Neural Decoder for Topological Codes using Pseudo-Inverse of Parity Check Matrix

Recent developments in the field of deep learning have motivated many researchers to apply these methods to problems in quantum information. Torlai and Melko first proposed a decoder for surface codes based on neural networks. Since then, many other researchers have applied neural networks to study a variety of problems in the context of decoding. An important development in this regard was due to Varsamopoulos et al. who proposed a two-step decoder using neural networks. Subsequent work of Maskara et al. used the same concept for decoding for various noise models. We propose a similar two-step neural decoder using inverse parity-check matrix for topological color codes. We show that it outperforms the state-of-the-art performance of non-neural decoders for independent Pauli errors noise model on a 2D hexagonal color code. Our final decoder is independent of the noise model and achieves a threshold of $10 \%$. Our result is comparable to the recent work on neural decoder for quantum error correction by Maskara et al.. It appears that our decoder has significant advantages with respect to training cost and complexity of the network for higher lengths when compared to that of Maskara et al.. Our proposed method can also be extended to arbitrary dimension and other stabilizer codes.Comment: 12 pages, 12 figures, 2 tables, submitted to the 2019 IEEE International Symposium on Information Theor

Learning Optimal Deep Projection of 18^{18}F-FDG PET Imaging for Early Differential Diagnosis of Parkinsonian Syndromes

Several diseases of parkinsonian syndromes present similar symptoms at early stage and no objective widely used diagnostic methods have been approved until now. Positron emission tomography (PET) with $^{18}$F-FDG was shown to be able to assess early neuronal dysfunction of synucleinopathies and tauopathies. Tensor factorization (TF) based approaches have been applied to identify characteristic metabolic patterns for differential diagnosis. However, these conventional dimension-reduction strategies assume linear or multi-linear relationships inside data, and are therefore insufficient to distinguish nonlinear metabolic differences between various parkinsonian syndromes. In this paper, we propose a Deep Projection Neural Network (DPNN) to identify characteristic metabolic pattern for early differential diagnosis of parkinsonian syndromes. We draw our inspiration from the existing TF methods. The network consists of a (i) compression part: which uses a deep network to learn optimal 2D projections of 3D scans, and a (ii) classification part: which maps the 2D projections to labels. The compression part can be pre-trained using surplus unlabelled datasets. Also, as the classification part operates on these 2D projections, it can be trained end-to-end effectively with limited labelled data, in contrast to 3D approaches. We show that DPNN is more effective in comparison to existing state-of-the-art and plausible baselines.Comment: 8 pages, 3 figures, conference, MICCAI DLMIA, 201

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process