Background: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. Findings: To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O √ n -time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

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Second-generation PLINK: rising to the challenge of larger and richer datasets

This paper presents and characterizes the Princeton Application Repository for Shared-Memory Computers (PARSEC), a benchmark suite for studies of Chip-Multiprocessors (CMPs). Previous available benchmarks for multiprocessors have focused on high-performance computing applications and used a limited number of synchronization methods. PARSEC includes emerging applications in recognition, mining and synthesis (RMS) as well as systems applications which mimic large-scale multithreaded commercial programs. Our characterization shows that the benchmark suite covers a wide spectrum of working sets, locality, data sharing, synchronization and off-chip traffic. The benchmark suite has been made available to the public.

/pdf/the-parsec-benchmark-suite-characterization-and-jiajft2rem.pdf

The PARSEC benchmark suite: characterization and architectural implications

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. 
To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. 
The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.

We explore the effect of dimensionality on the nearest neighbor problem. We show that under a broad set of conditions (much broader than independent and identically distributed dimensions), as dimensionality increases, the distance to the nearest data point approaches the distance to the farthest data point. To provide a practical perspective, we present empirical results on both real and synthetic data sets that demonstrate that this effect can occur for as few as 10-15 dimensions. These results should not be interpreted to mean that high-dimensional indexing is never meaningful; we illustrate this point by identifying some high-dimensional workloads for which this effect does not occur. However, our results do emphasize that the methodology used almost universally in the database literature to evaluate high-dimensional indexing techniques is flawed, and should be modified. In particular, most such techniques proposed in the literature are not evaluated versus simple linear scan, and are evaluated over workloads for which nearest neighbor is not meaningful. Often, even the reported experiments, when analyzed carefully, show that linear scan would outperform the techniques being proposed on the workloads studied in high (10-15) dimensionality!.

When is nearest neighbor meaningful

Similarity search finds application in specialized database systems handling complex data such as images or videos, which are typically represented by high-dimensional features and require specific indexing structures. This paper tackles the problem of better utilizing GPUs for this task. While GPUs excel at data-parallel tasks, prior approaches are bottlenecked by algorithms that expose less parallelism, such as k-min selection, or make poor use of the memory hierarchy. 
We propose a design for k-selection that operates at up to 55% of theoretical peak performance, enabling a nearest neighbor implementation that is 8.5x faster than prior GPU state of the art. We apply it in different similarity search scenarios, by proposing optimized design for brute-force, approximate and compressed-domain search based on product quantization. In all these setups, we outperform the state of the art by large margins. Our implementation enables the construction of a high accuracy k-NN graph on 95 million images from the Yfcc100M dataset in 35 minutes, and of a graph connecting 1 billion vectors in less than 12 hours on 4 Maxwell Titan X GPUs. We have open-sourced our approach for the sake of comparison and reproducibility.

Billion-scale similarity search with GPUs

An interpolation unit, such as may be found in a texture unit or texture sampler, may be used utilized to perform general purpose mathematical computations such as dot products. This enables some general purpose computations and operations to be offloaded from a central processing unit to an interpolation unit. The interpolation unit may use linear interpolators in order to perform the dot product calculations.

Using a Texture Unit for General Purpose Computing

A semiconductor chip is described that includes an instruction execution unit having a functional unit, said functional unit having minimum and maximum comparison circuitry followed by interleaving circuitry, said minimum and maximum comparison circuitry to respectively identify minimums and maximums of same positioned elements from two different sets of sorted elements, said interleaving circuitry to interleave said minimums and maximums to help form a third sorted set composed of elements from said different sets and being larger than each of said different sets.

Method and apparatus of instruction that merges and sorts smaller sorted vectors into larger sorted vector

Techniques for extraction of body parameters, dimensions and shape of a customer are presented herein. A model descriptive of a garment, a corresponding calibration factor and reference garment shapes can be assessed. A garment shape corresponding to the three-dimensional model can be selected from the reference garment shapes based on a comparison of the three-dimensional model with the reference garment shapes. A reference feature from the plurality of reference features may be associated with the model feature. A measurement of the reference feature may be calculated based on the association and the calibration factor. The computed measurement can be stored in a body profile associated with a user. An avatar can be generated for the user based on the body profile and be used to show or indicate fit of a garment, as well as make fit and size recommendations.

Extraction of body dimensions from planar garment photographs of fitting garments

One embodiment includes a method of pre-computing a support map which includes a run-time environment comprising at least one three dimensional convex body having a plurality of vertices on each of at least six sides, each side being divided into a predetermined number of sample regions. The embodiment includes determining, for each of at least six input directions, which of the plurality of vertices extends farthest from the body within each of the sample regions. The embodiment also includes storing resulting output data for each sample region in a memoization structure.

System and method for acceleration of collision detection

A region or group of pixels may be textured as a unit, using a range specifier and one or more anchor pixels to define the group. In some embodiments, processing grouped pixels improves efficiency.

Jatin Chhugani

Papers

Using a Texture Unit for General Purpose Computing

Method and apparatus of instruction that merges and sorts smaller sorted vectors into larger sorted vector

Extraction of body dimensions from planar garment photographs of fitting garments

System and method for acceleration of collision detection

Grouping Pixels to be Textured