A High-Throughput Solver for Marginalized Graph Kernels on GPU

We present the design and optimization of a linear solver on General Purpose GPUs for the efficient and high-throughput evaluation of the marginalized graph kernel between pairs of labeled graphs. The solver implements a preconditioned conjugate gradient (PCG) method to compute the solution to a generalized Laplacian equation associated with the tensor product of two graphs. To cope with the gap between the instruction throughput and the memory bandwidth of current generation GPUs, our solver forms the tensor product linear system on-the-fly without storing it in memory when performing matrix-vector dot product operations in PCG. Such on-the-fly computation is accomplished by using threads in a warp to cooperatively stream the adjacency and edge label matrices of individual graphs by small square matrix blocks called tiles, which are then staged in registers and the shared memory for later reuse. Warps across a thread block can further share tiles via the shared memory to increase data reuse. We exploit the sparsity of the graphs hierarchically by storing only non-empty tiles using a coordinate format and nonzero elements within each tile using bitmaps. Besides, we propose a new partition-based reordering algorithm for aggregating nonzero elements of the graphs into fewer but denser tiles to improve the efficiency of the sparse format.We carry out extensive theoretical analyses on the graph tensor product primitives for tiles of various density and evaluate their performance on synthetic and real-world datasets. Our solver delivers three to four orders of magnitude speedup over existing CPU-based solvers such as GraKeL and GraphKernels. The capability of the solver enables kernel-based learning tasks at unprecedented scales

A 'normal' baby for every pregnancy: dream or reality

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Axial alignment of the lower extremity in Chinese adults

Background: The restoration of normal axial alignment of the lower extremity is important to surgeons who perform reconstructive surgery of the knee. However, data on the normal alignment of the lower extremity in Chinese adults are not available. Methods: The axial alignment of the lower extremity in twenty-five adult male and twenty-five adult female volunteers of southern Chinese origin was measured on weight-bearing radiographs of the entire lower limb. The mean age was twenty-four years for the male volunteers and twenty-three years for the female volunteers. The results were compared with those of two similar studies of white volunteers in the United States. Results: The medial inclination of the tibial plateau in the Chinese subjects (mean and standard deviation, 5.4 ± 2.5 degrees for women and 4.9 ± 2.3 degrees for men) was greater than the commonly reported 3 degrees. The extremities of the Chinese women were found to have a mean of 2.2 ± 2.5 degrees of varus alignment, and those of the Chinese men had a mean of 2.2 ± 2.7 degrees of varus alignment. Conclusions: Compared with the white subjects described in the studies by Moreland et al. and Hsu et al., the Chinese subjects had significantly larger medial inclination of the knee joint (knee-joint obliquity) (p < 0.005) and the female Chinese subjects had significantly more varus alignment of the lower extremity (p < 0.025). Clinical Relevance: Five degrees of external rotation of the femoral component, instead of the commonly reported 3 degrees, may be required to obtain a rectangular flexion gap in total knee arthroplasty in Chinese patients. The racial difference in the knee-joint obliquity may contribute to the racial difference in the ratio of knee osteoarthritis to hip osteoarthritis. Additional studies are necessary to confirm this relationship.published_or_final_versio

Isolated foetal ascites.

The prenatal diagnosis and perinatal outcome of two patients with isolated foetal ascites compatible with chyloperitoneum is described. The foetal ascites resolved spontaneously after delivery with good perinatal outcome in both cases. A good prognosis can be anticipated in such cases. Antepartum and intrapartum interventions are seldom necessary.published_or_final_versio

Case study on user knowledge and design knowledge in product form design

2003-2004 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Asymmetric-detection time-stretch optical microscopy (ATOM) for high-contrast and high-speed microfluidic cellular imaging

High-throughput cellular imaging is acclaimed as captivating yet challenging in biomedical diagnostics. We have demonstrated a new imaging modality, asymmetric-detection time-stretch optical microscopy (ATOM), by incorporating a simple detection scheme which is a further advancement in time-stretch microscopy - a viable solution to achieve high-speed and high-throughput cellular imaging. Through the asymmetric-detection scheme in ATOM, the time-stretch image contrast is enhanced through accessing to the phase-gradient information. With the operation in the 1 μm wavelength range, we demonstrate high-resolution and high-contrast cellular imaging in ultrafast microfluidic flow (up to 10 m/s) by ATOM - achieving an imaging throughput equivalent to 100,000 cells/sec. © 2014 SPIE.published_or_final_versio

Quantification of the performance of chaotic micromixers on the basis of finite time Lyapunov exponents

Chaotic micromixers such as the staggered herringbone mixer developed by Stroock et al. allow efficient mixing of fluids even at low Reynolds number by repeated stretching and folding of the fluid interfaces. The ability of the fluid to mix well depends on the rate at which "chaotic advection" occurs in the mixer. An optimization of mixer geometries is a non trivial task which is often performed by time consuming and expensive trial and error experiments. In this paper an algorithm is presented that applies the concept of finite-time Lyapunov exponents to obtain a quantitative measure of the chaotic advection of the flow and hence the performance of micromixers. By performing lattice Boltzmann simulations of the flow inside a mixer geometry, introducing massless and non-interacting tracer particles and following their trajectories the finite time Lyapunov exponents can be calculated. The applicability of the method is demonstrated by a comparison of the improved geometrical structure of the staggered herringbone mixer with available literature data.Comment: 9 pages, 8 figure

Gut microbiota-derived propionate reduces cancer cell proliferation in the liver

Peer reviewedPublisher PD