Reviewerly/exHarmony huggingface dataset:
Improved non-local self-similarity measures for effective speckle noise reduction in ultrasound images

In the observed medical ultrasound image, there is always some speckle noise which suppress the details of images and impairs the value of ultrasonography in diagnosis. This work present a novel despeckling method which effectively exploit non-local self-similarity for restoration of corrupted ultrasound images. The proposed approach consist of three stages. First, an improved optimized Bayesian non-local means (OBNLM) filter in which pixel patch is represented by a new vector form is used to get an preliminary estimation of noise-free image. Then, a new index called redundancy index of each pixel patch is calculated for determining which areas in image have low redundancy. Finally, another new vector form is used to represent pixel patch in areas with low redundancy obtained in second stage to recalculate filtered output, and the recalculated output is superimposed on preliminary estimation to generate final result of proposed method. The performance of proposed approach is evaluated on simulated and real ultrasound images. The experiments conducted on various test image illustrate that our proposed algorithm outperforms the various classic denoising algorithms included block matching 3-D (BM3D) and optimized Bayesian non-local means filter. The objective evaluations and subjective visual inspection of denoised simulated and real ultrasound images demonstrate that the proposed algorithm can achieve superior performance than previously developed methods for speckle noise suppression. The combined use of two new representations improve denoising and edge preserving capability of proposed filter apparently. The success of proposed algorithm would help in building the lay foundation for inventing the despeckling algorithms that can make fuller use of information in images.
Efficient logging and querying for blockchain-based cross-site genomic dataset access audit

Abstract Background Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module plays an essential role in ensuring the accountability. A centralized access log audit system is vulnerable to the single point of attack and also lack transparency since the log could be tampered by a malicious system administrator or internal adversaries. Several studies have proposed blockchain-based access audit to solve this problem but without considering the efficiency of the audit queries. The 2018 iDASH competition first track provides us with an opportunity to design efficient logging and querying system for cross-site genomic dataset access audit. We designed a blockchain-based log system which can provide a light-weight and widely compatible module for existing blockchain platforms. The submitted solution won the third place of the competition. In this paper, we report the technical details in our system. Methods We present two methods: baseline method and enhanced method. We started with the baseline method and then adjusted our implementation based on the competition evaluation criteria and characteristics of the log system. To overcome obstacles of indexing on the immutable Blockchain system, we designed a hierarchical timestamp structure which supports efficient range queries on the timestamp field. Results We implemented our methods in Python3, tested the scalability, and compared the performance using the test data supplied by competition organizer. We successfully boosted the log retrieval speed for complex AND queries that contain multiple predicates. For the range query, we boosted the speed for at least one order of magnitude. The storage usage is reduced by 25%. Conclusion We demonstrate that Blockchain can be used to build a time and space efficient log and query genomic dataset audit trail. Therefore, it provides a promising solution for sharing genomic data with accountability requirement across multiple sites.
Boosting Deep Open World Recognition by Clustering

While convolutional neural networks have brought significant advances in robot vision, their ability is often limited to closed world scenarios, where the number of semantic concepts to be recognized is determined by the available training set. Since it is practically impossible to capture all possible semantic concepts present in the real world in a single training set, we need to break the closed world assumption, equipping our robot with the capability to act in an open world. To provide such ability, a robot vision system should be able to (i) identify whether an instance does not belong to the set of known categories (i.e., open set recognition), and (ii) extend its knowledge to learn new classes over time (i.e., incremental learning). In this work, we show how we can boost the performance of deep open world recognition algorithms by means of a new loss formulation enforcing a global to local clustering of class-specific features. In particular, a first loss term, i.e., global clustering, forces the network to map samples closer to the class centroid they belong to while the second one, local clustering, shapes the representation space in such a way that samples of the same class get closer in the representation space while pushing away neighbours belonging to other classes. Moreover, we propose a strategy to learn class-specific rejection thresholds, instead of heuristically estimating a single global threshold, as in previous works. Experiments on three benchmarks show the effectiveness of our approach.
Conquering Data Variations in Resolution: A Slice-Aware Multi-Branch Decoder Network

Fully convolutional neural networks have made promising progress in joint liver and liver tumor segmentation. Instead of following the debates over 2D versus 3D networks (for example, pursuing the balance between large-scale 2D pretraining and 3D context), in this paper, we novelly identify the wide variation in the ratio between intra- and inter-slice resolutions as a crucial obstacle to the performance. To tackle the mismatch between the intra- and inter-slice information, we propose a slice-aware 2.5D network that emphasizes extracting discriminative features utilizing not only in-plane semantics but also out-of-plane coherence for each separate slice. Specifically, we present a slice-wise multi-input multi-output architecture to instantiate such a design paradigm, which contains a Multi-Branch Decoder (MD) with a Slice-centric Attention Block (SAB) for learning slice-specific features and a Densely Connected Dice (DCD) loss to regularize the inter-slice predictions to be coherent and continuous. Based on the aforementioned innovations, we achieve state-of-the-art results on the MICCAI 2017 Liver Tumor Segmentation (LiTS) dataset. Besides, we also test our model on the ISBI 2019 Segmentation of THoracic Organs at Risk (SegTHOR) dataset, and the result proves the robustness and generalizability of the proposed method in other segmentation tasks.
Cultural Perspectives on InfantCaregiver Interaction

This chapter reviews the available evidence that the Euro-American–derived model of social interaction is not universally applicable. In Euro-American middle-class culture, infants are most often raised in nuclear families with few siblings and with primary care being given by the mother. Caregivers look and talk to their infants often, holding the infant away from their bodies to allow them to look at the infant face to face. Caregivers are particularly good at understanding the source of the negative expression and therefore can quickly fix whatever is wrong. Their adeptness at reading body cues means that often infants’ problems are addressed before they escalate into overt negative expression of experience. The Euro-American interaction rules transmitted to infants are quite complex. Caregivers mediate infants’ actions in the world only out of concern for the infant’s well-being and safety. A different pattern of social interaction is found with young infants in a rural African American community in the southern United States.
Graph convolutional neural networks with node transition probability-based message passing and DropNode regularization

Graph convolutional neural networks (GCNNs) have received much attention recently, owing to their capability in handling graph-structured data. Among the existing GCNNs, many methods can be viewed as instances of a neural message passing motif; features of nodes are passed around their neighbors, aggregated and transformed to produce better nodes’ representations. Nevertheless, these methods seldom use node transition probabilities, a measure that has been found useful in exploring graphs. Furthermore, when the transition probabilities are used, their transition direction is often improperly considered in the feature aggregation step, resulting in an inefficient weighting scheme. In addition, although a great number of GCNN models with increasing level of complexity have been introduced, the GCNNs often suffer from over-fitting when being trained on small graphs. Another issue of the GCNNs is over-smoothing, which tends to make nodes’ representations indistinguishable. This work presents a new method to improve the message passing process based on node transition probabilities by properly considering the transition direction, leading to a better weighting scheme in nodes’ features aggregation compared to the existing counterpart. Moreover, we propose a novel regularization method termed DropNode to address the over-fitting and over-smoothing issues simultaneously. DropNode randomly discards part of a graph, thus it creates multiple deformed versions of the graph, leading to data augmentation regularization effect. Additionally, DropNode lessens the connectivity of the graph, mitigating the effect of over-smoothing in deep GCNNs. Extensive experiments on eight benchmark datasets for node and graph classification tasks demonstrate the effectiveness of the proposed methods in comparison with the state of the art.
Texture Classification Using Pair-Wise Difference Pooling-Based Bilinear Convolutional Neural Networks

Texture is normally represented by aggregating local features based on the assumption of spatial homogeneity. Effective texture features are always the research focus even though both hand-crafted and deep learning approaches have been extensively investigated. Motivated by the success of Bilinear Convolutional Neural Networks (BCNNs) in fine-grained image recognition, we propose to incorporate the BCNN with the Pair-wise Difference Pooling (i.e. BCNN-PDP) for texture classification. The BCNN-PDP is built on top of a set of feature maps extracted at a convolutional layer of the pre-trained CNN. Compared with the outer product used by the original BCNN feature set, the pair-wise difference not only captures the pair-wise relationship between two sets of features but also encodes the difference between each pair of features. Considering the importance of the gradient data to the representation of image structures, we further generalise the BCNN-PDP feature set to two sets of feature maps computed from the original image and its gradient magnitude map respectively, i.e. the Fused BCNN-PDP (F-BCNN-PDP) feature set. In addition, the BCNN-PDP can be applied to two different CNNs and is referred to as the Asymmetric BCNN-PDP (A-BCNN-PDP). The three PDP-based BCNN feature sets can also be extracted at multiple scales. Since the dimensionality of the BCNN feature vectors is very high, we propose a new yet simple Block-wise PCA (BPCA) method in order to derive more compact feature vectors. The proposed methods are tested on seven different datasets along with 21 baseline feature sets. The results show that the proposed feature sets are superior, or at least comparable, to their counterparts across different datasets.
Applying a Random Projection Algorithm to Optimize Machine Learning Model for Breast Lesion Classification

Machine learning is widely used in developing computer-aided diagnosis (CAD) schemes of medical images. However, CAD usually computes large number of image features from the targeted regions, which creates a challenge of how to identify a small and optimal feature vector to build robust machine learning models. In this study, we investigate feasibility of applying a random projection algorithm to build an optimal feature vector from the initially CAD-generated large feature pool and improve performance of machine learning model. We assemble a retrospective dataset involving 1,487 cases of mammograms in which 644 cases have confirmed malignant mass lesions and 843 have benign lesions. A CAD scheme is first applied to segment mass regions and initially compute 181 features. Then, support vector machine (SVM) models embedded with several feature dimensionality reduction methods are built to predict likelihood of lesions being malignant. All SVM models are trained and tested using a leave-one-case-out cross-validation method. SVM generates a likelihood score of each segmented mass region depicting on one-view mammogram. By fusion of two scores of the same mass depicting on two-view mammograms, a case-based likelihood score is also evaluated. Comparing with the principle component analyses, nonnegative matrix factorization, and Chi-squared methods, SVM embedded with the random projection algorithm yielded a significantly higher case-based lesion classification performance with the area under ROC curve of 0.84+0.01 (p<0.02). The study demonstrates that the random project algorithm is a promising method to generate optimal feature vectors to help improve performance of machine learning models of medical images.
Quantifying the usage of small public spaces using deep convolutional neural network

Small public spaces are the key built environment elements that provide venues for various of activities. However, existing measurements or approaches could not efficiently and effectively quantify how small public spaces are being used. In this paper, we utilized a deep convolutional neural network to quantify the usage of small public spaces through recorded videos as a reliable and robust method to bridge the literature gap. To start with, we deployed photographic devices to record videos that cover the minimum enclosing square of a small public space for a certain period of time, then utilized a deep convolutional neural network to detect people in these videos and converted their location from image-based position to real-world projected coordinates. To validate the accuracy and robustness of the method, we experimented our approach in a residential community in Beijing, and our results confirmed that the usage of small public spaces could be measured and quantified effectively and efficiently.
An Introduction to Quantum Computing, without the Physics

This paper is a gentle but rigorous introduction to quantum computing intended for discrete mathematicians. Starting from a small set of assumptions on the behavior of quantum computing devices, we analyze their main characteristics, stressing the differences with classical computers, and finally describe two well-known algorithms (Simon's algorithm and Grover's algorithm) using the formalism developed in previous sections. This paper does not touch on the physics of the devices, and therefore does not require any notion of quantum mechanics. Numerical examples based on an implementation of Grover's algorithm using open-source software are provided.
Spectra of perfect state transfer Hamiltonians on fractal-like graphs

Abstract In this paper we study the spectral features, on fractal-like graphs, of Hamiltonians which exhibit the special property of perfect quantum state transfer (PQST): the transmission of quantum states without dissipation. The essential goal is to develop the theoretical framework for understanding the interplay between PQST, spectral properties, and the geometry of the underlying graph, in order to design novel protocols for applications in quantum information science. We present a new lifting and gluing construction, and use this to prove results concerning an inductive spectral structure, applicable to a wide variety of fractal-like graphs. We illustrate this construction with explicit examples for several classes of diamond graphs.
Classical Verification of Quantum Computations with Efficient Verifier

In this paper, we extend the protocol of classical verification of quantum computations (CVQC) recently proposed by Mahadev to make the verification efficient. Our result is obtained in the following three steps:
Experimental Demonstration of Secure Quantum Remote Sensing

Quantum metrology aims to enhance the precision of various measurement tasks by taking advantages of quantum properties. In many scenarios, precision is not the sole target; the acquired information must be protected once it is generated in the sensing process. Considering a remote sensing scenario where a local site performs cooperative sensing with a remote site to collect sensitive information at the remote site, the loss of sensing data inevitably causes sensitive information to be revealed. Quantum key distribution is known to be a reliable solution for secure data transmission; however, it fails if an eavesdropper accesses the sensing data generated at a remote site. In this study we demonstrate that, by sharing entanglement between local and remote sites, secure quantum remote sensing can be realized, and the secure level is characterized by asymmetric Fisher information gain. Concretely, only the local site can acquire the estimated parameter accurately with Fisher information approaching 1. In contrast, the accessible Fisher information for an eavesdropper is nearly zero even if he or she obtains the raw sensing data at the remote site. This achievement is primarily due to the nonlocal calibration and control of the probe state at the remote site. Our results explore one significant advantage of ``quantumness'' and extend the notion of quantum metrology to the security realm.
A comparative evaluation of novelty detection algorithms for discrete sequences

The identification of anomalies in temporal data is a core component of numerous research areas such as intrusion detection, fault prevention, genomics and fraud detection. This article provides an experimental comparison of candidate methods for the novelty detection problem applied to discrete sequences. The objective of this study is to identify which state-of-the-art methods are efficient and appropriate candidates for a given use case. These recommendations rely on extensive novelty detection experiments based on a variety of public datasets in addition to novel industrial datasets. We also perform thorough scalability and memory usage tests resulting in new supplementary insights of the methods’ performance, key selection criteria to solve problems relying on large volumes of data and to meet the expectations of applications subject to strict response time constraints.
An Experimental Study of Building Blocks of Lattice-Based NIST Post-Quantum Cryptographic Algorithms

Security of currently deployed public-key cryptography algorithms is foreseen to be vulnerable against quantum computer attacks. Hence, a community effort exists to develop post-quantum cryptography (PQC) algorithms, most notably the NIST PQC standardization competition. In this work, we have investigated how lattice-based candidate algorithms fare when implemented in hardware. To achieve this, we have assessed 12 lattice-based algorithms in order to identify their basic building blocks. We assume the algorithms will be implemented in an application-specific integrated circuit (ASIC) platform and the targeted technology is 65 nm. To estimate the characteristics of each algorithm, we have assessed the following characteristics: memory requirements, use of multipliers, and use of hashing functions. Furthermore, for these building blocks, we have collected area and power figures for all studied algorithms by making use of commercial memory compilers and standard cells. Our results reveal interesting insights about the relative importance of each building block for the overall cryptosystem, which can be used for guiding ASIC designers when selecting an algorithm or when deciding where to focus optimization efforts such that the final design respects requirements and design constraints.
Volumetric Medical Image Segmentation: A 3D Deep Coarse-to-Fine Framework and Its Adversarial Examples

Although deep neural networks have been a dominant method for many 2D vision tasks, it is still challenging to apply them to 3D tasks, such as medical image segmentationImage segmentation, due to the limited amount of annotated 3D data and limited computational resources. In this chapter, by rethinking the strategy to apply 3D Convolutional Neural NetworksConvolutional Neural Networks (CNNs) to segment medical images, we propose a novel 3D-based coarse-to-fineCoarse-to-fine framework to efficiently tackle these challenges. The proposed 3D-based framework outperforms their 2D counterparts by a large margin since it can leverage the rich spatial information along all three axes. We further analyze the threat of adversarial attacksAdversarial attack on the proposed framework and show how to defend against the attack. We conduct experiments on three datasets, the NIH pancreas dataset, the JHMI pancreas dataset and the JHMI pathological cyst dataset, where the first two and the last one contain healthy and pathological pancreases, respectively, and achieve the current state of the art in terms of Dice-Sørensen Coefficient (DSC) on all of them. Especially, on the NIH pancreas dataset, we outperform the previous best by an average of over $$2\%$$ , and the worst case is improved by $$7\%$$ to reach almost $$70\%$$ , which indicates the reliability of our framework in clinical applications.
Spatial concept-based navigation with human speech instructions via probabilistic inference on Bayesian generative model

Robots are required to not only learn spatial concepts autonomously but also utilize such knowledge for various tasks in a domestic environment. Spatial concept represents a multimodal place category acquired from the robot's spatial experience including vision, speech-language, and self-position. The aim of this study is to enable a mobile robot to perform navigational tasks with human speech instructions, such as `Go to the kitchen', via probabilistic inference on a Bayesian generative model using spatial concepts. Specifically, path planning was formalized as the maximization of probabilistic distribution on the path-trajectory under speech instruction, based on a control-as-inference framework. Furthermore, we described the relationship between probabilistic inference based on the Bayesian generative model and control problem including reinforcement learning. We demonstrated path planning based on human instruction using acquired spatial concepts to verify the usefulness of the proposed approach in the simulator and in real environments. Experimentally, places instructed by the user's speech commands showed high probability values, and the trajectory toward the target place was correctly estimated. Our approach, based on probabilistic inference concerning decision-making, can lead to further improvement in robot autonomy.