S. Shah

2papers

2 Papers

28.8HEP-EXApr 21
Neural posterior estimation of the neutrino direction in IceCube using transformer-encoded normalizing flows on the sphere

R. Abbasi, M. Ackermann, J. Adams et al.

IceCube is a cubic-kilometer-scale neutrino detector located at the geographic South Pole. A precise directional reconstruction of IceCube neutrinos is vital for associations with astronomical objects. In this context, we discuss neural posterior estimation of the neutrino direction via a transformer encoder that maps to a normalizing flow on the 2-sphere. It achieves a new state-of-the-art angular resolution for the two main event morphologies in IceCube - tracks and showers - while being significantly faster than traditional B-spline-based likelihood reconstructions. All-sky scans can be performed within seconds rather than hours, and take constant computation time, regardless of whether the posterior extent is arc-minutes or spans the whole sky. We utilize a combination of $C^2$-smooth rational-quadratic splines, scale transformations and rotations to define a novel spherical normalizing-flow distribution whose parameters are predicted as a whole as the output of the transformer encoder. We test several structural choices diverting from the vanilla transformer architecture. In particular, we find dual residual streams, nonlinear QKV projection and a separate class token with its own cross-attention processing to boost test-time performance. The angular resolution for both showers and tracks improves substantially over the whole trained energy range from 100 GeV to 100 PeV. At 100 TeV deposited energy, for example, the median angular resolution improves by a factor of $1.3$ for throughgoing tracks, by a factor of $1.7$ for showers and by a factor of $2.5$ for starting tracks compared to state-of-the art likelihood reconstructions based on B-splines. While previous machine-learning (ML) efforts have managed to obtain competitive shower resolutions, this is the first time an ML-based method outperforms likelihood-based muon reconstructions above 100 GeV.

IVNov 20, 2019
Yottixel -- An Image Search Engine for Large Archives of Histopathology Whole Slide Images

S. Kalra, C. Choi, S. Shah et al.

With the emergence of digital pathology, searching for similar images in large archives has gained considerable attention. Image retrieval can provide pathologists with unprecedented access to the evidence embodied in already diagnosed and treated cases from the past. This paper proposes a search engine specialized for digital pathology, called Yottixel, a portmanteau for "one yotta pixel," alluding to the big-data nature of histopathology images. The most impressive characteristic of Yottixel is its ability to represent whole slide images (WSIs) in a compact manner. Yottixel can perform millions of searches in real-time with a high search accuracy and low storage profile. Yottixel uses an intelligent indexing algorithm capable of representing WSIs with a mosaic of patches by converting them into a small number of methodically extracted barcodes, called "Bunch of Barcodes" (BoB), the most prominent performance enabler of Yottixel. The performance of the prototype platform is qualitatively tested using 300 WSIs from the University of Pittsburgh Medical Center (UPMC) and 2,020 WSIs from The Cancer Genome Atlas Program (TCGA) provided by the National Cancer Institute. Both datasets amount to more than 4,000,000 patches of 1000x1000 pixels. We report three sets of experiments that show that Yottixel can accurately retrieve organs and malignancies, and its semantic ordering shows good agreement with the subjective evaluation of human observers.