Efficient data structures for piecewise-smooth video processing

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 95-102).A number of useful image and video processing techniques, ranging from low level operations such as denoising and detail enhancement to higher level methods such as object manipulation and special effects, rely on piecewise-smooth functions computed from the input data. In this thesis, we present two computationally efficient data structures for representing piecewise-smooth visual information and demonstrate how they can dramatically simplify and accelerate a variety of video processing algorithms. We start by introducing the bilateral grid, an image representation that explicitly accounts for intensity edges. By interpreting brightness values as Euclidean coordinates, the bilateral grid enables simple expressions for edge-aware filters. Smooth functions defined on the bilateral grid are piecewise-smooth in image space. Within this framework, we derive efficient reinterpretations of a number of edge-aware filters commonly used in computational photography as operations on the bilateral grid, including the bilateral filter, edgeaware scattered data interpolation, and local histogram equalization. We also show how these techniques can be easily parallelized onto modern graphics hardware for real-time processing of high definition video. The second data structure we introduce is the video mesh, designed as a flexible central data structure for general-purpose video editing. It represents objects in a video sequence as 2.5D "paper cutouts" and allows interactive editing of moving objects and modeling of depth, which enables 3D effects and post-exposure camera control. In our representation, we assume that motion and depth are piecewise-smooth, and encode them sparsely as a set of points tracked over time. The video mesh is a triangulation over this point set and per-pixel information is obtained by interpolation. To handle occlusions and detailed object boundaries, we rely on the user to rotoscope the scene at a sparse set of frames using spline curves. We introduce an algorithm to robustly and automatically cut the mesh into local layers with proper occlusion topology, and propagate the splines to the remaining frames. Object boundaries are refined with per-pixel alpha mattes. At its core, the video mesh is a collection of texture-mapped triangles, which we can edit and render interactively using graphics hardware. We demonstrate the effectiveness of our representation with special effects such as 3D viewpoint changes, object insertion, depthof- field manipulation, and 2D to 3D video conversion.by Jiawen Chen.Ph.D

Load-balanced rendering on a general-purpose tiled architecture

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 77-80).Commodity graphics hardware has become increasingly programmable over the last few years, but has been limited to a fixed resource allocation. These architectures handle some workloads well, others poorly; load-balancing to maximize graphics hardware performance has become a critical issue. I have designed a system that solves the load-balancing problem in real-time graphics by using compile-time resource allocation on general-purpose hardware. I implemented a flexible graphics pipeline on Raw, a tile-based multicore processor. The complete graphics pipeline is expressed using StreamIt, a high-level language based on the stream programming model. The StreamIt compiler automatically maps the stream computation onto the Raw architecture. The system is evaluated by comparing the performance of the flexible pipeline with a fixed allocation representative of commodity hardware on common rendering tasks. The benchmarks place workloads on different parts of the pipeline to determine the effectiveness of the load-balance. The flexible pipeline achieves up to twice the throughput of a static allocation.by Jiawen Chen.M.Eng

rs641738C>T near MBOAT7 is associated with liver fat, ALT, and fibrosis in NAFLD: a meta-analysis

Background & aims: A common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in non-alcoholic fatty liver disease (NAFLD), however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and characterize its role in the regulation of related metabolic phenotypes through meta-analysis. Methods: We performed meta-analysis of studies with data on the association between rs641738C>T genotype and: liver fat, NAFLD histology, and serum ALT, lipids, or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed random effects meta-analysis using recessive, additive, and dominant genetic models. Results: Data from 1,066,175 participants (9,688 with liver biopsies) across 42 studies were included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI: 0.02 - 0.05], pz=4.8x10-5) and diagnosis of NAFLD (OR 1.17 [95% CI 1.05 - 1.3], pz=0.003) in Caucasian adults. The variant was also positively associated with presence of advanced fibrosis (OR 1.22 [95% CI: 1.03 - 1.45], pz=0.021) in Caucasian adults using a recessive model of inheritance (CC+CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (pz=0.002) and lower serum triglycerides (pz=1.5x10-4). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD. Conclusion: Our study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent

rs641738C>T near MBOAT7 is associated with liver fat, ALT and fibrosis in NAFLD: A meta-analysis.

BACKGROUND & AIMS: A common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in NAFLD; however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and to characterise its role in the regulation of related metabolic phenotypes through a meta-analysis. METHODS: We performed a meta-analysis of studies with data on the association between rs641738C>T genotype and liver fat, NAFLD histology, and serum alanine aminotransferase (ALT), lipids or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed a random effects meta-analysis using recessive, additive and dominant genetic models. RESULTS: Data from 1,066,175 participants (9,688 with liver biopsies) across 42 studies were included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI 0.02-0.05], pz = 4.8×10-5) and diagnosis of NAFLD (odds ratio [OR] 1.17 [95% CI 1.05-1.3], pz = 0.003) in Caucasian adults. The variant was also positively associated with presence of advanced fibrosis (OR 1.22 [95% CI 1.03-1.45], pz = 0.021) in Caucasian adults using a recessive model of inheritance (CC + CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (pz = 0.002) and lower serum triglycerides (pz = 1.5×10-4). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD. CONCLUSIONS: Our study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent. LAY SUMMARY: Fatty liver disease is a common condition where fat builds up in the liver, which can cause liver inflammation and scarring (including 'cirrhosis'). It is closely linked to obesity and diabetes, but some genes are also thought to be important. We did this study to see whether one specific change ('variant') in one gene ('MBOAT7') was linked to fatty liver disease. We took data from over 40 published studies and found that this variant near MBOAT7 is linked to more severe fatty liver disease. This means that drugs designed to work on MBOAT7 could be useful for treating fatty liver disease.JPM is supported by a Wellcome Trust Fellowship (216329/Z/19/Z

rs641738C>T near MBOAT7 is associated with liver fat, ALT, and fibrosis in NAFLD : a meta-analysis

Background & Aims: A common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in NAFLD; however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and to characterise its role in the regulation of related metabolic phenotypes through a meta-analysis. Methods: We performed a meta-analysis of studies with data on the association between rs641738C>T genotype and liver fat, NAFLD histology, and serum alanine aminotransferase (ALT), lipids or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed a random effects meta-analysis using recessive, additive and dominant genetic models. Results: Data from 1,066,175 participants (9,688 with liver biopsies) across 42 studies were included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI 0.02\u20130.05], pz = 4.8 710\u20135) and diagnosis of NAFLD (odds ratio [OR] 1.17 [95% CI 1.05\u20131.3], pz = 0.003) in Caucasian adults. The variant was also positively associated with presence of advanced fibrosis (OR 1.22 [95% CI 1.03\u20131.45], pz = 0.021) in Caucasian adults using a recessive model of inheritance (CC + CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (pz = 0.002) and lower serum triglycerides (pz = 1.5 710\u20134). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD. Conclusions: Our study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent. Lay summary: Fatty liver disease is a common condition where fat builds up in the liver, which can cause liver inflammation and scarring (including \u2018cirrhosis\u2019). It is closely linked to obesity and diabetes, but some genes are also thought to be important. We did this study to see whether one specific change (\u2018variant\u2019) in one gene (\u2018MBOAT7\u2019) was linked to fatty liver disease. We took data from over 40 published studies and found that this variant near MBOAT7 is linked to more severe fatty liver disease. This means that drugs designed to work on MBOAT7 could be useful for treating fatty liver disease

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease

ILC Reference Design Report Volume 1 - Executive Summary

The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2s^-1. This report is the Executive Summary (Volume I) of the four volume Reference Design Report. It gives an overview of the physics at the ILC, the accelerator design and value estimate, the detector concepts, and the next steps towards project realization.The International Linear Collider (ILC) is a 200-500 GeV center-of-mass high-luminosity linear electron-positron collider, based on 1.3 GHz superconducting radio-frequency (SCRF) accelerating cavities. The ILC has a total footprint of about 31 km and is designed for a peak luminosity of 2x10^34 cm^-2s^-1. This report is the Executive Summary (Volume I) of the four volume Reference Design Report. It gives an overview of the physics at the ILC, the accelerator design and value estimate, the detector concepts, and the next steps towards project realization