Reviewerly/exHarmony huggingface dataset:
The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition

Abstract Background The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. Although the ELIXIR Core Data Resources and other established infrastructures provide comprehensive and long-term stable services and platforms for FAIR data management, a large quantity of research data is still hidden or at risk of getting lost. Currently, high-throughput plant genomics and phenomics technologies are producing research data in abundance, the storage of which is not covered by established core databases. This concerns the data volume, e.g., time series of images or high-resolution hyper-spectral data; the quality of data formatting and annotation, e.g., with regard to structure and annotation specifications of core databases; uncovered data domains; or organizational constraints prohibiting primary data storage outside institional boundaries. Results To share these potentially dark data in a FAIR way and master these challenges the ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) implements a “bring the infrastructure to the data” approach, which allows research data to be kept in place and wrapped in a FAIR-aware software infrastructure. This article presents new features of the e!DAL infrastructure software and the PGP repository as a best practice on how to easily set up FAIR-compliant and intuitive research data services. Furthermore, the integration of the ELIXIR Authentication and Authorization Infrastructure (AAI) and data discovery services are introduced as means to lower technical barriers and to increase the visibility of research data. Conclusion The e!DAL software matured to a powerful and FAIR-compliant infrastructure, while keeping the focus on flexible setup and integration into existing infrastructures and into the daily research process.
TzanckNet: a convolutional neural network to identify cells in the cytology of erosive-vesiculobullous diseases

Abstract Tzanck smear test is a low-cost, rapid and reliable tool which can be used for the diagnosis of many erosive-vesiculobullous, tumoral and granulomatous diseases. Currently its use is limited mainly due to lack of experience in interpretation of the smears. We developed a deep learning model, TzanckNet, that can identify cells in Tzanck smear test findings. TzanckNet was trained on a retrospective development dataset of 2260 Tzanck smear images collected between December 2006 and December 2019. The finalized model was evaluated using a prospective validation dataset of 359 Tzanck smear images collected from 15 patients during January 2020. It is designed to recognize six cell types (acantholytic cells, eosinophils, hypha, multinucleated giant cells, normal keratinocytes and tadpole cells). For 359 images and 6 cell types, TzanckNet made 2154 predictions. The accuracy was 94.3% (95% CI 93.4–95.3), the sensitivity was 83.7% (95% CI 80.3–87.0) and the specificity was 97.3% (95% CI 96.5–98.1). The area under the receiver operating characteristic curve was 0.974. Our results show that TzanckNet has the potential to lower the experience barrier needed to use this test, broadening its user base, and hence improving patient well-being.
Uncertain-DeepSSM: From Images to Probabilistic Shape Models

Statistical shape modeling (SSM) has recently taken advantage of advances in deep learning to alleviate the need for a time-consuming and expert-driven workflow of anatomy segmentation, shape registration, and the optimization of population-level shape representations. DeepSSM is an end-to-end deep learning approach that extracts statistical shape representation directly from unsegmented images with little manual overhead. It performs comparably with state-of-the-art shape modeling methods for estimating morphologies that are viable for subsequent downstream tasks. Nonetheless, DeepSSM produces an overconfident estimate of shape that cannot be blindly assumed to be accurate. Hence, conveying what DeepSSM does not know, via quantifying granular estimates of uncertainty, is critical for its direct clinical application as an on-demand diagnostic tool to determine how trustworthy the model output is. Here, we propose Uncertain-DeepSSM as a unified model that quantifies both, data-dependent aleatoric uncertainty by adapting the network to predict intrinsic input variance, and model-dependent epistemic uncertainty via a Monte Carlo dropout sampling to approximate a variational distribution over the network parameters. Experiments show an accuracy improvement over DeepSSM while maintaining the same benefits of being end-to-end with little pre-processing.
Optical Axons for Electro-Optical Neural Networks

Recently, neuromorphic sensors, which convert analogue signals to spiking frequencies, have been reported for neurorobotics. In bio-inspired systems these sensors are connected to the main neural unit to perform post-processing of the sensor data. The performance of spiking neural networks has been improved using optical synapses, which offer parallel communications between the distanced neural areas but are sensitive to the intensity variations of the optical signal. For systems with several neuromorphic sensors, which are connected optically to the main unit, the use of optical synapses is not an advantage. To address this, in this paper we propose and experimentally verify optical axons with synapses activated optically using digital signals. The synaptic weights are encoded by the energy of the stimuli, which are then optically transmitted independently. We show that the optical intensity fluctuations and link’s misalignment result in delay in activation of the synapses. For the proposed optical axon, we have demonstrated line of sight transmission over a maximum link length of 190 cm with a delay of 8 μs. Furthermore, we show the axon delay as a function of the illuminance using a fitted model for which the root mean square error (RMS) similarity is 0.95.
GAZEV: GAN-Based Zero-Shot Voice Conversion Over Non-Parallel Speech Corpus

Non-parallel many-to-many voice conversion is recently attract-ing huge research efforts in the speech processing community. A voice conversion system transforms an utterance of a source speaker to another utterance of a target speaker by keeping the content in the original utterance and replacing by the vocal features from the target speaker. Existing solutions, e.g., StarGAN-VC2, present promising results, only when speech corpus of the engaged speakers is available during model training. AUTOVCis able to perform voice conversion on unseen speakers, but it needs an external pretrained speaker verification model. In this paper, we present our new GAN-based zero-shot voice conversion solution, called GAZEV, which targets to support unseen speakers on both source and target utterances. Our key technical contribution is the adoption of speaker embedding loss on top of the GAN framework, as well as adaptive instance normalization strategy, in order to address the limitations of speaker identity transfer in existing solutions. Our empirical evaluations demonstrate significant performance improvement on output speech quality and comparable speaker similarity to AUTOVC.
Image memorability is predicted by discriminability and similarity in different stages of a convolutional neural network

The features of an image can be represented at multiple levels—from its low-level visual properties to high-level meaning. What drives some images to be memorable while others are forgettable? We address this question across two behavioral experiments. In the first, different layers of a convolutional neural network (CNN), which represent progressively higher levels of features, were used to select the images that would be shown to 100 participants through a form of prospective assignment. Here, the discriminability/similarity of an image with others, according to different CNN layers dictated the images presented to different groups, who made a simple indoor versus outdoor judgment for each scene. We found that participants remember more scene images that were selected based on their low-level discriminability or high-level similarity. A second experiment replicated these results in an independent sample of 50 participants, with a different order of postencoding tasks. Together, these experiments provide evidence that both discriminability and similarity, at different visual levels, predict image memorability.
Dissipative dynamics in a tunable Rabi dimer with periodic harmonic driving

Recent progress on qubit manipulation allows application of periodic driving signals on qubits. In this study, a harmonic driving field is added to a Rabi dimer to engineer photon and qubit dynamics in a circuit quantum electrodynamics device. To model environmental effects, qubits in the Rabi dimer are coupled to a phonon bath with a sub-Ohmic spectral density. A nonperturbative treatment, the Dirac-Frenkel time-dependent variational principle together with the multiple Davydov D2 ansatz, is employed to explore the dynamical behavior of the tunable Rabi dimer. In the absence of the phonon bath, the amplitude damping of the photon number oscillation is greatly suppressed by the driving field, and photons can be created, thanks to the resonance between the periodic driving field and the photon frequency. In the presence of the phonon bath, one can still change the photon numbers in two resonators and indirectly alter the photon imbalance in the Rabi dimer by directly varying the driving signal in one qubit. It is shown that qubit states can be manipulated directly by the harmonic driving. The environment is found to strengthen the interqubit asymmetry induced by the external driving, opening up a new venue to engineer the qubit states.
End-to-End Adversarial Shape Learning for Abdomen Organ Deep Segmentation

Automatic segmentation of abdomen organs using medical imaging has many potential applications in clinical workflows. Recently, the state-of-the-art performance for organ segmentation has been achieved by deep learning models, i.e., convolutional neural network (CNN). However, it is challenging to train the conventional CNN-based segmentation models that aware of the shape and topology of organs. In this work, we tackle this problem by introducing a novel end-to-end shape learning architecture – organ point-network. It takes deep learning features as inputs and generates organ shape representations as points that located on organ surface. We later present a novel adversarial shape learning objective function to optimize the point-network to capture shape information better. We train the point-network together with a CNN-based segmentation model in a multi-task fashion so that the shared network parameters can benefit from both shape learning and segmentation tasks. We demonstrate our method with three challenging abdomen organs including liver, spleen, and pancreas. The point-network generates surface points with fine-grained details and it is found critical for improving organ segmentation. Consequently, the deep segmentation model is improved by the introduced shape learning as significantly better Dice scores are observed for spleen and pancreas segmentation.
A quantum secret sharing scheme with verifiable function

In the (t, n) threshold quantum secret sharing scheme, it is difficult to ensure that internal participants are honest. In this paper, a verifiable (t, n) threshold quantum secret sharing scheme is designed to combine with classical secret sharing scheme. First of all, the distributor uses the asymmetric binary polynomial to generate the shares and sends them to each participant. Secondly, the distributor sends the initial quantum state with the secret to the first participant, and each participant performs unitary operation that uses the mutually unbiased bases on the obtained d dimension single bit quantum state (d is a large odd prime number). In this process, distributor can randomly check the participants, and find out the internal fraudsters. Then the secret is reconstructed after all other participants publicly transmit it at the same time. The analysis of this scheme includes correctness analysis, completeness analysis and security analysis. And the security analysis shows that the scheme can resist both external and internal attacks.
Memory effects in quantum processes

Understanding temporal processes and their correlations in time is of paramount importance for the development of near-term technologies that operate under realistic conditions. Capturing the complete multi-time statistics that define a stochastic process lies at the heart of any proper treatment of memory effects. This is well understood in classical theory, where a hierarchy of joint probability distributions completely characterizes the process at hand. However, attempting to generalize this notion to quantum mechanics is problematic: observing realizations of a quantum process necessarily disturbs the state of the system, breaking an implicit, and crucial, assumption in the classical setting. This issue can be overcome by separating the experimental interventions from the underlying process, enabling an unambiguous description of the process itself and accounting for all possible multi-time correlations for any choice of interrogating instruments. In this paper, using a novel framework for the characterization of quantum stochastic processes, we first solve the long standing question of unambiguously describing the memory length of a quantum processes. This is achieved by constructing a quantum Markov order condition, which naturally generalizes its classical counterpart for the quantification of finite-length memory effects. As measurements are inherently invasive in quantum mechanics, one has no choice but to define Markov order with respect to the interrogating instruments that are used to probe the process at hand: different memory effects are exhibited depending on how one addresses the system, in contrast to the standard classical setting. We then fully characterize the structural constraints imposed on quantum processes with finite Markov order, shedding light on a variety of memory effects that can arise through various examples. Finally, we introduce an instrument-specific notion of memory strength that allows for a meaningful quantification of the temporal correlations between the history and the future of a process for a given choice of experimental intervention. These findings are directly relevant to both characterizing and exploiting memory effects that persist for a finite duration. In particular, immediate applications range from developing efficient compression and recovery schemes for the description of quantum processes with memory to designing coherent control protocols that efficiently perform information-theoretic tasks, amongst a plethora of others.
Interval Temporal Logic Decision Tree Learning

Decision trees are simple, yet powerful, classification models used to classify categorical and numerical data, and, despite their simplicity, they are commonly used in operations research and management, as well as in knowledge mining. From a logical point of view, a decision tree can be seen as a structured set of logical rules written in propositional logic. Since knowledge mining is rapidly evolving towards temporal knowledge mining, and since in many cases temporal information is best described by interval temporal logics, propositional logic decision trees may evolve towards interval temporal logic decision trees. In this paper, we define the problem of interval temporal logic decision tree learning, and propose a solution that generalizes classical decision tree learning.
Progressive Object Transfer Detection

Recent development of object detection mainly depends on deep learning with large-scale benchmarks. However, collecting such fully-annotated data is often difficult or expensive for real-world applications, which restricts the power of deep neural networks in practice. Alternatively, humans can detect new objects with little annotation burden, since humans often use the prior knowledge to identify new objects with few elaborately-annotated examples, and subsequently generalize this capacity by exploiting objects from wild images. Inspired by this procedure of learning to detect, we propose a novel Progressive Object Transfer Detection (POTD) framework. Specifically, we make three main contributions in this paper. First, POTD can leverage various object supervision of different domains effectively into a progressive detection procedure. Via such human-like learning, one can boost a target detection task with few annotations. Second, POTD consists of two delicate transfer stages, i.e., Low-Shot Transfer Detection (LSTD), and Weakly-Supervised Transfer Detection (WSTD). In LSTD, we distill the implicit object knowledge of source detector to enhance target detector with few annotations. It can effectively warm up WSTD later on. In WSTD, we design a recurrent object labelling mechanism for learning to annotate weakly-labeled images. More importantly, we exploit the reliable object supervision from LSTD, which can further enhance the robustness of target detector in the WSTD stage. Finally, we perform extensive experiments on a number of challenging detection benchmarks with different settings. The results demonstrate that, our POTD outperforms the recent state-of-the-art approaches.
Mathematical model and topology evaluation of quantum key distribution network

Due to the intrinsic point-to-point characteristic of quantum key distribution (QKD) systems, it is necessary to study and develop QKD network technology to provide a secure communication service for a large-scale of nodes over a large area. Considering the quality assurance required for such a network and the cost limitations, building an effective mathematical model of a QKD network becomes a critical task. In this paper, a flow-based mathematical model is proposed to describe a QKD network using mathematical concepts and language. In addition, an investigation on QKD network topology evaluation was conducted using a unique and novel QKD network performance indicator, the Information-Theoretic Secure communication bound, and the corresponding linear programming-based calculation algorithm. A large number of simulation results based on the SECOQC network and NSFNET network validate the effectiveness of the proposed model and indicator.
Exploring classical correlations in noise to recover quantum information using local filtering

Abstract A general quantum channel consisting of a decohering and a filtering element carries one qubit of an entangled photon pair. As we apply a local filter to the other qubit, some mutual quantum information between the two qubits is restored depending on the properties of the noise mixed into the signal. We demonstrate a drastic difference between channels with bit-flip and phase-flip noise and further suggest a scheme for maximal recovery of the quantum information.
TSXplain: Demystification of DNN Decisions for Time-Series Using Natural Language and Statistical Features

Neural networks (NN) are considered as black-boxes due to the lack of explainability and transparency of their decisions. This significantly hampers their deployment in environments where explainability is essential along with the accuracy of the system. Recently, significant efforts have been made for the interpretability of these deep networks with the aim to open up the black-box. However, most of these approaches are specifically developed for visual modalities. In addition, the interpretations provided by these systems require expert knowledge and understanding for intelligibility. This indicates a vital gap between the explainability provided by the systems and the novice user. To bridge this gap, we present a novel framework i.e. Time-Series eXplanation (TSXplain) system which produces a natural language based explanation of the decision taken by a NN. It uses the extracted statistical features to describe the decision of a NN, merging the deep learning world with that of statistics. The two-level explanation provides ample description of the decision made by the network to aid an expert as well as a novice user alike. Our survey and reliability assessment test confirm that the generated explanations are meaningful and correct. We believe that generating natural language based descriptions of the network's decisions is a big step towards opening up the black-box.
Locally Maximally Entangled States of Multipart Quantum Systems

For a multipart quantum system, a locally maximally entangled (LME) state is one where each elementary subsystem is maximally entangled with its complement. This paper is a sequel to arXiv:1708.01645, which gives necessary and sufficient conditions for a system to admit LME states in terms of its subsystem dimensions $(d_1, d_2, \dots, d_n)$, and computes the dimension of the space ${\cal H}_{LME}/K$ of LME states up to local unitary transformations for all non-empty cases. In this paper, we provide a pedagogical overview and physical interpretation of the the underlying mathematics that leads to these results and give a large class of explicit constructions for LME states. In particular, we construct all LME states for tripartite systems with subsystem dimensions $(2,A,B)$ and give a general representation-theoretic construction for a special class of stabilizer LME states. The latter construction provides a common framework for many known LME states. Our results also give the dimension of the space of SLOCC equivalence classes for states with "generic" entanglement for all multipart systems since this space is equivalent to ${\cal H}_{LME}/K$. Finally, we give the dimension of the stabilizer subgroup $S \subset SL(d_1, \mathbb{C}) \times \cdots \times SL(d_n, \mathbb{C})$ for a generic state in an arbitrary multipart system and identify all cases where this stabilizer is trivial.
Quantum Fourier transform revisited

Summary The fast Fourier transform (FFT) is one of the most successful numerical algorithms of the 20th century and has found numerous applications in many branches of computational science and engineering. The FFT algorithm can be derived from a particular matrix decomposition of the discrete Fourier transform (DFT) matrix. In this paper, we show that the quantum Fourier transform (QFT) can be derived by further decomposing the diagonal factors of the FFT matrix decomposition into products of matrices with Kronecker product structure. We analyze the implication of this Kronecker product structure on the discrete Fourier transform of rank‐1 tensors on a classical computer. We also explain why such a structure can take advantage of an important quantum computer feature that enables the QFT algorithm to attain an exponential speedup on a quantum computer over the FFT algorithm on a classical computer. Further, the connection between the matrix decomposition of the DFT matrix and a quantum circuit is made. We also discuss a natural extension of a radix‐2 QFT decomposition to a radix‐ d QFT decomposition. No prior knowledge of quantum computing is required to understand what is presented in this paper. Yet, we believe this paper may help readers to gain some rudimentary understanding of the nature of quantum computing from a matrix computation point of view.