Orienting to a novel event is a rapid shift in attention to a change in one’s surroundings that appears to be a fundamental biological mechanism for survival and essentially functions as a “what is it” detector. Orienting appears to play a central role in human learning and development, as it facilitates adaptation to an ever-changing environment. Thus, orienting can be viewed as an allocational mechanism in which attention sifts through the complex multi-sensory world and selects relevant stimuli for further processing. The selection of stimuli for further processing has implications for what will be encoded into memories and how strong those memory traces will be. The ability to differentiate between relevant and irrelevant input, to inhibit the processing of irrelevant stimuli, and to sustain attention requires control, and inhibitory processes that improve with age.

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We aim to augment recovery in spinal cord (SC) injured patients. Electrical stimulation of the SC can facilitate recovery, but the mechanisms are not yet understood. One knowledge gap lies in the exact pathways that are recruited by stimulation. To close this gap, we have tested the effects of SC stimulation in people undergoing clinically indicated surgery. By testing the distribution and size of muscle responses to SC stimulation, we can infer which circuits are activated. We are also examining how SC injury changes those responses. We propose to use Bayesian methods to understand the interaction between muscle responses to stimulation and the MRI indicated pattern of damage. The project will involve construction of models linking multiple data modalities that predict muscle activity, followed by the modification of these models to account for patterns of damage. Construction of such models would enable a deeper understanding of SC stimulation leading to more effective stimulation paradigms.

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Our goal is to use deep learning networks to understand which neurons in the brain encode fine motor movements in mice. We collected large datasets entailing calcium imaging data of active neurons and high-resolution videos when mice perform motor tasks. We want to use recent advances in deep learning to (1) estimate the poses of mouse body parts at a high spatiotemporal resolution (2) extract behaviorally-relevant information and (3) align them with neural activity data. Behavioral video analysis is made possible by transfer learning, the ability to take a network that was trained on a task with a large supervised dataset and utilize it on a small supervised dataset. This has been used e.g. in a human pose–estimation algorithm called DeeperCut. Recently, such algorithms were tailored for use in the laboratory in a Python-based toolbox known as DeepLabCut, providing a tool for high-throughput behavioral video analysis.

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42% of New York City greenhouse gas emissions result from on-site fossil fuel combustion in residential and commercial buildings; space heating is, by far, the majority contributor. Both New York State and NYC have policies to dramatically reduce emissions that will require a transformation in the way buildings are heated, including major efforts in existing buildings. This transition is inextricably linked to existing energy equity issues that we believe significantly overlap across NYC (and elsewhere). These include unreliable heating in the winter, susceptibility to extreme heat (an increasing occurrence with climate change) and struggles to afford energy needs. Various known data sources for NYC are available, though they are disparate and have not been analyzed holistically. Further, we believe there are potential engineering and policy solutions to these challenges. In this project, the DSI scholar will access (and search for where not yet known to qSEL researchers) relevant data sets, analyze those data sets to identify communities exposed to all or a subset of these issues, and assist qSEL researchers in developing models to evaluate possible solutions. The project has the possibility of extending through Summer 2020, subject to fundraising efforts and the success of the Spring 2020 project.

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The function for much of the 3 billion letters in the human genome remain to be understood. Advances in DNA sequencing technology have generated enormous amount of data, yet we don’t have the tool to extract rules of how the genome works. Deep learning holds great potential in decoding the genome, in particular due to the digital nature of DNA sequences and the ability to handle large data sets. However, like many other applications, the interpretability of deep learning models hampers its ability to help understand the genome. We are developing deep learning architectures embedded with the principles of gene regulation and we will be leveraging billions of existing measurements of gene activity to learn a mechanistic model of gene regulation in human cells.

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This project will be focused on creating a deep learning framework for tracking individual molecules and proteins as they move within a cell under various conditions. Using total internal reflection (TIRF) microscopy, we have accumulated more than 10 million trajectories over dozens of experimental preparations with differences in both the imaging approaches as well as the biological context. In our experiments we have captured particles under a wide variety of conditions including increased protein expression level, and a range of drug concentrations. Our biggest challenge is being able to stably track the movement of a particle as it passes by other particles or groups of particles, and to do this in a way that generalizes over novel conditions. The Data Science Institute Scholar chosen for this project would work with scientists in the Javitch laboratory and others across the Columbia campus to conceive of an approach for efficiently and effectively tracking particles. The resulting work would be of great interest to an increasing number of scientists working in this field who currently rely on methods based on feature engineering that are often inaccurate or inflexible compared to modern deep learning methods.

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Columbia Data Science Institute (DSI) Scholars Program

The DSI Scholars Program is to engage and support undergraduate and master students in participating data science related research with Columbia faculty. The program’s unique enrichment activities will foster a learning and collaborative community in data science at Columbia.

Columbia University DSI

New York, NY