Workflow and Atlas System for Brain-Wide Mapping of Axonal Connectivity in Rat

Detailed knowledge about the anatomical organization of axonal connections is important for understanding normal functions of brain systems and disease-related dysfunctions. Such connectivity data are typically generated in neuroanatomical tract-tracing experiments in which specific axonal connections are visualized in histological sections. Since journal publications typically only accommodate restricted data descriptions and example images, literature search is a cumbersome way to retrieve overviews of brain connectivity. To explore more efficient ways of mapping, analyzing, and sharing detailed axonal connectivity data from the rodent brain, we have implemented a workflow for data production and developed an atlas system tailored for online presentation of axonal tracing data. The system is available online through the Rodent Brain WorkBench (www.rbwb.org; Whole Brain Connectivity Atlas) and holds experimental metadata and high-resolution images of histological sections from experiments in which axonal tracers were injected in the primary somatosensory cortex. We here present the workflow and the data system, and exemplify how the online image repository can be used to map different aspects of the brain-wide connectivity of the rat primary somatosensory cortex, including not only presence of connections but also morphology, densities, and spatial organization. The accuracy of the approach is validated by comparing results generated with our system with findings reported in previous publications. The present study is a contribution to a systematic mapping of rodent brain connections and represents a starting point for further large-scale mapping efforts

Moving from Data-Constrained to Data-Enabled Research: Experiences and Challenges in Collecting, Validating and Analyzing Large-Scale e-Commerce Data

Widespread e-commerce activity on the Internet has led to new opportunities to collect vast amounts of micro-level market and nonmarket data. In this paper we share our experiences in collecting, validating, storing and analyzing large Internet-based data sets in the area of online auctions, music file sharing and online retailer pricing. We demonstrate how such data can advance knowledge by facilitating sharper and more extensive tests of existing theories and by offering observational underpinnings for the development of new theories. Just as experimental economics pushed the frontiers of economic thought by enabling the testing of numerous theories of economic behavior in the environment of a controlled laboratory, we believe that observing, often over extended periods of time, real-world agents participating in market and nonmarket activity on the Internet can lead us to develop and test a variety of new theories. Internet data gathering is not controlled experimentation. We cannot randomly assign participants to treatments or determine event orderings. Internet data gathering does offer potentially large data sets with repeated observation of individual choices and action. In addition, the automated data collection holds promise for greatly reduced cost per observation. Our methods rely on technological advances in automated data collection agents. Significant challenges remain in developing appropriate sampling techniques integrating data from heterogeneous sources in a variety of formats, constructing generalizable processes and understanding legal constraints. Despite these challenges, the early evidence from those who have harvested and analyzed large amounts of e-commerce data points toward a significant leap in our ability to understand the functioning of electronic commerce.Comment: Published at http://dx.doi.org/10.1214/088342306000000231 in the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Latent Space Model for Multi-Modal Social Data

With the emergence of social networking services, researchers enjoy the increasing availability of large-scale heterogenous datasets capturing online user interactions and behaviors. Traditional analysis of techno-social systems data has focused mainly on describing either the dynamics of social interactions, or the attributes and behaviors of the users. However, overwhelming empirical evidence suggests that the two dimensions affect one another, and therefore they should be jointly modeled and analyzed in a multi-modal framework. The benefits of such an approach include the ability to build better predictive models, leveraging social network information as well as user behavioral signals. To this purpose, here we propose the Constrained Latent Space Model (CLSM), a generalized framework that combines Mixed Membership Stochastic Blockmodels (MMSB) and Latent Dirichlet Allocation (LDA) incorporating a constraint that forces the latent space to concurrently describe the multiple data modalities. We derive an efficient inference algorithm based on Variational Expectation Maximization that has a computational cost linear in the size of the network, thus making it feasible to analyze massive social datasets. We validate the proposed framework on two problems: prediction of social interactions from user attributes and behaviors, and behavior prediction exploiting network information. We perform experiments with a variety of multi-modal social systems, spanning location-based social networks (Gowalla), social media services (Instagram, Orkut), e-commerce and review sites (Amazon, Ciao), and finally citation networks (Cora). The results indicate significant improvement in prediction accuracy over state of the art methods, and demonstrate the flexibility of the proposed approach for addressing a variety of different learning problems commonly occurring with multi-modal social data.Comment: 12 pages, 7 figures, 2 table

Scratchpad Sharing in GPUs

GPGPU applications exploit on-chip scratchpad memory available in the Graphics Processing Units (GPUs) to improve performance. The amount of thread level parallelism present in the GPU is limited by the number of resident threads, which in turn depends on the availability of scratchpad memory in its streaming multiprocessor (SM). Since the scratchpad memory is allocated at thread block granularity, part of the memory may remain unutilized. In this paper, we propose architectural and compiler optimizations to improve the scratchpad utilization. Our approach, Scratchpad Sharing, addresses scratchpad under-utilization by launching additional thread blocks in each SM. These thread blocks use unutilized scratchpad and also share scratchpad with other resident blocks. To improve the performance of scratchpad sharing, we propose Owner Warp First (OWF) scheduling that schedules warps from the additional thread blocks effectively. The performance of this approach, however, is limited by the availability of the shared part of scratchpad. We propose compiler optimizations to improve the availability of shared scratchpad. We describe a scratchpad allocation scheme that helps in allocating scratchpad variables such that shared scratchpad is accessed for short duration. We introduce a new instruction, relssp, that when executed, releases the shared scratchpad. Finally, we describe an analysis for optimal placement of relssp instructions such that shared scratchpad is released as early as possible. We implemented the hardware changes using the GPGPU-Sim simulator and implemented the compiler optimizations in Ocelot framework. We evaluated the effectiveness of our approach on 19 kernels from 3 benchmarks suites: CUDA-SDK, GPGPU-Sim, and Rodinia. The kernels that underutilize scratchpad memory show an average improvement of 19% and maximum improvement of 92.17% compared to the baseline approach