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Non-invasive reconstruction of electrophysiological activity in the heart is of great significance for clinical disease prevention and surgical treatment. The distribution of transmembrane potential (TMP) in three-dimensional myocardium can help us diagnose heart diseases such as myocardial ischemia and ectopic pacing. However, the problem of solving TMP is ill-posed, and appropriate constraints need to be added. The existing state-of-art method total variation minimisation only takes advantage of the local similarity in space, which has the problem of over-smoothing, and fails to take into account the relationship among frames in the dynamic TMP sequence. In this work, the authors introduce a novel regularisation method called graph-based total variation to make up for the above shortcomings. The graph structure takes the TMP value of a time sequence on each heart node as the criterion to establish the similarity relationship among the heart. Two sets of phantom experiments were set to verify the superiority of the proposed method over the traditional constraints: infarct scar reconstruction and activation wavefront reconstruction. In addition, experiments with ten real premature ventricular contractions patient data were used to demonstrate the accuracy of the authors' method in clinical applications.

SAD phasing of XFEL data is shown to require accurate error estimates from the merged reflection intensities. Various methods of treating the errors are presented, including a best-practice approach that refines error-correction terms using a nonlinear least-squares method., A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

A hybrid communication network with a common analog signal and an independent digital data stream as input to each node in a multiple access network is considered. The receiver/base-station has to estimate the analog signal with a given fidelity, and decode the digital streams with a low error probability. Treating the analog signal as a common state process, we set up a joint state estimation and communication problem in a Gaussian multiple access channel (MAC) with additive state. The transmitters have non-causal knowledge of the state process, and need to communicate independent data streams in addition to facilitating state estimation at the receiver. We first provide a complete characterization of the optimal trade-off between mean squared error distortion performance in estimating the state and the data rates for the message streams from two transmitting nodes. This is then generalized to an N-sender MAC. To this end, we show a natural connection between the state-dependent MAC model and a hybrid multi-sensor network in which a common source phenomenon is observed at N transmitting nodes. Each node encodes the source observations as well as an independent message stream over a Gaussian MAC without any state process. The receiver is interested estimating the source and all the messages. Again the distortion-rate performance is characterized., 12 pages, Journal submission

Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved inter‐residue contact prediction, contact‐based structure prediction has gradually reached the performance ceiling. New methods have been proposed to predict the inter‐residue distance, but unanimously by simplifying the real‐valued distance prediction into a multiclass classification problem. Here, a lightweight regression‐based distance prediction method is shown, which adopts the generative adversarial network to capture the delicate geometric relationship between residue pairs and thus could predict the continuous, real‐valued inter‐residue distance rapidly and satisfactorily. The predicted residue distance map allows quick structure modeling by the CNS suite, and the constructed models approach the same level of quality as the other state‐of‐the‐art protein structure prediction methods when tested on CASP13 targets. Moreover, this method can be used directly for the structure prediction of membrane proteins without transfer learning., A lightweight GAN‐based protein inter‐residue distance prediction method is reported. This method is capable of capturing the delicate geometric relationship between residue pairs and thus could predict the continuous, real‐valued distance rapidly and satisfactorily. Pipelined with structure modeling software like the CNS suite, this method could construct protein structure models with the state‐of‐the‐art quality.

The chemi-thermo-mechanical pulping (CTMP) is an important process that produces fibers for paper-making, whose output fiber length distribution (FLD) directly determines the energy consumption and product quality of the subsequent papermaking production. Therefore, study on modeling and control of the output FLD is essential for improving pulp quality and saving energy in refining process. However, the output FLD of refining process has non-Gaussian stochastic distribution property, making it difficult to use conventional methods to establish the output FLD model effectively. Under the framework of stochastic distribution control theory, this paper presents a novel modeling approach for output probability density function (PDF) of fiber length in CTMP by combining with the improved wavelet neural network (WNN). In this context, the square root B-spline approximation principle is firstly adopted to extract the B-spline weights of fiber length PDF shape as the target outputs for the WNN based B-spline weights model. Secondly, a novel two-stage hybrid learning algorithm is proposed to establish the parameters system for the WNN based weighs model by defining a multi-objective evaluation index for modeling accuracy in advance. This learning algorithm integrates multi-objective NSGA II algorithm in the first stage for better initial solutions at a global scope, and gradient descent method is employed in the second stage for accurate solutions of WNN model parameters inside a local range. As a result, the final output PDF of fiber length is reconstructed by the estimated B-spline weights using the B-spline approximation principle again. Experiments using actual industrial data have demonstrated the superiority and practicability of the proposed method.

Random unitary beamforming (RUB) achieves multiuser diversity gain over multiple-input multiple-output broadcast channels with partial channel state information (CSI). RUB can asymptotically achieve the same growth of rate $M\log \log K$ as the optimal dirty paper coding or sub-optimal zero-forcing beamforming, which need full CSI at the transmitter. In this paper, we propose energy efficient RUB systems that select the optimal number of streams and transmission power to maximize energy efficiency (EE). In contrast to other beamforming schemes that use full CSI, optimizing RUB in terms of EE is a difficult task due to the CSI constraints. To solve this problem, we first select the EE-optimal number of streams and transmission power by using the statistical characteristics of RUB, which have been studied in previous works. Next, based on partial CSI feedback from users, we propose the method whereby the transmitter of RUB can adaptively control the transmission power. Simulation results demonstrate that our proposed systems can improve the EE performance of RUB and that the analytical results derived in this paper are accurate.

It is difficult to ensure that the scanned document will not be skewed due to the high speed scanning of the paper document by the mechanical feed or the document itself. This will not only affect the visual effects, but also seriously affect the accuracy and speed of subsequent processing. Therefore, this paper presents a Hough transform algorithm based on automatic scanning image correction and cropping, the first to determine whether the scanned image is a text or non-text image, the image preprocessing based on different types of scanned images of the image binarization, Compared with the traditional algorithm has a good anti-interference ability, can accurately detect the scan image skew angle.

The purpose of the present study was to reconstruct the energy spectrum of a poly-energetic neutron source using an algorithm developed based on an Adaptive Neuro-Fuzzy Inference System (ANFIS). ANFIS is a kind of artificial neural network based on the Takagi–Sugeno fuzzy inference system. The ANFIS algorithm uses the advantages of both fuzzy inference systems and artificial neural networks to improve the effectiveness of algorithms in various applications such as modeling, control and classification. The neutron pulse height distributions used as input data in the training procedure for the ANFIS algorithm were obtained from the simulations performed by MCNPX-ESUT computational code (MCNPX-Energy engineering of Sharif University of Technology). Taking into account the normalization condition of each energy spectrum, 4300 neutron energy spectra were generated randomly. (The value in each bin was generated randomly, and finally a normalization of each generated energy spectrum was performed). The randomly generated neutron energy spectra were considered as output data of the developed ANFIS computational code in the training step. To calculate the neutron energy spectrum using conventional methods, an inverse problem with an approximately singular response matrix (with the determinant of the matrix close to zero) should be solved. The solution of the inverse problem using the conventional methods unfold neutron energy spectrum with low accuracy. Application of the iterative algorithms in the solution of such a problem, or utilizing the intelligent algorithms (in which there is no need to solve the problem), is usually preferred for unfolding of the energy spectrum. Therefore, the main reason for development of intelligent algorithms like ANFIS for unfolding of neutron energy spectra is to avoid solving the inverse problem. In the present study, the unfolded neutron energy spectra of 252Cf and 241Am-9Be neutron sources using the developed computational code were found to have excellent agreement with the reference data. Also, the unfolded energy spectra of the neutron sources as obtained using ANFIS were more accurate than the results reported from calculations performed using artificial neural networks in previously published papers.

Background Patient data is considered particularly sensitive personal data. Privacy regulations strictly govern the use of patient data and restrict their exchange. However, medical research can benefit from multicentric studies in which patient data from different institutions are pooled and evaluated together. Thus, the goals of data utilization and data protection are in conflict. Secure multiparty computation (SMPC) solves this conflict because it allows direct computation on distributed proprietary data—held by different data owners—in a secure way without exchanging private data. Objective The objective of this work was to provide a proof-of-principle of secure and privacy-preserving multicentric computation by SMPC with real-patient data over the free internet. A privacy-preserving log-rank test for the Kaplan-Meier estimator was implemented and tested in both an experimental setting and a real-world setting between two university hospitals. Methods The domain of survival analysis is particularly relevant in clinical research. For the Kaplan-Meier estimator, we provided a secure version of the log-rank test. It was based on the SMPC realization SPDZ and implemented via the FRESCO framework in Java. The complexity of the algorithm was explored both for synthetic data and for real-patient data in a proof-of-principle over the internet between two clinical institutions located in Munich and Berlin, Germany. Results We obtained a functional realization of an SMPC-based log-rank evaluation. This implementation was assessed with respect to performance and scaling behavior. We showed that network latency strongly influences execution time of our solution. Furthermore, we identified a lower bound of 2 Mbit/s for the transmission rate that has to be fulfilled for unimpeded communication. In contrast, performance of the participating parties have comparatively low influence on execution speed, since the peer-side processing is parallelized and the computational time only constitutes 30% to 50% even with optimal network settings. In the real-world setting, our computation between three parties over the internet, processing 100 items each, took approximately 20 minutes. Conclusions We showed that SMPC is applicable in the medical domain. A secure version of commonly used evaluation methods for clinical studies is possible with current implementations of SMPC. Furthermore, we infer that its application is practically feasible in terms of execution time.

The incorporation of prior knowledge about the structures of biological macromolecules into the reconstruction process of cryo-EM structure determination is proposed. Using a novel algorithm inspired by regularization by denoising, it is shown how convolutional neural networks can be used within this framework to improve reconstructions from simulated data., Three-dimensional reconstruction of the electron-scattering potential of biological macromolecules from electron cryo-microscopy (cryo-EM) projection images is an ill-posed problem. The most popular cryo-EM software solutions to date rely on a regularization approach that is based on the prior assumption that the scattering potential varies smoothly over three-dimensional space. Although this approach has been hugely successful in recent years, the amount of prior knowledge that it exploits compares unfavorably with the knowledge about biological structures that has been accumulated over decades of research in structural biology. Here, a regularization framework for cryo-EM structure determination is presented that exploits prior knowledge about biological structures through a convolutional neural network that is trained on known macromolecular structures. This neural network is inserted into the iterative cryo-EM structure-determination process through an approach that is inspired by regularization by denoising. It is shown that the new regularization approach yields better reconstructions than the current state of the art for simulated data, and options to extend this work for application to experimental cryo-EM data are discussed.

Background As a common mental disease, depression seriously affects people’s physical and mental health. According to the statistics of the World Health Organization, depression is one of the main reasons for suicide and self-harm events in the world. Therefore, strengthening depression detection can effectively reduce the occurrence of suicide or self-harm events so as to save more people and families. With the development of computer technology, some researchers are trying to apply natural language processing techniques to detect people who are depressed automatically. Many existing feature engineering methods for depression detection are based on emotional characteristics, but these methods do not consider high-level emotional semantic information. The current deep learning methods for depression detection cannot accurately extract effective emotional semantic information. Objective In this paper, we propose an emotion-based attention network, including a semantic understanding network and an emotion understanding network, which can capture the high-level emotional semantic information effectively to improve the depression detection task. Methods The semantic understanding network module is used to capture the contextual semantic information. The emotion understanding network module is used to capture the emotional semantic information. There are two units in the emotion understanding network module, including a positive emotion understanding unit and a negative emotion understanding unit, which are used to capture the positive emotional information and the negative emotional information, respectively. We further proposed a dynamic fusion strategy in the emotion understanding network module to fuse the positive emotional information and the negative emotional information. Results We evaluated our method on the Reddit data set. The experimental results showed that the proposed emotion-based attention network model achieved an accuracy, precision, recall, and F-measure of 91.30%, 91.91%, 96.15%, and 93.98%, respectively, which are comparable results compared with state-of-the-art methods. Conclusions The experimental results showed that our model is competitive with the state-of-the-art models. The semantic understanding network module, the emotion understanding network module, and the dynamic fusion strategy are effective modules for depression detection. In addition, the experimental results verified that the emotional semantic information was effective in depression detection.

We study communication systems over state-dependent channels in the presence of a malicious state-aware jamming adversary. The channel has a memoryless state with an underlying distribution. The adversary introduces a jamming signal into the channel. The state sequence is known non-causally to both the encoder and the adversary. Taking an Arbitrarily Varying Channel (AVC) approach, we consider two setups, namely, the discrete memoryless Gel'fand-Pinsker (GP) AVC and the additive white Gaussian Dirty Paper (DP) AVC. We determine the randomized coding capacity of both the AVCs under a maximum probability of error criterion. Similar to other randomized coding setups, we show that the capacity is the same even under the average probability of error criterion. Even with non-causal knowledge of the state, we prove that the state-aware adversary cannot affect the rate any worse than when it employs a memoryless strategy which depends only on the instantaneous state. Thus, the AVC capacity characterization is given in terms of the capacity of the worst memoryless channels with state, induced by the adversary employing such memoryless jamming strategies. For the DP-AVC, it is further shown that among memoryless jamming strategies, none impact the communication more than a memoryless Gaussian jamming strategy which completely disregards the knowledge of the state. Thus, the capacity of the DP-AVC equals that of a standard AWGN channel with two independent sources of additive white Gaussian noise, i.e., the channel noise and the jamming noise., Comment: 24 pages, 3 figures

Motivation Data splitting is a fundamental step for building classification models with spectral data, especially in biomedical applications. This approach is performed following pre-processing and prior to model construction, and consists of dividing the samples into at least training and test sets; herein, the training set is used for model construction and the test set for model validation. Some of the most-used methodologies for data splitting are the random selection (RS) and the Kennard-Stone (KS) algorithms; here, the former works based on a random splitting process and the latter is based on the calculation of the Euclidian distance between the samples. We propose an algorithm called the Morais-Lima-Martin (MLM) algorithm, as an alternative method to improve data splitting in classification models. MLM is a modification of KS algorithm by adding a random-mutation factor. Results RS, KS and MLM performance are compared in simulated and six real-world biospectroscopic applications using principal component analysis linear discriminant analysis (PCA-LDA). MLM generated a better predictive performance in comparison with RS and KS algorithms, in particular regarding sensitivity and specificity values. Classification is found to be more well-equilibrated using MLM. RS showed the poorest predictive response, followed by KS which showed good accuracy towards prediction, but relatively unbalanced sensitivities and specificities. These findings demonstrate the potential of this new MLM algorithm as a sample selection method for classification applications in comparison with other regular methods often applied in this type of data. Availability and implementation MLM algorithm is freely available for MATLAB at https://doi.org/10.6084/m9.figshare.7393517.v1.

A new fully automatic search–match procedure based on a Rietveld full-pattern-fitting method is presented. The method does not rely on peak positions and permits not only phase identification but also a quantification of the phases and their gross microstructural features., A new search–match procedure has been developed and tested which, in contrast to previously existing methods, does not use a set of lines identified from a diffraction pattern, but an optimized Rietveld fitting on the raw data. Modern computers with multicore processors allow the routine to be fast enough to perform the entire search in a reasonable time using quite large databases of crystal structures. The search–match is done using the crystal structures for all phases and the instrumental geometry, and as such can be applied to every kind of diffraction experiment, including X-rays, thermal/time-of-flight neutrons and electrons. The methodology can also be applied to nanocrystalline samples for which peak identification may be a problem. A web interface has been developed to permit easy testing and evaluation of the procedure. The quality of the results mainly depends on the availability of the sought phase in the structure database. The method permits not only phase identification but also a rapid quantification of the phases and their gross microstructural features, provided the instrumental function is known.

Motivation How to partition a dataset into a set of distinct clusters is a ubiquitous and challenging problem. The fact that data vary widely in features such as cluster shape, cluster number, density distribution, background noise, outliers and degree of overlap, makes it difficult to find a single algorithm that can be broadly applied. One recent method, clusterdp, based on search of density peaks, can be applied successfully to cluster many kinds of data, but it is not fully automatic, and fails on some simple data distributions. Results We propose an alternative approach, clusterdv, which estimates density dips between points, and allows robust determination of cluster number and distribution across a wide range of data, without any manual parameter adjustment. We show that this method is able to solve a range of synthetic and experimental datasets, where the underlying structure is known, and identifies consistent and meaningful clusters in new behavioral data. Availability and implementation The clusterdv is implemented in Matlab. Its source code, together with example datasets are available on: https://github.com/jcbmarques/clusterdv. Supplementary information Supplementary data are available at Bioinformatics online.

A bead-modelling approach is presented to determine the structural motifs of helical and rod-like systems from small-angle solution scattering data. The implemented algorithm is verified using analytical models and is further applied to reconstruct from experimental scattering data the building block of a self-assembled peptide double helix., The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a ‘projection scheme’: by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif. This building block is fitted by allowing random dummy-atom movements without an underlying grid. The proposed method is verified using a variety of analytical models, and examples are presented of successful shape reconstruction from experimental data sets. To make the algorithm available to the scientific community, it is implemented in a graphical computer program that encourages user interaction during the fitting process and also includes an option for shape reconstruction of globular particles.

Background Financial codes are often used to extract diagnoses from electronic health records. This approach is prone to false positives. Alternatively, queries are constructed, but these are highly center and language specific. A tantalizing alternative is the automatic identification of patients by employing machine learning on format-free text entries. Objective The aim of this study was to develop an easily implementable workflow that builds a machine learning algorithm capable of accurately identifying patients with rheumatoid arthritis from format-free text fields in electronic health records. Methods Two electronic health record data sets were employed: Leiden (n=3000) and Erlangen (n=4771). Using a portion of the Leiden data (n=2000), we compared 6 different machine learning methods and a naïve word-matching algorithm using 10-fold cross-validation. Performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision recall curve (AUPRC), and F1 score was used as the primary criterion for selecting the best method to build a classifying algorithm. We selected the optimal threshold of positive predictive value for case identification based on the output of the best method in the training data. This validation workflow was subsequently applied to a portion of the Erlangen data (n=4293). For testing, the best performing methods were applied to remaining data (Leiden n=1000; Erlangen n=478) for an unbiased evaluation. Results For the Leiden data set, the word-matching algorithm demonstrated mixed performance (AUROC 0.90; AUPRC 0.33; F1 score 0.55), and 4 methods significantly outperformed word-matching, with support vector machines performing best (AUROC 0.98; AUPRC 0.88; F1 score 0.83). Applying this support vector machine classifier to the test data resulted in a similarly high performance (F1 score 0.81; positive predictive value [PPV] 0.94), and with this method, we could identify 2873 patients with rheumatoid arthritis in less than 7 seconds out of the complete collection of 23,300 patients in the Leiden electronic health record system. For the Erlangen data set, gradient boosting performed best (AUROC 0.94; AUPRC 0.85; F1 score 0.82) in the training set, and applied to the test data, resulted once again in good results (F1 score 0.67; PPV 0.97). Conclusions We demonstrate that machine learning methods can extract the records of patients with rheumatoid arthritis from electronic health record data with high precision, allowing research on very large populations for limited costs. Our approach is language and center independent and could be applied to any type of diagnosis. We have developed our pipeline into a universally applicable and easy-to-implement workflow to equip centers with their own high-performing algorithm. This allows the creation of observational studies of unprecedented size covering different countries for low cost from already available data in electronic health record systems.

Background Over the past decade, the emergence of several large federated clinical data networks has enabled researchers to access data on millions of patients at dozens of health care organizations. Typically, queries are broadcast to each of the sites in the network, which then return aggregate counts of the number of matching patients. However, because patients can receive care from multiple sites in the network, simply adding the numbers frequently double counts patients. Various methods such as the use of trusted third parties or secure multiparty computation have been proposed to link patient records across sites. However, they either have large trade-offs in accuracy and privacy or are not scalable to large networks. Objective This study aims to enable accurate estimates of the number of patients matching a federated query while providing strong guarantees on the amount of protected medical information revealed. Methods We introduce a novel probabilistic approach to running federated network queries. It combines an algorithm called HyperLogLog with obfuscation in the form of hashing, masking, and homomorphic encryption. It is tunable, in that it allows networks to balance accuracy versus privacy, and it is computationally efficient even for large networks. We built a user-friendly free open-source benchmarking platform to simulate federated queries in large hospital networks. Using this platform, we compare the accuracy, k-anonymity privacy risk (with k=10), and computational runtime of our algorithm with several existing techniques. Results In simulated queries matching 1 to 100 million patients in a 100-hospital network, our method was significantly more accurate than adding aggregate counts while maintaining k-anonymity. On average, it required a total of 12 kilobytes of data to be sent to the network hub and added only 5 milliseconds to the overall federated query runtime. This was orders of magnitude better than other approaches, which guaranteed the exact answer. Conclusions Using our method, it is possible to run highly accurate federated queries of clinical data repositories that both protect patient privacy and scale to large networks.

Background COVID-19 is a global pandemic that is affecting more than 200 countries worldwide. Efficient diagnosis and treatment are crucial to combat the disease. Computer-interpretable guidelines (CIGs) can aid the broad global adoption of evidence-based diagnosis and treatment knowledge. However, currently, no internationally shareable CIG exists. Objective The aim of this study was to establish a rapid CIG development and dissemination approach and apply it to develop a shareable CIG for COVID-19. Methods A 6-step rapid CIG development and dissemination approach was designed and applied. Processes, roles, and deliverable artifacts were specified in this approach to eliminate ambiguities during development of the CIG. The Guideline Definition Language (GDL) was used to capture the clinical rules. A CIG for COVID-19 was developed by translating, interpreting, annotating, extracting, and formalizing the Chinese COVID-19 diagnosis and treatment guideline. A prototype application was implemented to validate the CIG. Results We used 27 archetypes for the COVID-19 guideline. We developed 18 GDL rules to cover the diagnosis and treatment suggestion algorithms in the narrative guideline. The CIG was further translated to object data model and Drools rules to facilitate its use by people who do not employ the non-openEHR archetype. The prototype application validated the correctness of the CIG with a public data set. Both the GDL rules and Drools rules have been disseminated on GitHub. Conclusions Our rapid CIG development and dissemination approach accelerated the pace of COVID-19 CIG development. A validated COVID-19 CIG is now available to the public.

Background It is well established that lack of physical activity is detrimental to the overall health of an individual. Modern-day activity trackers enable individuals to monitor their daily activities to meet and maintain targets. This is expected to promote activity encouraging behavior, but the benefits of activity trackers attenuate over time due to waning adherence. One of the key approaches to improving adherence to goals is to motivate individuals to improve on their historic performance metrics. Objective The aim of this work was to build a machine learning model to predict an achievable weekly activity target by considering (1) patterns in the user’s activity tracker data in the previous week and (2) behavior and environment characteristics. By setting realistic goals, ones that are neither too easy nor too difficult to achieve, activity tracker users can be encouraged to continue to meet these goals, and at the same time, to find utility in their activity tracker. Methods We built a neural network model that prescribes a weekly activity target for an individual that can be realistically achieved. The inputs to the model were user-specific personal, social, and environmental factors, daily step count from the previous 7 days, and an entropy measure that characterized the pattern of daily step count. Data for training and evaluating the machine learning model were collected over a duration of 9 weeks. Results Of 30 individuals who were enrolled, data from 20 participants were used. The model predicted target daily count with a mean absolute error of 1545 (95% CI 1383-1706) steps for an 8-week period. Conclusions Artificial intelligence applied to physical activity data combined with behavioral data can be used to set personalized goals in accordance with the individual’s level of activity and thereby improve adherence to a fitness tracker; this could be used to increase engagement with activity trackers. A follow-up prospective study is ongoing to determine the performance of the engagement algorithm.

The COVID-19 pandemic has captivated scientific activity since its early days. Particular attention has been dedicated to the identification of underlying dynamics and prediction of future trend. In this work, a switching Kalman filter formalism is applied on dynamics learning and forecasting of the daily new cases of COVID-19. The main feature of this dynamical system is its ability to switch between different linear Gaussian models based on the observations and specified probabilities of transitions between these models. It is thus able to handle the problem of hidden state estimation and forecasting for models with non-Gaussian and nonlinear effects. The potential of this method is explored on the daily new cases of COVID-19 both at the state-level and the country-level in the US. The results suggest a common disease dynamics across states that share certain features. We also demonstrate the ability to make short to medium term predictions with quantifiable error bounds.

Motivation Predicting the folding dynamics of RNAs is a computationally difficult problem, first and foremost due to the combinatorial explosion of alternative structures in the folding space. Abstractions are therefore needed to simplify downstream analyses, and thus make them computationally tractable. This can be achieved by various structure sampling algorithms. However, current sampling methods are still time consuming and frequently fail to represent key elements of the folding space. Method We introduce RNAxplorer, a novel adaptive sampling method to efficiently explore the structure space of RNAs. RNAxplorer uses dynamic programming to perform an efficient Boltzmann sampling in the presence of guiding potentials, which are accumulated into pseudo-energy terms and reflect similarity to already well-sampled structures. This way, we effectively steer sampling toward underrepresented or unexplored regions of the structure space. Results We developed and applied different measures to benchmark our sampling methods against its competitors. Most of the measures show that RNAxplorer produces more diverse structure samples, yields rare conformations that may be inaccessible to other sampling methods and is better at finding the most relevant kinetic traps in the landscape. Thus, it produces a more representative coarse graining of the landscape, which is well suited to subsequently compute better approximations of RNA folding kinetics. Availabilityand implementation https://github.com/ViennaRNA/RNAxplorer/. Supplementary information Supplementary data are available at Bioinformatics online.

The process of extracting gold by biological oxidation involves oxidizing the refractory high-sulfur and high-arsenic ore with the help of bacteria to decompose the wrapping material of gold to extract the gold. Therefore, maximizing the activity of bacteria will directly affect the efficiency of gold extraction, for which it is particularly important to maintain the pulp temperature in the oxidation tank at the optimal bacteria breeding temperature. However, gold mines are generally located in mountainous areas, and the large temperature difference between day and night in winter, coupled with the influence of wind and snow, creates variations in the temperature in the oxidation tank. The traditional temperature measurement method cannot fully reflect the temperature change of the oxidation tank. As a multi-field application method, sensor information fusion can effectively address the problem of pulp temperature measurement. First, we analyzed the heat transfer principle inside the oxidation tank, and designed the cluster hierarchical sensor network according to the spatial position of each oxidation tank and the environmental interference factors. The network structure is divided into three layers, the bottom of the sensor to collect pulp temperature data shows a spiral distribution in the inner wall of the oxidation tank. Each cluster head node sensor is used as an intermediate layer to complete local measurement fusion estimation. Finally, the fusion center is taken as the upper layer to realize the global state fusion estimation. Secondly, in the data processing of the bottom temperature sensor, the traditional unscented Kalman filter (UKF) algorithm is improved and the fading memory matrix is added to improve the identification of nonlinear modeling errors. The sequential observation fusion estimator (SOFE) algorithm is embedded in the measurement update to improve the performance of local measurement fusion. Finally, in the global state fusion estimation, the sequential analysis is combined with the inverse covariance intersection, and the sequential analysis and inverse covariance intersection-global state fusion estimation (SICI-GSFE) algorithm is proposed. Through calculation and simulation, the results show that the external interference can be reduced by combining all the temperature state estimations, and the accuracy of the best global temperature state estimation is improved.

In our previous work, we have introduced an extension of signal temporal logic called STL* that allows expressing freezing of values referred within temporal operators. The extension is important especially to express several aspects of signals that cannot be expressed in plain STL (e.g., presence of local extremes and their mutual relationships, non-trivial oscillatory behaviour such as damped oscillations, etc.). In this short paper, we address the tool Parasim that includes an implementation of the algorithm for computing robustness with respect to an STL* specification. The tool is in its current version considered as a prototype implementation of the algorithms for STL* robust monitoring of ODE models.

Aiming to co-channel interference (CCI) and multi-stream for LTE downlink multi-user multiple input multiple output orthogonal frequency division multiple (MIMO-OFDM) system, a successive signal to leakage plus noise ratio (SLNR) with geometric mean decomposition (GMD) for downlink multi-user multi-stream MIMO systems based on pre-processing matrix is proposed. The algorithm utilizes precoding matrix based on SSLNR scheme to process emission signal at the transmitter, and the known leakages is canceled by dirty paper coding (DPC) algorithm. GMD is applied to cancel the known leakages, as all subchannels for this system have identical signal noise ratio (SNR), it is more convenient to reduce the influence of gain. Moreover, the received signal is treated by preconditioned matrix, the interference between different users is eliminated in further, the sum-capacity is improved by pre-processing Matrix. Meanwhile, the proposed scheme has no restriction of the number of antennas. The performance improvement is verified by simulation, the proposed scheme has superior bit error rate (BER) performance compared with the existing algorithm, when BER is 10−4, SNR is improved about 4 dB.

Time-varying connectivity analysis based on sources reconstructed using inverse modeling of electroencephalographic (EEG) data is important to understand the dynamic behaviour of the brain. We simulated cortical data from a visual spatial attention network with a time-varying connectivity structure, and then simulated the propagation to the scalp to obtain EEG data. Distributed EEG source modeling using sLORETA was applied. We compared different dipole (representing a source) selection strategies based on their time series in a region of interest. Next, we estimated multivariate autoregressive (MVAR) parameters using classical Kalman filter and general linear Kalman filter approaches followed by the calculation of partial directed coherence (PDC). MVAR parameters and PDC values for the selected sources were compared with the ground-truth. We found that the best strategy to extract the time series of a region of interest was to select a dipole with time series showing the highest correlation with the average time series in the region of interest. Dipole selection based on power or based on the largest singular value offer comparable alternatives. Among the different Kalman filter approaches, the use of a general linear Kalman filter was preferred to estimate PDC based connectivity except when only a small number of trials are available. In the latter case, the classical Kalman filter can be an alternative.

MotivationIn the analysis of metabolism using omics data, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and Stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, produce results that are readily interpretable in terms of metabolic flux modes, however, they are not best suited for exploratory analysis on a large set of samples.ResultsWe propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and Stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a Stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology.AvailabilityMatlab software for PMFA and SPMFA is available in https://github.com/ aalto-ics-kepaco/PMFA.Contactsahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fiSupplementary informationDetailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

We propose a complete-search algorithm for solving a class of non-convex, possibly infinite-dimensional, optimization problems to global optimality. We assume that the optimization variables are in a bounded subset of a Hilbert space, and we determine worst-case run-time bounds for the algorithm under certain regularity conditions of the cost functional and the constraint set. Because these run-time bounds are independent of the number of optimization variables and, in particular, are valid for optimization problems with infinitely many optimization variables, we prove that the algorithm converges to an \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\varepsilon $$\end{document}ε-suboptimal global solution within finite run-time for any given termination tolerance \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\varepsilon > 0$$\end{document}ε>0. Finally, we illustrate these results for a problem of calculus of variations.

A data correction sequence is presented, consisting of ordered elementary steps that extract the small-angle X-ray scattering cross section from the original detector signal(s). It is applicable to a wide range of samples, including solids and dispersions., Data correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates. The method can be applied without modification to any pinhole-collimated instruments with photon-counting direct-detection area detectors.

A new method is presented for healing X-ray scattering images, allowing gaps in images to be filled and extending the image beyond the borders of the original detector exposure. This method exploits symmetry analysis to reconstruct the sample structure and thereby fill-in unmeasured regions of reciprocal space based on this automatically determined symmetry model., X-ray scattering images contain numerous gaps and defects arising from detector limitations and experimental configuration. We present a method to heal X-ray scattering images, filling gaps in the data and removing defects in a physically meaningful manner. Unlike generic inpainting methods, this method is closely tuned to the expected structure of reciprocal-space data. In particular, we exploit statistical tests and symmetry analysis to identify the structure of an image; we then copy, average and interpolate measured data into gaps in a way that respects the identified structure and symmetry. Importantly, the underlying analysis methods provide useful characterization of structures present in the image, including the identification of diffuse versus sharp features, anisotropy and symmetry. The presented method leverages known characteristics of reciprocal space, enabling physically reasonable reconstruction even with large image gaps. The method will correspondingly fail for images that violate these underlying assumptions. The method assumes point symmetry and is thus applicable to small-angle X-ray scattering (SAXS) data, but only to a subset of wide-angle data. Our method succeeds in filling gaps and healing defects in experimental images, including extending data beyond the original detector borders.

The capacity of frequency-flat multiuser MIMO downlinks is achieved with nonlinear dirty paper coding (DPC). Linear processing techniques, such as block diagonalization (BD), offer relatively low computational cost with respect to DPC and can also achieve capacity in certain cases. However, BD is not easily translated to frequency-selective channels since the channel matrix has a space-time structure (unlike the space-only information in frequency-flat channels), which induces an additional inter-symbol interference (ISI) component in the received signal. In this paper, we demonstrate that BD is feasible in frequency- selective channels when the transmitted block length is sufficiently large and the number of transmit antennas is greater than or equal to the number of users. We also present three novel techniques based on BD for frequency-selective MU- MIMO systems: time-reversal-based BD (TRBD), equalized BD (EBD), and joint processing BD (JPBD). These techniques use perfect channel state information at the transmitter (and also at the receiver, in the case of JPBD) to mitigate or eliminate both ISI and inter-user interference. We demonstrate that TRBD and EBD yield zero multiplexing gain (high SNR regime) but perform well under low SNR, while JPBD has a multiplexing gain approximately equal to the number of users for a sufficiently large transmit block length. Extensive numerical simulations show that the achievable rate performance of the proposed techniques improves that of time-reversal beamforming, a common technique for frequency- selective MU-MIMO downlinks.

This paper studies the downlink of a wireless system with an M-antenna base station, K single-antenna legitimate users and a single-antenna eavesdropper. A limited feedback-based scheduling and precoding scenario is considered that employs the orthogonal random beamforming (ORBF). The sum-rate of ORBF exhibits an identical growth rate as that of dirty paper coding for a large number of users. Unfortunately, for more realistic (low to moderate) K values, ORBF yields degraded performance. It is shown that having as many active beams as the number of transmit antennas is not always optimal for sparse network, thus scheduling strategies for ORBF with beam selection is investigated. Several user-beam selection algorithms featuring different complexity levels are proposed and their performance in terms of secrecy sum-rate is assessed. Numerical results are provided to illustrate the impact of the number of active beams on the secrecy performance.

In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably the first one capable of discovering with accuracy exceeding 50% multiple complex patterns in real gene expression datasets. It is also one of the very few biclustering methods designed for parallel environments with multiple graphics processing units (GPUs). We demonstrate that EBIC outperforms state-of-the-art biclustering methods, in terms of recovery and relevance, on both synthetic and genetic datasets. EBIC also yields results over 12 times faster than the most accurate reference algorithms. The proposed algorithm is anticipated to be added to the repertoire of unsupervised machine learning algorithms for the analysis of datasets, including those from large-scale genomic studies., 9 pages, 7 figures

In this paper, a two-stage filter for removing salt-and-pepper noise using noise detector based on characteristic difference parameter and adaptive directional mean filter is proposed. The first stage firstly detects the noise corrupted pixels by combining characteristic difference parameter and gray level extreme, then develops an improved adaptive median filter to firstly restore them. The second stage introduces a restoration scheme to further restore the noise corrupted pixels, which firstly divides them into two types and then applies different restoration skills for the pixels based on the classification result. One type of pixels is restored by the mean filter and the other type of pixels is restored by the proposed adaptive directional mean filter. The new filter firstly adaptively selects the optimal filtering window and direction template, then replaces the gray level of noise corrupted pixel by the mean value of pixels on the optimal template. Experimental results show that the proposed filter outperforms many existing main filters in terms of noise suppression and detail preservation.

Background The COVID-19 epidemic is still spreading globally. Contact tracing is a vital strategy in epidemic emergency management; however, traditional contact tracing faces many limitations in practice. The application of digital technology provides an opportunity for local governments to trace the contacts of individuals with COVID-19 more comprehensively, efficiently, and precisely. Objective Our research aimed to provide new solutions to overcome the limitations of traditional contact tracing by introducing the organizational process, technical process, and main achievements of digital contact tracing in Hainan Province. Methods A graph database algorithm, which can efficiently process complex relational networks, was applied in Hainan Province; this algorithm relies on a governmental big data platform to analyze multisource COVID-19 epidemic data and build networks of relationships among high-risk infected individuals, the general population, vehicles, and public places to identify and trace contacts. We summarized the organizational and technical process of digital contact tracing in Hainan Province based on interviews and data analyses. Results An integrated emergency management command system and a multi-agency coordination mechanism were formed during the emergency management of the COVID-19 epidemic in Hainan Province. The collection, storage, analysis, and application of multisource epidemic data were realized based on the government’s big data platform using a centralized model. The graph database algorithm is compatible with this platform and can analyze multisource and heterogeneous big data related to the epidemic. These practices were used to quickly and accurately identify and trace 10,871 contacts among hundreds of thousands of epidemic data records; 378 closest contacts and a number of public places with high risk of infection were identified. A confirmed patient was found after quarantine measures were implemented by all contacts. Conclusions During the emergency management of the COVID-19 epidemic, Hainan Province used a graph database algorithm to trace contacts in a centralized model, which can identify infected individuals and high-risk public places more quickly and accurately. This practice can provide support to government agencies to implement precise, agile, and evidence-based emergency management measures and improve the responsiveness of the public health emergency response system. Strengthening data security, improving tracing accuracy, enabling intelligent data collection, and improving data-sharing mechanisms and technologies are directions for optimizing digital contact tracing.

Introduction: Intelligent Diagnostic Assistant can be used for complicated diagnosis of skin diseases, which are among the most common causes of disability. The aim of this study was to design and implement a computerized intelligent diagnostic assistant for complicated skin diseases through C5’s Algorithm. Method: An applied-developmental study was done in 2015. Knowledge base was developed based on interviews with dermatologists through questionnaires and checklists. Knowledge representation was obtained from the train data in the database using Excel Microsoft Office. Clementine Software and C5’s Algorithms were applied to draw the decision tree. Analysis of test accuracy was performed based on rules extracted using inference chains. The rules extracted from the decision tree were entered into the CLIPS programming environment and the intelligent diagnostic assistant was designed then. Results: The rules were defined using forward chaining inference technique and were entered into Clips programming environment as RULE. The accuracy and error rates obtained in the training phase from the decision tree were 99.56% and 0.44%, respectively. The accuracy of the decision tree was 98% and the error was 2% in the test phase. Conclusion: Intelligent diagnostic assistant can be used as a reliable system with high accuracy, sensitivity, specificity, and agreement.

Motivation Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. Results The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Conclusions Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines. Availability and Implementation Source code: https://github.com/SBU-BMI/region-templates/. Supplementary information Supplementary data are available at Bioinformatics online.

Blood vascular reconstruction plays an important role in vessel disease diagnosis and prognosis, treatment planning and surgery. Based on adjacent vector projection, a simple and robust explicit algorithm is presented for vascular reconstruction. It generates the base mesh and utilizes the Loop algorithm for perceptual refinement by mesh subdivision. In the end, the reconstructed vascular tree is rendered for volumetric visualization and localization of vascular malformations. Experimental results on the Aneurisk database have validated the capacity of the proposed algorithm in generating smooth surface and natural transition of high tortuosity in real time, while on clinical cases has verified its accuracy on pinning vascular stenosis.

본 논문에서는 다른 셀로부터 발생하는 간섭을 고려하여 다중사용자 다중안테나 하향링크 채널에서 최소평균제곱오차(MMSE: minimum mean-squared error)에 기반한 비선형 연속 프리코딩(precoding) 기법을 제안한다. 기존의 zero forcing(ZF) 기반의 방법과 달리 제안하는 방식은 다른 셀로부터의 간섭을 고려하여 셀 내의 다중사용자 간섭을 억제하는 방식을 취하여 수신단에서의 신호 대 간섭 잡음비를 향상시킬 수 있다. 모의 실험 결과를 통해 제안하는 최소평균제곱오차에 기반한 비선형 전처리 기법이 다양한 셀 간섭 환경에서 기존 방법보다 좋은 성능을 가지는 것을 확인할 수 있다.

Methods for efficient data extraction for neutron spin-echo spectroscopy with multipixel area detectors and – at a pulsed neutron source – multiple time-of-flight wavelength bins are presented., Neutron spin-echo spectrometers with a position-sensitive detector and operating with extended time-of-flight-tagged wavelength frames are able to collect a comprehensive set of data covering a large range of wavevector and Fourier time space with only a few instrumental settings in a quasi-continuous way. Extracting all the information contained in the raw data and mapping them to a suitable physical space in the most efficient way is a challenge. This article reports algorithms employed in dedicated software, DrSpine (data reduction for spin echo), that achieves this goal and yields reliable representations of the intermediate scattering function S(Q, t) independent of the selected ‘binning’.

We present a scheme for accelerating hybrid continuum-atomistic models in multiscale fluidic systems by using Gaussian process regression as a surrogate model for computationally expensive molecular dynamics simulations. Using Gaussian process regression, we are able to accurately predict atomic-scale information purely by consideration of the macroscopic continuum-model inputs and outputs and judge on the fly whether the uncertainty of our prediction is at an acceptable level, else a new molecular simulation is performed to continually augment the database, which is never required to be complete. This provides a substantial improvement over the current generation of hybrid methods, which often require many similar atomistic simulations to be performed, discarding information after it is used once. We apply our hybrid scheme to nano-confined unsteady flow through a high-aspect-ratio converging-diverging channel, and make comparisons between the new scheme and full molecular dynamics simulations for a range of uncertainty thresholds and initial databases. For low thresholds, our hybrid solution is highly accurate-around that of thermal noise. As the uncertainty threshold is raised, the accuracy of our scheme decreases and the computational speed-up increases (relative to a full molecular simulation), enabling the compromise between accuracy and efficiency to be tuned. The speed-up of our hybrid solution ranges from an order of magnitude, with no initial database, to cases where an extensive initial database ensures no new MD simulations are required.

A numerical scheme is proposed for the detection of multiple cracks in three dimensional (3D) structures. The scheme is based on a variant of the extended finite element method (XFEM) and a hybrid optimizer solution. The proposed XFEM variant is particularly well-suited for the simulation of 3D fracture problems, and as such serves as an efficient solution to the so-called forward problem. A set of heuristic optimization algorithms are recombined into a multiscale optimization scheme. The introduced approach proves effective in tackling the complex inverse problem involved, where identification of multiple flaws is sought on the basis of sparse measurements collected near the structural boundary. The potential of the scheme is demonstrated through a set of numerical case studies of varying complexity., Computational Mechanics, 62 (4), ISSN:0178-7675, ISSN:1432-0924

Background: While health literacy is important for people to maintain good health and manage diseases, medical educational texts are often written beyond the reading level of the average individual. To mitigate this disconnect, text simplification research provides methods to increase readability and, therefore, comprehension. One method of text simplification is to isolate particularly difficult terms within a document and replace them with easier synonyms (lexical simplification) or an explanation in plain language (semantic simplification). Unfortunately, existing dictionaries are seldom complete, and consequently, resources for many difficult terms are unavailable. This is the case for English and Spanish resources. Objective: Our objective was to automatically generate explanations for difficult terms in both English and Spanish when they are not covered by existing resources. The system we present combines existing resources for explanation generation using a novel algorithm (SubSimplify) to create additional explanations. Methods: SubSimplify uses word-level parsing techniques and specialized medical affix dictionaries to identify the morphological units of a term and then source their definitions. While the underlying resources are different, SubSimplify applies the same principles in both languages. To evaluate our approach, we used term familiarity to identify difficult terms in English and Spanish and then generated explanations for them. For each language, we extracted 400 difficult terms from two different article types (General and Medical topics) balanced for frequency. For English terms, we compared SubSimplify’s explanation with the explanations from the Consumer Health Vocabulary, WordNet Synonyms and Summaries, as well as Word Embedding Vector (WEV) synonyms. For Spanish terms, we compared the explanation to WordNet Summaries and WEV Embedding synonyms. We evaluated quality, coverage, and usefulness for the simplification provided for each term. Quality is the average score from two subject experts on a 1-4 Likert scale (two per language) for the synonyms or explanations provided by the source. Coverage is the number of terms for which a source could provide an explanation. Usefulness is the same expert score, however, with a 0 assigned when no explanations or synonyms were available for a term. Results: SubSimplify resulted in quality scores of 1.64 for English (P

Background Chest computed tomography (CT) is crucial for the detection of lung cancer, and many automated CT evaluation methods have been proposed. Due to the divergent software dependencies of the reported approaches, the developed methods are rarely compared or reproduced. Objective The goal of the research was to generate reproducible machine learning modules for lung cancer detection and compare the approaches and performances of the award-winning algorithms developed in the Kaggle Data Science Bowl. Methods We obtained the source codes of all award-winning solutions of the Kaggle Data Science Bowl Challenge, where participants developed automated CT evaluation methods to detect lung cancer (training set n=1397, public test set n=198, final test set n=506). The performance of the algorithms was evaluated by the log-loss function, and the Spearman correlation coefficient of the performance in the public and final test sets was computed. Results Most solutions implemented distinct image preprocessing, segmentation, and classification modules. Variants of U-Net, VGGNet, and residual net were commonly used in nodule segmentation, and transfer learning was used in most of the classification algorithms. Substantial performance variations in the public and final test sets were observed (Spearman correlation coefficient = .39 among the top 10 teams). To ensure the reproducibility of results, we generated a Docker container for each of the top solutions. Conclusions We compared the award-winning algorithms for lung cancer detection and generated reproducible Docker images for the top solutions. Although convolutional neural networks achieved decent accuracy, there is plenty of room for improvement regarding model generalizability.

For the conventional computational methods for structural reliability analysis, the common limitations are long computational time, large number of iteration and low accuracy. Thus, a new novel method for structural reliability analysis has been proposed in this paper based on response surface method incorporated with an improved genetic algorithm. The genetic algorithm is first improved from the conventional genetic algorithm. Then, it is used to produce the response surface and the structural reliability is finally computed using the proposed method. The proposed method can be used to compute structural reliability easily whether the limit state function is explicit or implicit. It has been verified by two practical engineering cases that the algorithm is simple, robust, high accuracy and fast computation.

Some of the most efficient algorithms for computing the length of a longest common subsequence (LLCS) between two strings are based on so-called “bit-parallelism”. They achieve \(O(\lceil m/w \rceil n)\) time, where m and n are the string lengths and w is the computer word size. The first such algorithm was presented by Allison and Dix [3] and performs 6 bit-vector operations per step. The number of operations per step has later been improved to 5 by Crochemore et al. [5] and to 4 by Hyyro [6]. In this short paper we explore whether further improvement is possible. We find that under fairly reasonable assumptions, the LLCS problem requires at least 4 bit-vector operations per step. As a byproduct we also present five new 4-operation bit-parallel LLCS algorithms.

Bats sonar algorithm (BSA) as a swarm intelligence approach utilises the concept of echolocation of bats to find prey. However, the algorithm is unable to achieve good precision and fast convergence rate to the optimum solution. With this in mind, an adaptive bats sonar algorithm is introduced with new paradigms of real bats echolocation behaviour. The performance of the algorithm is validated through rigorous tests with several single objective optimisation benchmark test functions. The obtained results show that the proposed scheme outperforms the BSA in terms of accuracy and convergence speed and can be efficiently employed to solve engineering problems.

In this paper, we propose a new speech enhancement algorithm based on wavelet packet decomposition and mask filtering. In the traditional mask filtering such as ideal binary mask (IBM), the basic idea is to classify speech components as target signal and non-speech components as background noises. However, speech and non-speech components cannot be well separated in target signal and background noise. Therefore, the IBM has residual noise and signal loss. To overcome this problem, the proposed algorithm used semi-soft mask filter to exponentially increase. The semi-soft mask minimizes signal loss and the exponential filter removes residual noise. We performed experiments using various types of speech and noise signals, and experimental results show that the proposed algorithm achieves better performances than the traditional other speech enhancement algorithms.

Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements relative to the reference. They can scale over orders of magnitude in query sequence length. Finally, they are trivially extensible to more complex reference structures, such as graphs, that incorporate additional variation. We demonstrate empirically the existence of high performance context schemes, and present efficient context scheme mapping algorithms. Availability and Implementation: The software test framework created for this work is available from https://registry.hub.docker.com/u/adamnovak/sequence-graphs/. Contact: benedict@soe.ucsc.edu Supplementary Information: Six supplementary figures and one supplementary section are available with the online version of this article., Submission for Bioinformatics

The aim of this document is to present how the interpretation of the RVM (Recovery Voltage Measurement) test can be improved through the use of a Debye equivalent circuit. As it is described in the literature, the interpretation of the RVM test requires expertise and if the transformer presents a high interfacial polarization it is not possible to diagnose it in detail. The Debye model is proposed in this work for enhancing RVM interpretation. This model is based on an electrical circuit that includes basic R-C components, that allows two interesting features: on one hand, insulation physical effects can be separately represented and, on the other, the values of the R-C components can be calculated from the RVM response. A method is proposed in which using a sweep with a constant number of predefined time constants branches allows us to determine the areas of influence of the different compounds present in the dielectric. Finally, several case studies are presented, in which it is correlated a dielectric oil treatment carried out and the equivalent circuit changes using a sweep allows us to analyze different branches’ sensitivity and to identify the areas of influence of each compound.