and Three-rious: Speeding Up Weak Supervision with Triplet Methods. Fu, D.Y., Chen, M.F., Sala, F., Hooper, S.M., Fatahalian, K., Re, C. International Conference on Machine learning (ICML) 2020. 

8. Extracting chemical reactions from text using Snorkel. Mallory, E.K., de Rochemonteix, M., Ratner, Acharya, A., Re, C., Bright, R.A., Altman, R.B. BMC Bioinformatics, 21:217. PMID: 32460703 PMCID: PMC7251675

9. Cross-Modal Data Programming Enables Rapid
Medical Machine Learning. Dunnmon, J. A., Ratner, A. J., Saab, K., Khandwala, N., Markert, M., Sagreiya, H., Goldman, R., Lee-Messer, C., Lungren, M. P., Rubin, D. L., & Ré, C. Patterns, 1(2), 100019. PMCID: PMC7413132

10. Low-Dimensional Knowledge Graph Embeddings via Hyperbolic Rotations. Chami, I., Wolf, A., Sala, F., Ré, C. Association for Computational Linguistics (ACL) 2020.

11. Contextual Embeddings: When Are They Worth It?. Arora, S., May, A., Zhang, J., Re, C. Association for Computational Linguistics (ACL) 2020.

12. Sparse Recovery for Orthogonal Polynomial Transforms. Gilbert, A., Gu, A., Re, C., Rudra, A. International Colloquium on Automata, Languages and Programming (ICALP) 2020.

13. Hidden Stratification Causes Clinically Meaningful Failures in Machine Learning for Medical Imaging. Oakden-Rayner, L., Dunnmon, J., Carneiro, G., Re, C. Conference on Innovative Data Systems Research (CIDR) 2020.

14. Ivy: Instrumental Variable Synthesis for Causal Inference. Kuang, Z., Sala, F., Sohoni, N., Wu, S., Cordova-Palomera, A., Dunnmon, J., Priest, J., Re, C. International Conference on Learning Representations (ICLR) 2020.

15. Weak supervision as an efficient approach for automatedseizure detection in electroencephalography. Saab, K., Dunnmon, J., Ré, C., Rubin, D., Lee-Messer, C. NPJ Digit Med, 3:59. PMCID: PMC7170880

16. The turning and barrier course reveals gait parameters for detecting freezing of gait and measuring the efficacy of deep brain stimulation. O’Day, J., Syrkin-Nikolau, J., Anidi, C., Kidzinski, L., Delp, S., Bronte-Stewart, H. PLoS One. PMCID: PMC7190141 PMID: 32348346

17. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Sailani, M.R., Metwally, A.A., Zhou, W. et al. Nature Communications. PMID: 33004787 PMCID: PMC7529769

18. Pre-operative gastrocnemius lengths in gait predict outcomes following gastrocnemius lengthening surgery in children with cerebral palsy. Rajagopal, A., Kidziński, Ł., McGlaughlin, A. S., Hicks, J. L., Delp, S. L., & Schwartz, M. H. PloS one. PMCID: PMC7274436 PMID: 32502157

19. Automated Classification of Radiographic Knee Osteoarthritis Severity Using Deep Neural Networks. Thomas, K. A., Kidziński, Ł., Halilaj, E., Fleming, S. L., Venkataraman, G. R., Oei, E., Gold, G. E., & Delp, S. L. Radiol Artif Intell. PMCID: PMC7104788 PMID: 32280948

20. High-fidelity musculoskeletal modeling reveals that motor planning variability contributes to the speed-accuracy tradeoff. Al Borno, M., Vyas, S., Shenoy, K. V., & Delp, S. L. Elife. PMID: 33325369 PMCID: PMC7787661

21. The effects of motor modularity on performance, learning and generalizability in upper-extremity reaching: a computational analysis. Al Borno, M., Hicks, J. L., & Delp, S. L. Journal of the Royal Society, Interface. PMID: 32486950 PMCID: PMC7328389

22. Foot strike pattern during running alters muscle-tendon dynamics of the gastrocnemius and the soleus. Yong, J. R., Dembia, C. L., Silder, A., Jackson, R. W., Fredericson, M., & Delp, S. L. Scientific Reports. PMID: 32245985 PMCID: PMC7125118

23. OpenSim Moco: Musculoskeletal optimal control. Dembia, C. L., Bianco, N. A., Falisse, A., Hicks, J. L., & Delp, S. L. PLOS Computational Biology. PMID: 33370252 PMCID: PMC7793308

24. Personalization improves the biomechanical efficacy of foot progression angle modifications in individuals with medial knee osteoarthritis. medRxiv. Uhlrich, S., Kolesar, J. A., Kidziński, L., Boswell, M. A., Slider, A., Gold, G. E., Delp, S. L. PMCID: Pending

25. Digital Care for Chronic Musculoskeletal Pain: 10,000 Participant Longitudinal Cohort Study. Bailey, J.F., Agarwal, V., Zheng, P., Smuck, M., Fredericson, M., Kennedy, D.J., Krauss, J. J Med Internet Res. PMID: 32208358 PMCID: PMC7248800

26. Gait features for discriminating between mobility-limiting musculoskeletal disorders: Lumbar spinal stenosis and knee osteoarthritis. Odonkor C, Kuwabara A, Tomkins-Lane C, Zhang W, Muaremi A, Leutheuser H, Sun R, Smuck M. Gait Posture. PMCID: Pending


1. Best practices for analyzing large-scale health data from commercial wearables and smartphone apps. Hicks, J.L., Althoff, T.A. Sosic, R., King, A.C., Leskovec, J., Delp, S.L. Nature Partner Journal in Digital Medicine, 2:45. PMID: 31304391. PMCID: PMC6550237 DOI: 10.1038/s41746-019-0121-1

2. Wearable Sleep Technology in Clinical and Research Settings. de Zambotti, M., Cellini, N., Goldstone, A,. Colrain, I.M., Baker, F.C. Med Sci Sports Exerc. 51(7):1538-1557. PMID: 30789439 PMCID: PMC6579636

3. Training Complex Models with Multi-Task Weak Supervision. Alex Ratner, Braden Hancock, Jared Dunnmon, Frederic Sala, Shreyash Pandey, Christopher Ré. AAAI 2019. PMCID: PMC6765366

4. Low-Precision Random Fourier Features for Memory-Constrained Kernel Approximation. Jian Zhang, Avner May, Tri Dao, Christopher Ré. International Conference on Artificial Intelligence and Statistics (AISTATS) 2019. March 2019. PMCID: PMC6879383

5. Scene Graph Prediction with Limited Labels. Vincent S Chen, Paroma Varma, Ranjay Krishna, Michael Bernstein, C. Ré, Li Fei-Fei. ICCV 2019. PMID: 32218709 PMCID: PMC7098690

6. Weakly supervised classification of aortic valve malformations using unlabeled cardiac MRI sequences. Jason Fries et al. Nature Comms 2019. PMID: 31308376 PMCID: PMC6629670 DOI: 10.1038/s41467-019-11012-3

7. Learning Fast Algorithms for Linear Transforms Using Butterfly Factorizations. Tri Dao, Albert Gu, Matthew Eichhorn, Atri Rudra, C. Ré. ICML 2019. PMCID: PMC6879380

8.  A Kernel Theory of Modern Data Augmentation. Tri Dao, Albert Gu, Alexander J. Ratner, Virginia Smith, Christopher De Sa, C. Ré. ICML 2019. PMCID: PMC6879382

9. Snorkel DryBell: A Case Study in Deploying Weak Supervision at Industrial Scale. Stephen Bach et al. SIGMOD 2019. PMCID: PMC6879379

10. Connecting the legs with a spring improves human running economy. Cole S. Simpson, Cara G. Welker, Scott D. Uhlrich, et al. Journal of Experimental Biology.8 August 2019. PMCID: PMC6765174

11. Predicting Dynamic Embedding Trajectory in Temporal Interaction Networks. S. Kumar, X. Zhang, J. Leskovec. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2019. PMCID: PMC6752886

12. Goal-setting And Achievement In Activity Tracking Apps: A Case Study Of MyFitnessPal. M. Gordon, T. Althoff, J. Leskovec. ACM International Conference on World Wide Web (WWW), 2019. PMCID: PMC7197296

13. Predicting pregnancy using large-scale data from a women’s health tracking mobile application. B. Liu, S. Shi, Y. Wu, D. Thomas, L. Sumul, E. Pierson, J. Leskovec. ACM International Conference on World Wide Web (WWW), 2019. PMCID: PMC6752881

14. Inferring Multidimensional Rates of Aging from Cross-Sectional Data. E. Pierson, P. W. Koh, T. Hashimoto, D. Koller, J. Leskovec, N. Eriksson, P. Liang. Artificial Intelligence and Statistics Conference (AISTATS), 2019. PMCID: PMC6752884

15. Learning Mixed-Curvature Representations in Product Spaces. Beliz Gunel, Albert Gu, C. Ré. Fred Sala. ICLR 2019. PMCID: N/A

16. Enhancing safe routes to school programs through community-engaged citizen science: two pilot investigations in lower density areas of Santa Clara County, California, USA. Rodriguez NM, Arce A, Kawaguchi A, Hua J, Broderick B, Winter SJ, King AC. BMC Public Health. 2019 Mar 1;19(1):256. PMCID: PMC6397479 

17. Slice-based Learning: A Programming Model for Residual Learning in Critical Data Slices. Vincent S. Chen, Sen Wu, Zhenzhen Weng, Alexander Ratner, Christopher Ré. NeurIPS 2019 (Conference on Neural Information Processing Systems). PMCID: PMC6927210

18. On the Downstream Performance of Compressed Word Embeddings. Avner May, Jian Zhang, Tri Dao, Christopher Ré. NeurIPS 2019 (Conference on Neural Information Processing Systems). PMCID: PMC6935262

19. G2SAT: Learning to Generate SAT Formulas. Jiaxuan You, Haoze Wu, Clark Barrett, Raghuram Ramanujan, Jure Leskovec. NeurIPS 2019 (Conference on Neural Information Processing Systems). PMCID: PMC7138247

20. Hyperbolic Graph Convolutional Neural Networks. Ines Chami, Rex Ying, Christopher Ré, Jure Leskovec. NeurIPS 2019 (Conference on Neural Information Processing Systems). PMCID: PMC7108814

21. GNNExplainer: Generating Explanations for Graph Neural Networks. Rex Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, Jure Leskovec. NeurIPS 2019 (Conference on Neural Information Processing Systems). PMCID: PMCID: PMC7138248

22. Artificial Intelligence for Prosthetics — challenge solutions. Łukasz Kidziński, Carmichael Ong, Sharada Prasanna Mohanty, Jennifer Hicks, … Scott Delp.  NeurIPS 2019 (Conference on Neural Information Processing Systems).  

23. Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations. Ong, C.F., Geijtenbeek, T., Hicks, J.L., Delp, S.L. PLoS Computational Biology, 15(10):e1006993. PMID: 31589597 PMCID: PMC6797212

24. Standardizing Analytic Methods and Reporting in Activity Monitor Validation Studies. Welk, G.J., Bai, Y., Lee, J.M., Godino, J., Saint-Maurice, P.F., Carr, L. Med Sci Sports Exerc. 51(8):1767-1780.PMID: 30913159 PMCID: PMC6693923 DOI: 10.1249/MSS.0000000000001966.

25. Rapid energy expenditure estimation for ankle assisted and inclined loaded walking. Slade, P., Troutman, R., Kochenderfer, M.J., Collins, S.H, Delp, S.L. Journal of NeuroEngineering and Rehabilitation, 16:67. PMID: 31171003 PMCID: PMC6555733

26. Automatic real-time gait event detection in children using deep neural networks. Kidzinski, L., Delp, S.L., and Schwartz, M.PLOS One, 14(1):e0211466. PMCID: PMC6354999 PMID: 30703141

27. Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities. Zitnik, M., Nguyen, F., Wang, B., Leskovec, J., Goldenberg, A., Hoffman, M.M. Inf Fusion, 50:71-91. PMID: 30467459 PMCID: PMC6242341

28. Learning one’s genetic risk changes physiology independent of actual genetic risk. Turnwald, B.P., Goyer, J.P., Boles, D.Z., Silder, A., Delp, S.L., Crum, A.J. Nature Human Behaviour, 3:48-56. PMID: 30932047 PMCID: PMC6874306

29. Medical device surveillance with electronic health records. Callahan, A., Fries, J.A., Ré, C., Huddleston, J. I., Giori, N.J., Delp, S. & Shah, N.H.npj Digital Medicine, 2(1):94. PMID: 31583282 PMCID: PMC6761113

30. Evolution of resilience in protein interactomes across the tree of life. M. Zitnik, R. Sosic, M. Feldman, J. Leskovec. Proceedings of the National Academy of Sciences (PNAS), 2019. Pubmed: 30765515 PMCID: 6410798

31. Muscle Contributions to Upper-Extremity Movement and Work From a Musculoskeletal Model of the Human Shoulder. Front Neurorobot. Seth, A., Dong, M., Matias, R., & Delp, S. PMID: 31780916 PMCID: PMC6856649


1. Multimodal teaching analytics: Automated extraction of orchestration graphs from wearable sensor data.Prieto LP, Sharma K, Kidzinski Ł, Rodríguez‐Triana MJ, Dillenbourg P. J Comput Assist Learn. 2018;34:193–203. https://doi.org/10.1111/jcal.12232. PMCID: PMC5909982 NIHMSID: NIHMS932156 PMID: 29686446

2. Large-scale analysis of disease pathways in the human interactome. Agrawal M, Zitnik M, Leskovec J. Pacific Symposium on Biocomputing, 2018. PMCID: PMC5731453

3.  “Learning to Run challenge: Synthesizing physiologically accurate motion using deep reinforcement learning“. Łukasz Kidziński, Sharada P. Mohanty, Carmichael Ong, Jennifer L. Hicks, Sean F. Carroll, Sergey Levine, Marcel Salathé, Scott L. Delp. NIPS 2017 Competition Book, Springer, 2018. PMCID: N/A

4. “Learning to Run challenge solutions: Adapting reinforcement learning methods for neuromusculoskeletal environments“. Łukasz Kidziński, Sharada Mohanty, Carmichael Ong, Zhewei Huang, Shuchang Zhou, Anton Pechenko, Adam Stelmaszczyk, Piotr Jarosik, Mikhail Pavlov, Sergey Kolesnikov, Sergey Plis, Zhibo Chen, Zhizheng Zhang, Jiale Chen, Jun Shi, Zhuobin Zheng, Chun Yuan, Zhihui Lin, Henryk Michalewski, Piotr Miłoś, Błażej Osiński, Andrew Melnik, Malte Schilling, Helge Ritter, Sean Carroll, Jennifer Hicks, Sergey Levine, Marcel Salathé, Scott Delp. NIPS 2017 Competition Book, Springer, 2018. PMCID: N/A

5.  I’ll Be Back: On the Multiple Lives of Users of a Mobile Activity Tracking Application. Z. Lin, T. Althoff, J. Leskovec. ACM International Conference on World Wide Web (WWW), 2018. PMCID: PMC5959281

6. Modeling Individual Cyclic Variation in Human Behavior. E. Pierson, T. Althoff, J.Leskovec. ACM International Conference on World Wide Web (WWW), 2018. PMCID: PMC5959299

7. Modeling Interdependent and Periodic Real-World Action Sequences. T. Kurashima, T. Althoff, J. Leskovec. ACM International Conference on World Wide Web (WWW), 2018. PMCID: PMC5959287

8. A two-pronged progress in structured dense matrixvector multiplication. De Sa C, Gu A, Puttagunta R, Ré C, Rudra A. Proc Annu ACM SIAM Symp Discret Algorithms. 2018;2018:1060–1079. PMCID: PMC6534155

9. Some methods for heterogeneous treatment effect estimation in high-dimensions  Statistics in Medicine. Scott Powers, Junyang Qian, Kenneth Jung, Alejandro Schuler, Nigam Shah, Trevor Hastie and Robert Tibshirani.January 2018. PMCID: PMC5938172

10. Paroma Varma and Christopher Ré. 2018. Snuba: automating weak supervision to label training dataProc. VLDB Endow. 12, 3 (November 2018), 223-236. DOI: https://doi.org/10.14778/3291264.3291268 PMCID: PMC6879381

11. Training Classifiers with Natural Language Explanations. Braden Hancock, Paroma Varma, Stephanie Wang, Percy Liang, C. Ré. ACL18. PMCID:6534135

12. Representation Tradeoffs for Hyperbolic Embeddings Christopher De Sa, Albert Gu, C. Ré, Frederic Sala. ICML18. PMCID: PMC6534139 NIHMSID: NIHMS993800 PMID: 31131375

13. Learning Compressed Transforms with Low Displacement Rank. Anna T. Thomas*, Albert Gu*, Tri Dao, Atri Rudra, Christopher Ré. NIPS18. PMCID: PMC6534145 NIHMSID: NIHMS993802 PMID: 31130799

14. Accelerated Stochastic Power Iteration. De Sa C, He B, Mitliagkas I, Ré C, Xu P. Proc Mach Learn Res. 2018;84:58–67. PMCID: PMC6557638 NIHMSID: NIHMS993807 PMID: 31187095

15. Acute changes in foot strike pattern and cadence affect running parameters associated with tibial stress fracturesJournal of biomechanics. Yong, J. R., Silder, A., Montgomery, K. L., Fredericson, M., Delp, S. L.2018. PMID: 29866518 DOI: 10.1016/j.jbiomech.2018.05.017. PMCID: PMC6203338

16. Exploring the Utility of Developer Exhaust. Jian Zhang, Max Lam, Stephanie Wang, Paroma Varma, Luigi Nardi, Kunle Olukotun and C. Ré. DEEM 2018. PMCID: PMC6534136 NIHMSID: NIHMS993811 PMID: 31131381

17. Snorkel MeTaL: Weak Supervision for Multi-Task Learning. Alex Ratner, Braden Hancock, Jared Dunnmon, Roger Goldman, C.Ré. DEEM 2018. PMCID: PMC6436830

18. Machine learning in human movement biomechanics: Best practices, common pitfalls, and new opportunitiesJournal of Biomechanics. Eni Halilaj, Apoorva Rajagopal, Madalina Fiterau, Jennifer L. Hicks, Trevor J. Hastie, Scott L. Delp. 8 September 2018. PMID: 30279002 DOI: 10.1016/j.jbiomech.2018.09.009 PMCID: PMC6879187

19. Physical activity is associated with changes in knee cartilage microstructureOsteoarthritis and cartilage. Halilaj, E., Hastie, T. J., Gold, G. E., Delp, S. L.2018; 26 (6): 770–74. PMID: 29605382 PMCID: PMC6086595 DOI: 10.1016/j.joca.2018.03.009

20. Modeling and Predicting Osteoarthritis Progression: Data from the Osteoarthritis InitiativeOsteoarthritis and cartilage. Halilaj, E., Le, Y., Hicks, J. L., Hastie, T. J., Delp, S. L. 2018.PMID: 30130590 PMCID: PMC6469859 [Available on 2019-12-01] DOI: 10.1016/j.joca.2018.08.003

21. Longitudinal data analysis using matrix completion. Kidziński, Łukasz,  Hastie, Trevor. eprint arXiv. September 25, 2018.

22. Estimating the effect size of surgery to improve walking in children with cerebral palsy from retrospective observational clinical data. Rajagopal A, Kidziński Ł, McGlaughlin AS, Hicks JL, Delp SL, Schwartz MH. Sci Rep. 2018 Nov 5;8(1):16344. doi: 10.1038/s41598-018-33962-2. PMID: PMC30397268 PMCID: PMC6218552

23. Network enhancement as a general method to denoise weighted biological networks. B. Wang, A. Pourshafeie, M. Zitnik, J. Zhu, C. D. Bustamante, S. Batzoglou, J Leskovec. Nature Communications. PubMed: 30082777 PMCID: 6078978

24. Communications, 2018. Prioritizing Network Communities. M. Zitnik, R. Sosic, J. Leskovec. Nature Communications. PubMed: 29959323 PMCID: 6026212

25. Modeling Polypharmacy Side Effects with Graph Convolutional Networks. M. Zitnik, M. Agrawal, J. Leskovec. Bioinformatics, 2018. PMCID: PMC6022705

26. Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. L. Mulugeta, A. Drach, A. Erdemir, C. A. Hunt, M. Horner, J. Ku, J. G. Myers, R. Vadigepalli, W. W. Lytton. Front Neuroinform. PMID: 29713272 PMCID: PMC5911506

27. Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research. Erdemir A, Hunter PJ, Holzapfel GA, Loew LM, Middleton J, Jacobs CR, Nithiarasu P, Löhner R, Wei G, Winkelstein BA, Barocas VH, Guilak F, Ku JP, Hicks JL, Delp SL, Sacks M, Weiss JA, Ateshian GA, Maas SA, McCulloch AD, Peng GCY. J Biomech Eng. 1;140(2). PMID: 29247253 PMCID: PMC5821103

28. OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement. Seth A, Hicks JL, Uchida TK, Habib A, Dembia CL, Dunne JJ, Ong CF, DeMers MS, Rajagopal A, Millard M, Hamner SR, Arnold EM, Yong JR, Lakshmikanth SK, Sherman MA, Ku JP, Delp SL. PLoS Comput Biol, 26;14(7):e1006223. PMID: 30048444 PMCID: PMC6061994


1. Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. Li X, Dunn J, Salinas D, Zhou G, Zhou W, Schussler-Forenza Rose SM, et al. PLoS Biol. 2017 Jan 12;15(1):e2001402. doi: 10.1371/journal.pbio.2001402. eCollection 2017 Jan. PubMed PMID: 28081144; PubMed Central PMCID: PMC5230763.

2. Objective measurement of free-living physical activity (performance) in lumbar spinal stenosis: are physical activity guidelines being met?. Norden J, Smuck M, Sinha A, Hu R, Tomkins-Lane C. Spine J. 2017 Jan;17(1):26-33. doi: 10.1016/j.spinee.2016.10.016. PubMed PMID: 27793759. PubMed Central PMCID: PMC5732871

3. Preparatory co-activation of the ankle muscles may prevent ankle inversion injuries. DeMers, M.S., Hicks, J.L., Delp, S.L. Journal of Biomechanics, Vol. 53, 17-23, 2017. PMCID: PMC5798431.

4. Online Actions with Offline Impact: How Online Social Networks Influence Online and Offline User Behavior. Althoff T, Jindal P, Leskovec J. Proc Int Conf Web Search Data Min. 2017 Feb;2017:537-546. doi: 10.1145/3018661.3018672. Epub 2017 Feb 2. PubMed PMID: 28345078; PubMed Central PMCID: PMC5361221.

5. SnapVX: A Network-Based Convex Optimization Solver. Hallac D, Wong C, Diamond S, Sosic R, Boyd S, et al. Journal of machine learning research:JMLR. PMCID: PMC5870756

6. Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking. Jackson, R.W., Dembia, C.L., Delp, S.L., Collins, S.H. Journal of Experimental Biology, 2017. PMCID: PMC6514464

7. Physical performance analysis: A new approach to assessing free-living physical activity in musculoskeletal pain and mobility-limited populations. Smuck M, Tomkins-Lane C, Ith MA, Jarosz R, Kao MJ. PLoS One. 2017 Feb 24;12(2):e0172804. doi: 10.1371/journal.pone.0172804. PubMed PMID: 28235039; PubMed Central PMCID: PMC5325560.

8. How Gamification Affects Physical Activity: Large-scale Analysis of Walking Challenges in a Mobile Application. Shameli A, Althoff T, Saberi A, Leskovec J. ACM International Conference on World Wide Web (WWW), 2017. PMCID: PMC5627651

9. Ensuring Rapid Mixing and Low Bias for Asynchronous Gibbs Sampling. De Sa C, Olukotun K, Re C. JMLR Workshop Conf Proc. 2016;48:1567-1576. PubMed PMID: 28344730; PubMed Central PMCID: PMC5360990.

10. Large-scale physical activity data reveal worldwide activity inequality. Althoff T, Sosič R, Hicks JL, King AC, Delp SL, Leskovec J. Nature. 2017 Jul 10. doi: 10.1038/nature23018. [Epub ahead of print] PubMed PMID: 28693034 PMCID: PMC5774986

11. Snorkel: Rapid Training Data Creation with Weak Supervision. Alex Ratner, Stephen Bach, Henry Ehrenberg, Jason Fries, Sen Wu, C. Ré. VLDB 18. PMCID: PMC5951191

12. Fonduer: Knowledge Base Construction from Richly Formatted Data. Sen Wu, Luke Hsiao, […], and Christopher Ré. SIGMOD 18. PMCID: PMC6013301

13. Anyone Can Become a Troll: Causes of Trolling Behavior in Online Discussions. J. Cheng, M. Bernstein, C. Danescu-Niculescu-Mizil, J. Leskovec. Computer-Supported Cooperative Work and Social Computing (CSCW), 2017. Best paper award. PMCID: PMC5791909. 

14. Population-Scale Pervasive Health Tim Althoff IEEE Pervasive Computing Year: 2017, Volume: 16, Issue: 4 Pages: 75 – 79 IEEE Journals & Magazines. PMCID: PMC5951162

15. Understanding and Optimizing Asynchronous Low-Precision Stochastic Gradient Descent. C. De Sa, Matt Feldman, C. Ré, Kunle Olukotun. ISCA 2017. PMCID: PMC5789782. 

16. Human Decisions and Machine Predictions. J. Kleinberg, H. Lakkaraju, J. Leskovec, J. Ludwig, S. Mullainathan. Quarterly Journal of Economics, 2017. PMCID: PMC5947971

17. Predicting multicellular function through multi-layer tissue networks. M. Zitnik, J. Leskovec.Bioinformatics, 33 (14): i190-i198, 2017. PMID: 28881986 PMCID: PMC5870717 

18. Local Higher-Order Graph Clustering. H. Yin, A. Benson, D. Gleich, J. Leskovec. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2017.PMCID: PMC5951164

19. The Selective Labels Problem: Evaluating Algorithmic Predictions in the Presence of Unobservables. H. Lakkaraju, J. Kleinberg, J. Leskovec, J. Ludwig, S. Mullainathan. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2017. PMCID: PMC5958915

20. Toeplitz Inverse Covariance-Based Clustering of Multivariate Time Series Data. D. Hallac, S. Vare, S. Boyd, J. Leskovec. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2017. Best paper runner-up. PMCID: PMC5951184

21. Network Inference via the Time-Varying Graphical Lasso. D. Hallac, Y. Park, S. Boyd, J. Leskovec.ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), 2017. PMCID: PMC5951186

22. Loyalty in Online Communities. W. Hamilton, J. Zhang, C. Danescu-Niculescu-Mizil, D. Jurafsky, J. Leskovec. AAAI International Conference on Weblogs and Social Media (ICWSM), 2017. PMCID: PMC5774975

23. Citizen science applied to building healthier community environments: Advancing the field through shared construct and measurement development. Hinckson E, Schneider M, Winter S, Stone E, Puhan M, Stathi A, Porter MM, Gardiner PA, Lopes dos Santos D, Wolff, King AC. (In press). IJBNPA [the International Journal of Behavioral Nutrition and Physical Activity]. PubMed Central PMCID: PMC5622546

24. Learning the Structure of Generative Models without Labeled DataStephen H. Bach, Bryan He, Alex Ratner, C. Ré. ICML 2017. PMCID: PMC6417840

25. Inferring Generative Model Structure with Static Analysis. Paroma Varma, Bryan He, Payal Bajaj, C. Ré, NIPS2017. PMCID: PMC5789796. 

26. Learning to Compose Domain-Specific Transformations for Data Augmentation. A. Ratner, H. Ehrenberg, Z. Hussain, J. Dunnmon, C. Ré, NIPS2017. PMCID: PMC5786274

27. Objective measurement of function following lumbar spinal stenosis decompression reveals improved functional capacity with stagnant real-life physical activity. Smuck M, Muaremi A, Zheng P, Norden J, Sinha A, Hu R, Tomkins-Lane C. Spine J. 2017 Sep 26. pii: S1529-9430(17)30979-8. doi: 10.1016/j.spinee.2017.08.262. [Epub ahead of print] PMID: 28962914 PMCID: PMC5732871

28. Gaussian Quadrature for Kernel Features. Tri Dao, Chris De Sa, C. Ré, NIPS2017. Spotlight.PMCID: PMC5791159

29. Weighted SGD for lp regression with Randomized Preconditioning. Jiyan Yang, Yin-Lam Chow, C. Ré, and Michael Mahoney. JMLR 17. PMCID: PMC5959301

30. Community Identity and User Engagement in a Multi-Community Landscape. J. Zhang, W. Hamilton, C. Danescu-Niculescu-Mizil, D. Jurafsky, J. Leskovec. AAAI International Conference on Weblogs and Social Media (ICWSM), 2017. PMCID: PMC5774974

31. Learning the Network Structure of Heterogeneous Data via Pairwise Exponential Markov Random Fields. Y. Park, D. Hallac, S. Boyd, J. Leskovec. Artificial Intelligence and Statistics Conference (AISTATS), 2017. PMCID: PMC6436845

32. Network Analysis: A novel Method for Mapping Neonatal Acute Transport Patterns in California. S.N. Kunz, J.A.F. Zupancic, J. Rigdon, C.S. Phibbs, H.C. Lee, J.B. Gould, J. Leskovec, J. Profit. Journal of Perinatology, 2017. PubMed Central PMCID: PMC5446293

33. ShortFuse: Biomedical Time Series Representations in the Presence of Structured Information. Madalina Fiterau, Suvrat Bhooshan, Jason Fries, Charles Bournhonesque, Jennifer Hicks, Eni Halilaj, Christopher Ré and Scott Delp. 3rd Conference on Machine Learning for Healthcare, MLHC 2017. PMCID: PMC6417829


1. Scan Order in Gibbs Sampling: Models in Which it Matters and Bounds on How Much. He B, De Sa C, Mitliagkas I, Re C. Adv Neural Inf Process Syst. 2016;29. pii: 6589. PubMed PMID: 28344429; PubMed Central PMCID: PMC5361064.

2. DeepDive: Declarative Knowledge Base Construction. De Sa C, Ratner A, Re C, Shin J, Wang F, et al. SIGMOD Rec. 2016 Mar;45(1):60-67. Epub 2016 Feb 6. PubMed PMID: 28344371; PubMed Central PMCID: PMC5361060.

3. The Use of Behavior Change Techniques and Theory in Technologies for Cardiovascular Disease Prevention and Treatment in Adults: A Comprehensive Review.  Winter SJ, Sheats JL, King AC. Prog Cardiovasc Dis. 2016 May-Jun;58(6):605-12. doi: 10.1016/j.pcad.2016.02.005. Epub 2016 Feb 20. Review. PubMed PMID: 26902519; PubMed Central PMCID: PMC4868665.

4. Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running. Uchida TK, Hicks JL, Dembia CL, Delp SL. PLoS One. 2016 Mar 1;11(3):e0150378. doi: 10.1371/journal.pone.0150378. eCollection 2016. PubMed PMID: 26930416; PubMed Central PMCID: PMC4773147.

5. CVXPY: A Python-Embedded Modeling Language for Convex Optimization. Diamond S, Boyd S. J Mach Learn Res. 2016 Apr;17. pii: 83. PubMed PMID: 27375369; PubMed Central PMCID: PMC4927437.

6. Growing Wikipedia Across Languages via Recommendation. Wulczyn E, West R, Zia L, Leskovec J. Proc Int World Wide Web Conf. 2016 Apr;2016:975-985. PubMed PMID: 27819073; PubMed Central PMCID: PMC5092237.

7. Large-scale Analysis of Counseling Conversations: An Application of Natural Language Processing to Mental Health. Althoff T, Clark K, Leskovec J. Trans Assoc Comput Linguist. 2016;4:463-476. PubMed PMID: 28344978; PubMed Central PMCID: PMC5361062.

8. Leveraging Citizen Science and Information Technology for Population Physical Activity Promotion. King AC, Winter SJ, Sheats JL, Rosas LG, Buman MP, Salvo D, Rodriguez NM, Seguin RA, Moran M, Garber R, Broderick B, Zieff SG, Sarmiento OL, Gonzalez SA, Banchoff A, Dommarco JR. Transl J Am Coll Sports Med. 2016 May 15;1(4):30-44. PubMed PMID: 27525309; PubMed Central PMCID: PMC4978140.

9. EmptyHeaded: A Relational Engine for Graph Processing. Aberger CR, Tu S, Olukotun K, Ré C. Proc ACM SIGMOD Int Conf Manag Data. 2016 Jun-Jul;2016:431-446. doi: 10.1145/2882903.2915213. PubMed PMID: 28077912; PubMed Central PMCID: PMC5221635.

10. Effects of Three Motivationally Targeted Mobile Device Applications on Initial Physical Activity and Sedentary Behavior Change in Midlife and Older Adults: A Randomized Trial. King AC, Hekler EB, Grieco LA, Winter SJ, Sheats JL, Buman MP, Banerjee B, Robinson TN, Cirimele J. PLoS One. 2016 Jun 28;11(6):e0156370. doi: 10.1371/journal.pone.0156370. eCollection 2016. Erratum in: PLoS One. 2016;11(7):e0160113. PubMed PMID: 27352250; PubMed Central PMCID: PMC4924838.

11. Extracting Databases from Dark Data with DeepDive. Zhang C, Cafarella M, Niu F, Re C, Shin J. Proc ACM SIGMOD Int Conf Manag Data. 2016 Jun-Jul;2016:847-859. doi: 10.1145/2882903.2904442. PubMed PMID: 28316365; PubMed Central PMCID: PMC5350112.

12. Higher-order organization of complex networks. Benson AR, Gleich DF, Leskovec J. Science. 2016 Jul 8;353(6295):163-6. doi: 10.1126/science.aad9029. PubMed PMID: 27387949; PubMed Central PMCID: PMC5133458.

13. node2vec: Scalable Feature Learning for Networks. Grover A, Leskovec J. KDD. 2016 Aug;2016:855-864. PubMed PMID: 27853626; PubMed Central PMCID: PMC5108654.

14. Interpretable Decision Sets: A Joint Framework for Description and Prediction. Lakkaraju H, Bach SH, Leskovec J.  KDD. 2016 Aug;2016:1675-1684. PubMed PMID: 27853627; PubMed Central PMCID: PMC5108651.

15. Large-scale extraction of gene interactions from full-text literature using DeepDive. Mallory EK, Zhang C, Ré C, Altman RB. Bioinformatics. 2016 Jan 1;32(1):106-13. doi: 10.1093/bioinformatics/btv476. Epub 2015 Sep 3. PubMed PMID:26338771; PubMed Central PMCID: PMC4681986.

16. Bias correction in species distribution models: pooling survey and collection data for multiple species. Methods in ecology and evolution / British Ecological Society. NIHMSID: 723170. PMID: 27840673. PMCID: PMC5102514

17. SNAP: A General Purpose Network Analysis and Graph Mining Library. Leskovec J, Sosic R. ACM Trans Intell Syst Technol. 2016 Oct;8(1). pii: 1. doi: 10.1145/2898361. Epub 2016 Oct 3. PubMed PMID: 28344853; PubMed Central PMCID: PMC5361061.

18. Inducing Domain-Specific Sentiment Lexicons from Unlabeled Corpora. Hamilton W, Leskovec J, Jurafasky D. Proc Conf Empir Methods Nat Lang Process. 2016 Nov;2016:595-605. doi: 10.18653/v1/D16-1057. PubMed PMID: 28660257; PubMed Central PMCID: PMC5483533.

19. Cultural Shift or Linguistic Drift? Comparing Two Computational Measures of Semantic Change. Hamilton W, Leskovec J, Jurafsky D. Proc Conf Empir Methods Nat Lang Process. 2016 Nov;2016:2116-2121. PubMed PMID: 28580459; PubMed Central PMCID: PMC5452980.

20. Data Programming: Creating Large Training Sets, Quickly. Ratner A, De Sa C, Wu S, Selsam D, Re C. NIPS 2016. PMCID: PMC5985238 NIHMSID: NIHMS961532 PMID: 29872252

21. Gait Biomechanics in the Era of Data Science. Ferber, R., Osis, S., Hicks, J., Delp, S. Journal of biomechanics. PMCID: PMC5407492 NIHMSID: NIHMS825844 PMID: 27814971

22. Full-Body Musculoskeletal Model for Muscle-Driven Simulation of Human Gait. Rajagopal A, Dembia CL, DeMers MS, Delp DD, Hicks JL, Delp SL. IEEE Trans Biomed Eng. 2016 Oct;63(10):2068-79. doi: 10.1109/TBME.2016.2586891. Epub 2016 Jul 7. PMID: 27392337 PMCID: PMC5507211


1. Donor Retention in Online Crowdfunding Communities: A Case Study of DonorsChoose.org. Althoff T, Leskovec J. Proc Int World Wide Web Conf. 2015 May;2015:34-44. PubMed PMID: 27077139; PubMed Central PMCID: PMC4827627.

2. Caffe con Troll: Shallow Ideas to Speed Up Deep Learning. Hadjis S, Abuzaid F, Zhang C, Ré C. Proc Fourth Workshop Data Anal Scale Danac 2015 (2015). 2015 May-Jun;2015. pii: 2. PubMed PMID: 27314106; PubMed Central PMCID: PMC4906251.

3. Ringo: Interactive Graph Analytics on Big-Memory Machines.  Perez Y, Sosič R, Banerjee A, Puttagunta R, Raison M, Shah P, Leskovec J. Proc ACM SIGMOD Int Conf Manag Data. 2015 May-Jun;2015:1105-1110. PubMed PMID: 27081215; PubMed Central PMCID: PMC4829061.

4. Making a meaningful impact: modelling simultaneous frictional collisions in spatial multibody systems. Uchida TK, Sherman MA, Delp SL. Proc Math Phys Eng Sci. 2015 May 8;471(2177):20140859. PubMed PMID: 27547093; PubMed Central PMCID: PMC4984984.

5. A Database Framework for Classifier Engineering.  Kimelfeld B, Ré C. CEUR Workshop Proc. 2015 May;1378. pii: http://ceur-ws.org/Vol-1378/AMW_2015_paper_1.pdf. Epub 2015 Jun 11. PubMed PMID: 27274719; PubMed Central PMCID: PMC4891810.

6. Incremental Knowledge Base Construction Using DeepDive.  Shin J, Wu S, Wang F, De Sa C, Zhang C, Ré C. Proceedings VLDB Endowment. 2015 Jul;8(11):1310-1321. PubMed PMID: 27144081; PubMed Central PMCID: PMC4852149.

7. Network Lasso: Clustering and Optimization in Large Graphs.Hallac D, Leskovec J, Boyd S.KDD. 2015 Aug;2015:387-396. PubMed PMID: 27398260; PubMed Central PMCID: PMC4937836.

8. The mobilize center: an NIH big data to knowledge center to advance human movement research and improve mobility. Ku JP, Hicks JL, Hastie T, Leskovec J, Ré C, Delp SL. J Am Med Inform Assoc. 2015 Nov;22(6):1120-5. doi:10.1093/jamia/ocv071. Epub 2015 Aug 13. PubMed PMID: 26272077; PubMed Central PMCID: PMC4639715.

9. Mindtagger: A Demonstration of Data Labeling in Knowledge Base Construction.  Shin J, Ré C, Cafarella M. Proceedings VLDB Endowment. 2015 Aug;8(12):1920-1923. PubMed PMID: 27144082; PubMed Central PMCID: PMC4852148.

10. Tensor Spectral Clustering for Partitioning Higher-order Network Structures. Benson A, Gleich D, Leskovec J. Proc SIAM Int Conf Data Min. 2015;2015:118-126. PubMed PMID: 27812399; PubMed Central PMCID: PMC5089081.

11. Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width. De Sa C, Zhang C, Olukotun K, Ré C. Adv Neural Inf Process Syst. 2015 Dec;28:3079-3087. PubMed PMID: 27279724; PubMed Central PMCID: PMC4894721.

12. Taming the Wild: A Unified Analysis of Hogwild!-Style Algorithms. De Sa C, Zhang C, Olukotun K, Ré C. Adv Neural Inf Process Syst. 2015 Dec;28:2656-2664. PubMed PMID: 27330264; PubMed Central PMCID: PMC4907892.