David Carlson | Scholars@Duke

David Carlson
Assistant Professor of Civil and Environmental Engineering

Current Research Interests

Machine learning, predictive modeling, health data science, statistical neuroscience

Current Appointments & Affiliations

Assistant Professor of Civil and Environmental Engineering, Civil and Environmental Engineering, Pratt School of Engineering 2017
Assistant Professor - Track V in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2017
Assistant Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2018
Assistant Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2018
Member of the Duke Clinical Research Institute, Duke Clinical Research Institute, Institutes and Centers 2017

Contact Information

Hudson Hall 165, 100 Science Dr, Durham, NC 27708
david.carlson@duke.edu (919) 660-5421

Background
Education, Training, & Certifications
- Ph.D., Duke University 2015
Recognition
In the News
- JAN 9, 2018 Duke Research Blog
  
  David Carlson: Engineering and Machine Learning for Better Medicine
- AUG 24, 2017 Pratt School of Engineering
  
  David Carlson: Generating Scientific Understanding from Machine Learning
Research
Selected Grants
- Dissecting and modifying temporal dynamics underlying major depressive disorder awarded by National Institutes of Health 2019 - 2024
- Duke University Program in Environmental Health awarded by National Institutes of Health 2013 - 2024
- Developing a comprehensive model for peripheral nerve stimulation of gastrointestinal function awarded by National Institutes of Health 2019 - 2023
- Network Dynamics of Negative and Positive Valence Systems in Decision Making awarded by National Institutes of Health 2019 - 2023
- Uncovering Population-Level Cellular Relationships to Behavior via Mesoscale Networks awarded by National Institutes of Health 2019 - 2022
- The neurophysiology of impulsive sensation seeking awarded by University of Pittsburgh 2018 - 2020
- Enabling Stress Resistance awarded by National Institutes of Health 2012 - 2018
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Zheng, T., M. H. Bergin, R. Sutaria, S. N. Tripathi, R. Caldow, and D. E. Carlson. “Gaussian process regression model for dynamically calibrating and surveilling a wireless low-cost particulate matter sensor network in Delhi.” Atmospheric Measurement Techniques 12, no. 9 (September 26, 2019): 5161–81. https://doi.org/10.5194/amt-12-5161-2019.
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  - Norris, Christina, Lin Fang, Karoline K. Barkjohn, David Carlson, Yinping Zhang, Jinhan Mo, Zhen Li, et al. “Sources of volatile organic compounds in suburban homes in Shanghai, China, and the impact of air filtration on compound concentrations..” Chemosphere 231 (September 2019): 256–68. https://doi.org/10.1016/j.chemosphere.2019.05.059.
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  - Carlson, David, and Lawrence Carin. “Continuing progress of spike sorting in the era of big data..” Current Opinion in Neurobiology 55 (April 2019): 90–96. https://doi.org/10.1016/j.conb.2019.02.007.
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  - Zheng, T., M. H. Bergin, K. K. Johnson, S. N. Tripathi, S. Shirodkar, M. S. Landis, R. Sutaria, and D. E. Carlson. “Field evaluation of low-cost particulate matter sensors in high-and low-concentration environments.” Atmospheric Measurement Techniques 11, no. 8 (August 22, 2018): 4823–46. https://doi.org/10.5194/amt-11-4823-2018.
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  - Goldstein, Benjamin A., David Carlson, and Nrupen A. Bhavsar. “Subject Matter Knowledge in the Age of Big Data and Machine Learning..” Jama Netw Open 1, no. 4 (August 3, 2018). https://doi.org/10.1001/jamanetworkopen.2018.1568.
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  - Hultman, Rainbo, Kyle Ulrich, Benjamin D. Sachs, Cameron Blount, David E. Carlson, Nkemdilim Ndubuizu, Rosemary C. Bagot, et al. “Brain-wide Electrical Spatiotemporal Dynamics Encode Depression Vulnerability..” Cell 173, no. 1 (March 22, 2018): 166-180.e14. https://doi.org/10.1016/j.cell.2018.02.012.
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  - Vu, Mai-Anh T., Tülay Adalı, Demba Ba, György Buzsáki, David Carlson, Katherine Heller, Conor Liston, et al. “A Shared Vision for Machine Learning in Neuroscience..” J Neurosci 38, no. 7 (February 14, 2018): 1601–7. https://doi.org/10.1523/JNEUROSCI.0508-17.2018.
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  - Carlson, David, Lisa K. David, Neil M. Gallagher, Mai-Anh T. Vu, Matthew Shirley, Rainbo Hultman, Joyce Wang, et al. “Dynamically Timed Stimulation of Corticolimbic Circuitry Activates a Stress-Compensatory Pathway..” Biol Psychiatry 82, no. 12 (December 15, 2017): 904–13. https://doi.org/10.1016/j.biopsych.2017.06.008.
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  - Gallagher, Neil, Kyle R. Ulrich, Austin Talbot, Kafui Dzirasa, Lawrence Carin, and David E. Carlson. “Cross-Spectral Factor Analysis..” Edited by Isabelle Guyon, Ulrike von Luxburg, Samy Bengio, Hanna M. Wallach, Rob Fergus, S. V. N. Vishwanathan, and Roman Garnett. Nips, 2017, 6845–55.
  - Lee, J. H., D. Carlson, H. Shokri, W. Yao, G. Goetz, E. Hagen, E. Batty, E. J. Chichilnisky, G. Einevoll, and L. Paninski. “YASS: Yet another spike sorter.” Advances in Neural Information Processing Systems 2017-December (January 1, 2017): 4003–13.
  - Li, Yitong, Michael Murias, Samantha Major, Geraldine Dawson, Kafui Dzirasa, Lawrence Carin, and David E. Carlson. “Targeting EEG/LFP Synchrony with Neural Nets..” Edited by Isabelle Guyon, Ulrike von Luxburg, Samy Bengio, Hanna M. Wallach, Rob Fergus, S. V. N. Vishwanathan, and Roman Garnett. Nips, 2017, 4623–33.
  - Hultman, Rainbo, Stephen D. Mague, Qiang Li, Brittany M. Katz, Nadine Michel, Lizhen Lin, Joyce Wang, et al. “Dysregulation of Prefrontal Cortex-Mediated Slow-Evolving Limbic Dynamics Drives Stress-Induced Emotional Pathology..” Neuron 91, no. 2 (July 20, 2016): 439–52. https://doi.org/10.1016/j.neuron.2016.05.038.
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  - Merel, Josh, David Carlson, Liam Paninski, and John P. Cunningham. “Neuroprosthetic Decoder Training as Imitation Learning..” Plos Computational Biology 12, no. 5 (May 18, 2016). https://doi.org/10.1371/journal.pcbi.1004948.
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  - Carlson, D., Y. P. Hsieh, E. Collins, L. Carin, and V. Cevher. “Stochastic Spectral Descent for Discrete Graphical Models.” Ieee Journal on Selected Topics in Signal Processing 10, no. 2 (March 1, 2016): 296–311. https://doi.org/10.1109/JSTSP.2015.2505684.
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  - Gan, Z., C. Li, R. Henao, D. Carlson, and L. Carin. “Deep temporal sigmoid belief networks for sequence modeling.” Advances in Neural Information Processing Systems 2015-January (January 1, 2015): 2467–75.
  - Carlson, David E., Joshua T. Vogelstein, Joshua T. Qisong Wu, Joshua T. Wenzhao Lian, Joshua T. Mingyuan Zhou, Colin R. Stoetzner, Daryl Kipke, Douglas Weber, David B. Dunson, and Lawrence Carin. “Multichannel electrophysiological spike sorting via joint dictionary learning and mixture modeling..” Ieee Transactions on Bio Medical Engineering 61, no. 1 (January 2014): 41–54. https://doi.org/10.1109/tbme.2013.2275751.
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  - Wang, L., D. E. Carlson, M. R. D. Rodrigues, R. Calderbank, and L. Carin. “A bregman matrix and the gradient of mutual information for vector poisson and gaussian channels.” Ieee Transactions on Information Theory 60, no. 5 (January 1, 2014): 2611–29. https://doi.org/10.1109/TIT.2014.2307068.
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  - Karumbaiah, Lohitash, Tarun Saxena, David Carlson, Ketki Patil, Radhika Patkar, Eric A. Gaupp, Martha Betancur, Garrett B. Stanley, Lawrence Carin, and Ravi V. Bellamkonda. “Relationship between intracortical electrode design and chronic recording function..” Biomaterials 34, no. 33 (November 2013): 8061–74. https://doi.org/10.1016/j.biomaterials.2013.07.016.
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  - Carlson, D., V. Rao, J. Vogelstein, and L. Carin. “Real-time inference for a gamma process model of neural spiking.” Advances in Neural Information Processing Systems, January 1, 2013.
  - Wang, L., D. Carlson, M. D. Rodrigues, D. Wilcox, R. Calderbank, and L. Carin. “Designed measurements for vector count data.” Advances in Neural Information Processing Systems, January 1, 2013.
  - Chen, Minhua, David Carlson, Aimee Zaas, Christopher W. Woods, Geoffrey S. Ginsburg, Alfred Hero, Joseph Lucas, and Lawrence Carin. “Detection of viruses via statistical gene expression analysis..” Ieee Trans Biomed Eng 58, no. 3 (March 2011): 468–79. https://doi.org/10.1109/TBME.2010.2059702.
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- Conference Papers
  - Li, Y., M. Murias, S. Major, G. Dawson, and D. E. Carlson. “Extracting relationships by multi-domain matching.” In Advances in Neural Information Processing Systems, 2018-December:6798–6809, 2018.
  - Li, Y., M. R. Min, D. Shen, D. Carlson, and L. Carin. “Video generation from text.” In 32nd Aaai Conference on Artificial Intelligence, Aaai 2018, 7065–72, 2018.
  - Liang, K. J., G. Heilmann, C. Gregory, S. O. Diallo, D. Carlson, G. P. Spell, J. B. Sigman, K. Roe, and L. Carin. “Automatic threat recognition of prohibited items at aviation checkpoint with x-ray imaging: A deep learning approach.” In Proceedings of Spie the International Society for Optical Engineering, Vol. 10632, 2018. https://doi.org/10.1117/12.2309484.
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  - Gallagher, N. M., K. Ulrich, A. Talbot, K. Dzirasa, L. Carin, and D. E. Carlson. “Cross-spectral factor analysis.” In Advances in Neural Information Processing Systems, 2017-December:6843–53, 2017.
  - Li, Y., M. Murias, S. Major, G. Dawson, K. Dzirasa, L. Carin, and D. E. Carlson. “Targeting EEG/LFP synchrony with neural nets.” In Advances in Neural Information Processing Systems, 2017-December:4621–31, 2017.
  - Pakman, A., D. Gilboa, D. Carlson, and L. Paninski. “Stochastic bouncy particle sampler.” In 34th International Conference on Machine Learning, Icml 2017, 6:4186–4208, 2017.
  - Carlson, D. E., P. Stinson, A. Pakman, and L. Paninski. “Partition functions from rao-blackwellized tempered sampling.” In 33rd International Conference on Machine Learning, Icml 2016, 6:4248–62, 2016.
    Open Access Copy
  - Chen, C., D. Carlson, Z. Gan, C. Li, and L. Carin. “Bridging the gap between stochastic gradient MCMC and stochastic optimization.” In Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, Aistats 2016, 1051–60, 2016.
  - Kaganovsky, Y., I. Odinaka, D. Carlson, and L. Carin. “Parallel majorization minimization with dynamically restricted domains for nonconvex optimization.” In Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, Aistats 2016, 1497–1505, 2016.
  - Li, C., C. Chen, D. Carlson, and L. Carin. “Preconditioned stochastic gradient langevin dynamics for deep neural networks.” In 30th Aaai Conference on Artificial Intelligence, Aaai 2016, 1788–94, 2016.
  - Song, Z., R. Henao, D. Carlson, and L. Carin. “Learning sigmoid belief networks via monte carlo expectation maximization.” In Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, Aistats 2016, 2016.
  - Carlson, D. E., E. Collins, Y. P. Hsieh, L. Carin, and V. Cevher. “Preconditioned spectral descent for deep learning.” In Advances in Neural Information Processing Systems, 2015-January:2971–79, 2015.
  - Carlson, D., V. Cevher, and L. Carin. “Stochastic spectral descent for restricted boltzmann machines.” In Journal of Machine Learning Research, 38:111–19, 2015.
  - Gan, Z., C. Chen, R. Henao, D. Carlson, and L. Carin. “Scalable deep Poisson factor analysis for topic modeling.” In 32nd International Conference on Machine Learning, Icml 2015, 3:1823–32, 2015.
  - Gan, Z., R. Henao, D. Carlson, and L. Carin. “Learning deep sigmoid belief networks with data augmentation.” In Journal of Machine Learning Research, 38:268–76, 2015.
  - Gan, Zhe, Chunyuan Li, Ricardo Henao, David E. Carlson, and Lawrence Carin. “Deep Temporal Sigmoid Belief Networks for Sequence Modeling..” In Nips, edited by Corinna Cortes, Neil D. Lawrence, Daniel D. Lee, Masashi Sugiyama, and Roman Garnett, 2467–75, 2015.
  - Ulrich, K., D. E. Carlson, K. Dzirasa, and L. Carin. “GP kernels for cross-spectrum analysis.” In Advances in Neural Information Processing Systems, 2015-January:1999–2007, 2015.
  - Carlson, D. E., J. S. Borg, K. Dzirasa, and L. Carin. “On the relationship between LFP & spiking data.” In Advances in Neural Information Processing Systems, 3:2060–68, 2014.
  - Carlson, David E., Jana Schaich Borg, Kafui Dzirasa, and Lawrence Carin. “On the relations of LFPs & Neural Spike Trains..” In Nips, edited by Zoubin Ghahramani, Max Welling, Corinna Cortes, Neil D. Lawrence, and Kilian Q. Weinberger, 2060–68, 2014.
  - Hu, C., E. Ryu, D. Carlson, Y. Wang, and L. Carin. “Latent Gaussian models for topic modeling.” In Journal of Machine Learning Research, 33:393–401, 2014.
  - Ulrich, K., D. E. Carlson, W. Lian, J. S. Borg, K. Dzirasa, and L. Carin. “Analysis of brain states from multi-region LFP time-series.” In Advances in Neural Information Processing Systems, 3:2483–91, 2014.
Teaching & Mentoring
Recent Courses

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Education, Training, & Certifications

In the News

Selected Grants

Selected Publications

Academic Articles

Conference Papers

Recent Courses