Visual Dynamics Models for Robotic Planning and Control

For a robot to interact with its environment, it must perceive the world and understand how the world evolves as a consequence of its actions. This thesis studies a few methods that a robot can use to respond to its observations, with a focus on instances that can leverage visual dynamic models. In general, these are models of how the visual observations of a robot evolves as a consequence of its actions. This could be in the form of predictive models that directly predict the future in the space of image pixels, in the space of visual features extracted from these images, or in the space of compact learned latent representations. The three instances that this thesis studies are in the context of visual servoing, visual planning, and representation learning for reinforcement learning. In the first case, we combine learned visual features with learning single-step predictive dynamics models and reinforcement learning to learn visual servoing mechanisms. In the second case, we use a deterministic multi-step video prediction model to achieve various manipulation tasks through visual planning. In addition, we show that conventional video prediction models are unequipped to model uncertainty and multiple futures, which could limit the planning capabilities of the robot. To address this, we propose a stochastic video prediction model that is trained with a combination of variational losses, adversarial losses, and perceptual losses, and show that this model can predict futures that are more realistic, diverse, and accurate. Unlike the first two cases, in which the dynamics model is used to make predictions for decision-making, the third case learns the model solely for representation learning. We learn a stochastic sequential latent variable model to learn a latent representation, and then use it as an intermediate representation for reinforcement learning. We show that this approach improves final performance and sample efficiency

Th17 Responses Are Not Induced in Dextran Sodium Sulfate Model of Acute Colitis

Dextran sodium sulfate (DSS) is a widely used chemical model for inflammatory bowel disease (IBD). It is thought that imbalances in the T helper (Th) cell subsets contribute to IBD. Recent studies suggest that the acute DSS-colitis model is polarized toward a Th1/Th17 profile based on RT-PCR analysis of colonic tissues. In the current study we determined whether colonic Th cells from DSS-colitis mice were skewed toward the Th17 profile. Mice were treated with 5% DSS for 7 days and colonic T cells isolated and examined for production of IFN-γ (Th1 cell), IL-4 (Th2 cell) and IL-17 (Th17 cell) by intracellular flow cytometry. We found that the percentage of colonic Th17 cells were similar to non-treated controls but the percentage of Th1 cells were elevated in DSS-colitis mice. These results suggest that in the acute DSS-colitis model the colonic Th cells exhibit a Th1 profile and not a Th17 profile

Second Data Release of the COSMOS Lyman-alpha Mapping and Tomographic Observation: The First 3D Maps of the Detailed Cosmic Web at 2.05<z<2.55

We present the second data release of the COSMOS Lyman-Alpha Mapping And Tomography Observations (CLAMATO) Survey conducted with the LRIS spectrograph on the Keck-I telescope. This project used Lyman-alpha forest absorption in the spectra of faint star forming galaxies and quasars at z ~ 2-3 to trace neutral hydrogen in the intergalactic medium. In particular, we use 320 objects over a footprint of ~0.2 deg^2 to reconstruct the absorption field at 2.05 < z < 2.55 at ~2 h^{-1}Mpc resolution. We apply a Wiener filtering technique to the observed data to reconstruct three dimensional maps of the field over a volume of 4.1 x 10^5 comoving cubic Mpc. In addition to the filtered flux maps, for the first time we infer the underlying dark matter field through a forward modeling framework from a joint likelihood of galaxy and Lyman-alpha forest data, finding clear examples of the detailed cosmic web consisting of cosmic voids, sheets, filaments, and nodes. In addition to traditional figures, we present a number of interactive three dimensional models to allow exploration of the data and qualitative comparisons to known galaxy surveys. We find that our inferred over-densities are consistent with those found from galaxy fields. Our reduced spectra, extracted Lyman-alpha forest pixel data, and reconstructed tomographic maps are available publicly at https://doi.org/10.5281/zenodo.5842842Comment: 20 pages, 15 figures. Data is available at https://doi.org/10.5281/zenodo.5842842 arXiv admin note: text overlap with arXiv:1710.0289

Honors Convocation

Program listing performers and works performe

ACOTES project: Advanced compiler technologies for embedded streaming

Streaming applications are built of data-driven, computational components, consuming and producing unbounded data streams. Streaming oriented systems have become dominant in a wide range of domains, including embedded applications and DSPs. However, programming efficiently for streaming architectures is a challenging task, having to carefully partition the computation and map it to processes in a way that best matches the underlying streaming architecture, taking into account the distributed resources (memory, processing, real-time requirements) and communication overheads (processing and delay). These challenges have led to a number of suggested solutions, whose goal is to improve the programmer’s productivity in developing applications that process massive streams of data on programmable, parallel embedded architectures. StreamIt is one such example. Another more recent approach is that developed by the ACOTES project (Advanced Compiler Technologies for Embedded Streaming). The ACOTES approach for streaming applications consists of compiler-assisted mapping of streaming tasks to highly parallel systems in order to maximize cost-effectiveness, both in terms of energy and in terms of design effort. The analysis and transformation techniques automate large parts of the partitioning and mapping process, based on the properties of the application domain, on the quantitative information about the target systems, and on programmer directives. This paper presents the outcomes of the ACOTES project, a 3-year collaborative work of industrial (NXP, ST, IBM, Silicon Hive, NOKIA) and academic (UPC, INRIA, MINES ParisTech) partners, and advocates the use of Advanced Compiler Technologies that we developed to support Embedded Streaming.Peer ReviewedPostprint (published version

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin