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Decision-support methods are crucial for analyzing complex alternatives and criteria in today’s data-driven world. This Systematic Literature Review (SLR) explores and synthesizes knowledge about decision support methodologies that integrate Multicriteria Decision Making (MCDM) and Principal Component Analysis (PCA), an unsupervised Machine Learning (ML) technique. Both techniques optimize complex decisions by combining multiple criteria and dimensional data analysis. Focusing on performance evaluations, criterion weighting, and validation testing, this review identifies significant gaps in existing methodologies. These include the lack of consideration for non-beneficial criteria in PCA, insufficient validation tests in over half of the studies, and the non-use of communalities (the contribution of each criterion to the main factors) in decision support approaches. Additionally, this SLR offers a comprehensive quantitative overview, analyzing data from the Scopus, IEEE, and Web of Science databases and identifying 16 relevant studies. Furthermore, the scarcity of systematic reviews integrating MCDM and PCA techniques impedes evidence-based decision-making practices and theoretical evolution. This is particularly crucial as ML and data analysis advance rapidly, requiring models that reflect technological innovations. This article addresses this gap in the literature by providing an analysis of decision support methods and guiding further improvement in this field.

Applied mathematics today is a vibrant field that keeps growing and is viewed as an essential part of the modern world as well as every profession on the planet. This research explores the emerging trends in applied mathematics and their far-reaching implications in various fields. Machine learning and artificial intelligence are revolutionizing healthcare, finance, and natural language processing. Big data analysis is enhancing decision-making in finance, healthcare, and logistics. Quantum computing promises to transform materials science and renewable energy. These trends are reshaping research and practice, offering innovative solutions and opportunities for interdisciplinary collaboration. Ethical considerations and the development of advanced algorithms are critical areas of future research. This study serves as a foundation for understanding and harnessing the potential of these trends, emphasizing the importance of continuous exploration and skill development in an evolving mathematical landscape. This overview explains why there is a need for individuals to remain updated as regard such trends to ensure that applied mathematics is availed to the world at its best to overcome the numerous challenges facing the world today. [ABSTRACT FROM AUTHOR]

Complex systems, as interwoven miscellaneous interacting entities that emerge and evolve through self-organization in a myriad of spiraling contexts, exhibit subtleties on global scale besides steering the way to understand complexity which has been under evolutionary processes with unfolding cumulative nature wherein order is viewed as the unifying framework. Indicating the striking feature of non-separability in components, a complex system cannot be understood in terms of the individual isolated constituents' properties per se, it can rather be comprehended as a way to multilevel approach systems behavior with systems whose emergent behavior and pattern transcend the characteristics of ubiquitous units composing the system itself. This observation specifies a change of scientific paradigm, presenting that a reductionist perspective does not by any means imply a constructionist view; and in that vein, complex systems science, associated with multiscale problems, is regarded as ascendancy of emergence over reductionism and level of mechanistic insight evolving into complex system. While evolvability being related to the species and humans owing their existence to their ancestors' capability with regards to adapting, emerging and evolving besides the relation between complexity of models, designs, visualization and optimality, a horizon that can take into account the subtleties making their own means of solutions applicable is to be entailed by complexity. Such views attach their germane importance to the future science of complexity which may probably be best regarded as a minimal history congruent with observable variations, namely the most parallelizable or symmetric process which can turn random inputs into regular outputs. Interestingly enough, chaos and nonlinear systems come into this picture as cousins of complexity which with tons of its components are involved in a hectic interaction with one another in a nonlinear fashion amongst the other related systems and fields. Relation, in mathematics, is a way of connecting two or more things, which is to say numbers, sets or other mathematical objects, and it is a relation that describes the way the things are interrelated to facilitate making sense of complex mathematical systems. Accordingly, mathematical modeling and scientific computing are proven principal tools toward the solution of problems arising in complex systems' exploration with sound, stimulating and innovative aspects attributed to data science as a tailored-made discipline to enable making sense out of voluminous (-big) data. Regarding the computation of the complexity of any mathematical model, conducting the analyses over the run time is related to the sort of data determined and employed along with the methods. This enables the possibility of examining the data applied in the study, which is dependent on the capacity of the computer at work. Besides these, varying capacities of the computers have impact on the results; nevertheless, the application of the method on the code step by step must be taken into consideration. In this sense, the definition of complexity evaluated over different data lends a broader applicability range with more realism and convenience since the process is dependent on concrete mathematical foundations. All of these indicate that the methods need to be investigated based on their mathematical foundation together with the methods. In that way, it can become foreseeable what level of complexity will emerge for any data desired to be employed. With relation to fractals, fractal theory and analysis are geared toward assessing the fractal characteristics of data, several methods being at stake to assign fractal dimensions to the datasets, and within that perspective, fractal analysis provides expansion of knowledge regarding the functions and structures of complex systems while acting as a potential means to evaluate the novel areas of research and to capture the roughness of objects, their nonlinearity, randomness, and so on. The idea of fractional-order integration and differentiation as well as the inverse relationship between them lends fractional calculus applications in various fields spanning across science, medicine and engineering, amongst the others. The approach of fractional calculus, within mathematics-informed frameworks employed to enable reliable comprehension into complex processes which encompass an array of temporal and spatial scales notably provides the novel applicable models through fractional-order calculus to optimization methods. Computational science and modeling, notwithstanding, are oriented toward the simulation and investigation of complex systems through the use of computers by making use of domains ranging from mathematics to physics as well as computer science. A computational model consisting of numerous variables that characterize the system under consideration allows the performing of many simulated experiments via computerized means. Furthermore, Artificial Intelligence (AI) techniques whether combined or not with fractal, fractional analysis as well as mathematical models have enabled various applications including the prediction of mechanisms ranging extensively from living organisms to other interactions across incredible spectra besides providing solutions to real-world complex problems both on local and global scale. While enabling model accuracy maximization, AI can also ensure the minimization of functions such as computational burden. Relatedly, level of complexity, often employed in computer science for decision-making and problem-solving processes, aims to evaluate the difficulty of algorithms, and by so doing, it helps to determine the number of required resources and time for task completion. Computational (-algorithmic) complexity, referring to the measure of the amount of computing resources (memory and storage) which a specific algorithm consumes when it is run, essentially signifies the complexity of an algorithm, yielding an approximate sense of the volume of computing resources and seeking to prove the input data with different values and sizes. Computational complexity, with search algorithms and solution landscapes, eventually points toward reductions vis à vis universality to explore varying degrees of problems with different ranges of predictability. Taken together, this line of sophisticated and computer-assisted proof approach can fulfill the requirements of accuracy, interpretability, predictability and reliance on mathematical sciences with the assistance of AI and machine learning being at the plinth of and at the intersection with different domains among many other related points in line with the concurrent technical analyses, computing processes, computational foundations and mathematical modeling. Consequently, as distinctive from the other ones, our special issue series provides a novel direction for stimulating, refreshing and innovative interdisciplinary, multidisciplinary and transdisciplinary understanding and research in model-based, data-driven modes to be able to obtain feasible accurate solutions, designed simulations, optimization processes, among many more. Hence, we address the theoretical reflections on how all these processes are modeled, merging all together the advanced methods, mathematical analyses, computational technologies, quantum means elaborating and exhibiting the implications of applicable approaches in real-world systems and other related domains. [ABSTRACT FROM AUTHOR]

The article proposes formulating and codifying a set of applied numerical methods, coined as Deep Learning Discrete Calculus (DLDC), that uses the knowledge from discrete numerical methods to interpret the deep learning algorithms through the lens of applied mathematics. The DLDC methods aim to leverage the flexibility and ever-increasing resources of deep learning and rich literature on numerical analysis to formulate a general class of numerical methods that can directly use data with uncertainty to predict the behavior of an unknown system as well as elevate the speed and accuracy of numerical solution of the governing equations for known systems. The article is structured into two major sections. In the first section, the building blocks of the DLDC methods are presented and deep learning structures analogous to traditional numerical methods such as finite difference and finite element methods are constructed with a view to incorporate these techniques in Science, Technology, Engineering, Mathematics syllabus for K-12 students. The second section builds upon the building blocks of the previous discussion and proposes new solution schemes for differential and integral equations pertinent to multiscale mechanics. Each section is accompanied by a mathematical formulation of the numerical methods, analogous DLDC formulation, and suitable examples. [ABSTRACT FROM AUTHOR]

Artificial intelligence (AI) methods have revolutionized and redefined the landscape of data analysis in business, healthcare, and technology. These methods have innovated the applied mathematics, computer science, and engineering fields and are showing considerable potential for risk science, especially in the disaster risk domain. The disaster risk field has yet to define itself as a necessary application domain for AI implementation by defining how to responsibly balance AI and disaster risk. (1) How is AI being used for disaster risk applications; and how are these applications addressing the principles and assumptions of risk science, (2) What are the benefits of AI being used for risk applications; and what are the benefits of applying risk principles and assumptions for AI‐based applications, (3) What are the synergies between AI and risk science applications, and (4) What are the characteristics of effective use of fundamental risk principles and assumptions for AI‐based applications? This study develops and disseminates an online survey questionnaire that leverages expertise from risk and AI professionals to identify the most important characteristics related to AI and risk, then presents a framework for gauging how AI and disaster risk can be balanced. This study is the first to develop a classification system for applying risk principles for AI‐based applications. This classification contributes to understanding of AI and risk by exploring how AI can be used to manage risk, how AI methods introduce new or additional risk, and whether fundamental risk principles and assumptions are sufficient for AI‐based applications. [ABSTRACT FROM AUTHOR]

Background. The coronavirus epidemic continues, but there is evidence that the society has already mastered effective measures for the prevention and treatment of this disease. The unresolved problems are prevention, early diagnosis and timely treatment of new viral epidemics, prevention and treatment of postcovid complications, the mortality from which manifests itself latently under the guise of other diseases and does not fall into the statistics of the coronavirus pandemic. Materials and methods. Based on the developed original data processing technique, designed for analyzing coronavirus genomic data, models of the anti-coronavirus multi-epitope vaccine were computed and tested in silico. In a series of computational experiments, evidence of their possible efficiency and safety was obtained. Results and conclusions. Based on research experiments and analysis of scientific literature, recommendations are formulated for the development and application of epitope antiviral vaccines using the example of the anti-coronavirus vaccine.

Purpose: This paper aims at making a comparison of three optimization algorithms – standard Genetic Algorithm and its two modifications: Extended Compact Genetic Algorithm and Population-based Incremental Learning. Design/methodology/approach: To reach the objectives of the paper the solver based on algorithms was developed. Certain test functions were applied to test them and evaluate their performance. Findings: Modifications of Genetic Algorithm reach optimal values faster and more precisely. Research limitations/implications: Problem of optimization of certain cost functions frequently occurs in many management problems of organizing the optimal workflow in organizations. It can be used also in engineering problems of designing optimal devices at lowest possible cost. Practical implications: One can optimize function faster using discussed algorithms than by using standard evolutionary algorithm. Originality/value: The paper shows results of comparisons of three algorithms, discusses how tuning meta parameters helps to increase their efficiency and accuracy. [ABSTRACT FROM AUTHOR]

This review paper was written on the occasion of the 40th anniversary of the Drying Technology Journal. Interestingly, most of the progress made in the domain of drying modeling and simulation has occurred over the last 40 years. Indeed, 40 years ago, the comprehensive formulation of coupled heat and mass transfer in porous media was available; however, its potential use for computational simulation was only in its nascent stage. This is therefore an ideal time span in which to take a full historical context, to present the state-of-the-art and to give insights into its future trajectory. All aspects are deliberately presented in a pedagogical manner with many illustrations to make the text accessible to young scientists. However, for the benefit of experts, detailed formulations are provided in the annexes. The main points addressed in this work include: The description of the comprehensive macroscopic formulation, An historical perspective of the progress made in computational simulation, The contribution of modeling in parameter characterization, The mechanical aspects of drying: strain and stress induced by drying, including the case of large deformations, The impact of non-local equilibrium, The promising domain of the digital twin in parameter tuning and control/command. [ABSTRACT FROM AUTHOR]

The planning and management of traffic flow networks with multiple input data sources for decision-making generate the need for a mathematical approach. The program of measures for the development of the transport infrastructure of the Russian Federation provides for the selection of pilot regions for the creation of intelligent transportation systems. With extensive knowledge of theoretical and applied mathematics, it is important to select and adapt mathematical methods for solving problems. In this regard, the aim of the study is to develop and validate an algorithm for solving the problem of classifying objects according to the potential of creating intelligent transportation systems. The main mathematical apparatus for classification is the «random forest» machine learning algorithm method. A bagging machine learning meta-algorithm for high accuracy of the algorithm was used. This paper proposes the author's method of sequential classification analysis for identifying objects with the potential to create intelligent transportation systems. The choice of using this method is justified by its best behavior under the large number of predictor variables required for an objective aggregate assessment of digital development and quality of territories. The proposed algorithm on the example of Russian regions was tested. A technique and algorithm for statistical data processing based on descriptive analytics tools have been developed. The quality of the classification analysis algorithm was assessed by the random forest method based on misclassification coefficients. The admissibility of retrained algorithms and formation of a «fine-grained» «random forest» model for solving classification problems under the condition of no prediction was proven to be successful. The most productive models with the highest probability of correct classification were «reached» and «finalized» on the basis of logistic regression analysis of relationships between predictors and categorical dependent variables. The regions of class 1 with «high potential for the creation of intelligent transportation systems» are most likely to be ready for the reorganization of infrastructure facilities; the introduction of digital technologies in the management of traffic flows was found. [ABSTRACT FROM AUTHOR]

The water quality monitoring of lotic and lentic ecosystems allows for informing the possible use in human activities and the consumption of the vital liquid. This work measures the biochemical parameters in Coyuca Lagoon and Tecpan River, localized in Guerrero, Mexico. A comparative statistical analysis of six physicochemical factors in lentic and lotic ecosystems was carried out, finding individual pH values slightly higher for the lagoon ecosystem and lower for the river. For electrical conductivity, we find river sites with parameters lower than 500 μS/cm ideal for human use and consumption. On the contrary, in sites of the lagoon system, the conductivity was higher. As for the total hardness of the river, the values are within the Mexican standard; however, for the lagoon ecosystem, the water has a higher amount of calcium and magnesium salts and is not recommended for human consumption. For chlorides, the lagoon system exceeds the limits of regulations for human consumption; otherwise, it happens with the lotic system. The values of total alkalinity and total dissolved solids are higher for the lentic system than for the lotic one. Finally, the machine learning method shows the importance of measuring other parameters to determine the water quality, especially the salinity and calcium hardness. [ABSTRACT FROM AUTHOR]

Perturbation bounds for singular subspaces have a wide range of applications, including high‐dimensional statistics, machine learning, and applied mathematics. This paper focuses on the perturbation bounds of singular subspaces under a signal matrix interfered by a special heteroscedastic noise matrix in which its same row or column shares similar variance. First of all, we extend homoscedastic results of T. Tony Cai and Anru Zhang (see Rate‐optimal perturbation bounds for singular subspaces with applications to high‐dimensional statistics, The Annals of Statistics, 2018, 46(1), 60–89) to heteroscedastic cases. Then we apply the developed tools to the heteroskedastic clustering model. We find out that our upper bound of clustering misclassification rate is better than the one of T. Tony Cai, Rungang Han, and Anru Zhang (see arXiv:2008.12434, 2020). [ABSTRACT FROM AUTHOR]

One approach to understanding complex data is to study its shape through the lens of algebraic topology. While the early development of topological data analysis focused primarily on static data, in recent years, theoretical and applied studies have turned to data that varies in time. A time-varying collection of metric spaces as formed, for example, by a moving school of fish or flock of birds, can contain a vast amount of information. There is often a need to simplify or summarize the dynamic behavior. We provide an introduction to topological summaries of time-varying metric spaces including vineyards [19], crocker plots [55], and multiparameter rank functions [37]. We then introduce a new tool to summarize time-varying metric spaces: a crocker stack. Crocker stacks are convenient for visualization, amenable to machine learning, and satisfy a desirable continuity property which we prove. We demonstrate the utility of crocker stacks for a parameter identification task involving an influential model of biological aggregations [57]. Altogether, we aim to bring the broader applied mathematics community up-to-date on topological summaries of time-varying metric spaces. [ABSTRACT FROM AUTHOR]

Numerous examples of physically unjustified neural networks, despite satisfactory performance, generate contradictions with logic and lead to many inaccuracies in the final applications. One of the methods to justify the typical black-box model already at the training stage involves extending its cost function by a relationship directly inspired by the physical formula. This publication explains the concept of Physics- guided neural networks (PGNN), makes an overview of already proposed solutions in the field and describes possibilities of implementing physics-based loss functions for spatial analysis. Our approach shows that the model predictions are not only optimal but also scientifically consistent with domain specific equations. Furthermore, we present two applications of PGNNs and illustrate their advantages in theory by solving Poisson's and Burger's partial differential equations. The proposed formulas describe various real-world processes and have numerous applications in the area of applied mathematics. Eventually, the usage of scientific knowledge contained in the tailored cost functions shows that our methods guarantee physics-consistent results as well as better generalizability of the model compared to classical, artificial neural networks. [ABSTRACT FROM AUTHOR]

Language is an integral part of society which enables communication among its members. To shed light on how words gain their meaning and how their meaning evolves over time, color naming is often used as a case study. The color domain can be defined by a physical space, making it a useful concept for studying denotation of meaning. Though humans can distinguish millions of colors, language provides us with a small, manageable set of terms for categorizing the space. Partitions of the color space vary across different language groups and evolve over time (e.g. new color terms may enter a language). Investigating universal patterns in color naming provides insight into the mechanisms that give rise to the observed data. Recently, computational techniques have been utilized to study this phenomenon. Here, we develop a methodology for transforming a color naming data set—namely, the World Color Survey—which is based on constraints imposed by the stimulus space. This transformed data is used to initialize a nonparametric Bayesian machine learning model in order to implement a culture and theory-independent study of universal color naming patterns across different language groups. All of the methods described are executed by our Python software package called ColorBBDP.• Data from the World Color Survey is transformed from its original format into binary features vectors which can be given as input to the Beta-Bernoulli Dirichlet Process Mixture Model.• This paper provides a specific application of Variational Inference on the Beta-Bernoulli Dirichlet Process Mixture Model towards a color naming data set.• New mathematical measures for performing post-cluster analyses are also detailed in this paper.

Gaussian processes are ubiquitous in machine learning, statistics, and applied mathematics. They provide a flexible modelling framework for approximating functions, whilst simultaneously quantifying uncertainty. However, this is only true when the model is well-specified, which is often not the case in practice. In this paper, we study the properties of Gaussian process means when the smoothness of the model and the likelihood function are misspecified. In this setting, an important theoretical question of practical relevance is how accurate the Gaussian process approximations will be given the chosen model and the extent of the misspecification. The answer to this problem is particularly useful since it can inform our choice of model and experimental design. In particular, we describe how the experimental design and choice of kernel and kernel hyperparameters can be adapted to alleviate model misspecification. [ABSTRACT FROM AUTHOR]

The problem of computing the vertices of the convex hull of a given input set S = { v i ∈ R m : i = 1 , ⋯ , n } is a classic and fundamental problem, studied in the context of computational geometry, linear and convex programming, machine learning and more. In this article we present All Vertex Triangle Algorithm (AVTA), a robust and efficient algorithm for this problem. On the one hand, without any assumptions, AVTA computes approximation to the subset S ¯ of all K vertices of the convex hull of S so that the convex hull of the approximate subset of vertices is as close to conv(S) as desired. On the other hand, assuming a known lower bound γ on the ratio Γ ∗ / R , where Γ ∗ the minimum of the distances from each vertex to the convex hull of the remaining vertices and R the diameter of S, AVTA can recover all of S ¯ . Furthermore, assuming that instead of S the input is an ε -perturbation of S, S ¯ ε , where ‖ v i - v i ε ‖ ≤ ε R , AVTA can compute approximation to c o n v (S ¯ ε) , to any prescribed accuracy. Also, given a lower bound to the ratio Σ ∗ / R , where Σ ∗ is the minimum of the distances from each vertex to the convex hull of the remaining point of S, AVTA can recover all of S ¯ ε . We show Σ ∗ ≥ ρ ∗ Γ ∗ / R , where ρ ∗ is the minimum distance between distinct pair of points in S and prove the following main results: Given any t ∈ (0 , 1) , AVTA computes a subset S ¯ t of S ¯ of cardinality K (t) in O (n K (t) (m + t - 2)) operations so that for any p ∈ c o n v (S) its Euclidean distance to c o n v (S ¯ t) is at most tR. Given γ ≤ γ ∗ = Γ ∗ / R , AVTA computes S ¯ in O (n K (m + γ - 2)) operations. If K is known, the complexity of AVTA is O (n K (m + γ ∗ - 2) log (γ ∗ - 1)) . Assuming instead of S, its ε -perturbation, S ε is given, we prove Given any t ∈ (0 , 1) , AVTA computes a subset S ¯ ε t ⊂ S ¯ ε of cardinality K ε (t) in O (n K ε (t) (m + t - 2)) operations so that for any p ∈ c o n v (S) its distance to c o n v (S ¯ ε t) is at most (t + ε) R . Given σ ∈ [ 4 ε , σ ∗ = Γ ∗ / R ] , AVTA computes S ¯ ε in O (n K ε (m + σ - 2)) operations, where K ≤ K ε ≤ n . If γ ≤ γ ∗ = Γ ∗ / R is known satisfying 4 ε ≤ γ ρ ∗ / R , AVTA computes S ¯ ε in O (n K ε (m + (γ ρ ∗) - 2)) operations. Given σ ∈ [ 4 ε , σ ∗ ] , if K is known, AVTA computes S ¯ ε in O (n K (m + σ ∗ - 2) log (σ ∗ - 1)) operations. We also consider the application of AVTA in the recovery of vertices through the projection of S or S ε under a Johnson–Lindenstrauss randomized linear projection L : R m → R m ′ . Denoting U = L (S) and U ε = L (S ε) , by relating the robustness parameters of conv(U) and c o n v (U ε) to those of conv(S) and c o n v (S ε) , we derive analogous complexity bounds for probabilistic computation of the vertex set of conv(U) or those of c o n v (U ε) , or an approximation to them. Finally, we apply AVTA to design new practical algorithms for two popular machine learning problems: topic modeling and non-negative matrix factorization. For topic models, our new algorithm leads to significantly better reconstruction of the topic-word matrix than state of the art approaches of Arora et al. (International conference on machine learning, pp 280–288, 2013) and Bansal et al. (Advances in neural information processing systems, pp 1997–2005, 2014). Additionally, we provide a robust analysis of AVTA and empirically demonstrate that it can handle larger amounts of noise than existing methods. For non-negative matrix factorization we show that AVTA is competitive with existing methods that are specialized for this task in Arora et al. (Proceedings of the forty-fourth annual ACM symposium on theory of computing, ACM, pp 145–162, 2012a). We also contrast AVTA with Blum et al. (Proceedings of the twenty-seventh annual ACM-SIAM symposium on discrete algorithms, Society for Industrial and Applied Mathematics, pp 548–557, 2016) Greedy Clustering coreset algorithm for computing approximation to the set of vertices and argue that not only there are regimes where AVTA outperforms that algorithm but it can also be used as a pre-processing step to their algorithm. Thus the two algorithms in fact complement each other. [ABSTRACT FROM AUTHOR]

The present survey is intended to serve as a comprehensive account of the main areas of the cryptography based on the Ring Learning With Errors Problem. We cover the major topics, from their mathematical foundations to the main primitives, as well as several open ends and recent progress with an emphasis in the connections with algebraic number theory. This work is based to a certain extent on an invited course and a seminar given by the author at the Basque Center for Applied Mathematics in 2018 and at the ICIAM 2019. [ABSTRACT FROM AUTHOR]

This problem can benefit from machine learning techniques, thanks to their capability of finding "hidden" relationships among the available data and therefore generate placement actions. In society, data producers and data consumers continuously exchange their roles. Since the very beginning, there has been a fruitful exchange between machine learning (ML) and optimization. [Extracted from the article]

In recent years, with the development of computer science, deep learning is held as competent enough to solve the problem of inference and learning in high dimensional space. Therefore, it has received unprecedented attention from both the academia and the business community. Compared with CPU/GPU, FPGA has attracted much attention for its high-energy efficiency, short development cycle and reconfigurability in the aspect of deep learning algorithm. However, because of the limited research on OpenCL optimization on FPGA of deep learning algorithms, OpenCL tools and models applied to CPU/GPU cannot be directly used on FPGA. This makes it difficult for software programmers to use FPGA when implementing deep learning algorithms for a rewarding performance. To solve this problem, this paper proposed an OpenCL computational model based on FPGA template architecture to optimize the time-consuming convolution layer in deep learning. The comparison between the program applying the computational model and the corresponding optimization program provided by Xilinx indicates that the former is 8-40 times higher than the latter in terms of performance. [ABSTRACT FROM AUTHOR]

Fundamental scientific advances can take decades to translate into improvements in human health. Shortening this interval would increase the rate at which scientific discoveries lead to successful treatment of human disease. One way to accomplish this would be to identify which advances in knowledge are most likely to translate into clinical research. Toward that end, we built a machine learning system that detects whether a paper is likely to be cited by a future clinical trial or guideline. Despite the noisiness of citation dynamics, as little as 2 years of postpublication data yield accurate predictions about a paper's eventual citation by a clinical article (accuracy = 84%, F1 score = 0.56; compared to 19% accuracy by chance). We found that distinct knowledge flow trajectories are linked to papers that either succeed or fail to influence clinical research. Translational progress in biomedicine can therefore be assessed and predicted in real time based on information conveyed by the scientific community's early reaction to a paper. [ABSTRACT FROM AUTHOR]

The prediction of cell-lines sensitivity to a given set of compounds is a very important factor in the optimization of in-vitro assays. To date, the most common prediction strategies are based upon machine learning or other quantitative structure-activity relationships (QSAR) based approaches. In the present research, we propose and discuss a straightforward strategy not based on any learning modelling but exclusively relying upon the chemical similarity of a query compound to reference compounds with annotated activity against cell lines. We also compare the performance of the proposed method to machine learning predictions on the same problem. A curated database of compounds-cell lines associations derived from ChemBL version 22 was created for algorithm construction and cross-validation. Validation was done using 10-fold cross-validation and testing the models on new data obtained from ChemBL version 25. In terms of accuracy, both methods perform similarly with values around 0.65 across 750 cell lines in 10-fold cross-validation experiments. By combining both methods it is possible to achieve 66% of correct classification rate in more than 26000 newly reported interactions comprising 11000 new compounds. A Web Service implementing the described approaches (both similarity and machine learning based models) is freely available at: . [ABSTRACT FROM AUTHOR]

Sensor network intrusion detection has attracted extensive attention. However, previous intrusion detection methods face the highly imbalanced attack class distribution problem, and they may not achieve a satisfactory performance. To solve this problem, we propose a new intrusion detection algorithm based on normalized cut spectral clustering for sensor network in this paper. The main aim is to reduce the imbalance degree among classes in an intrusion detection system. First, we design a normalized cut spectral clustering to reduce the imbalance degree between every two classes in the intrusion detection data set. Second, we train a network intrusion detection classifier on the new data set. Finally, we do extensive experiments and analyze the experimental results in detail. Simulation experiments show that our algorithm can reduce the imbalance degree among classes and reserves the distribution of the original data on the one hand, and improve effectively the detection performance on the other hand. [ABSTRACT FROM AUTHOR]

Temporal hierarchies have been widely used during the past few years as they are capable to provide more accurate coherent forecasts at different planning horizons. However, they still display some limitations, being mainly subject to the forecasting methods used for generating the base forecasts and the particularities of the examined series. This paper deals with such limitations by considering three different strategies: (i) combining forecasts of multiple methods, (ii) applying bias adjustments and (iii) selectively implementing temporal hierarchies to avoid seasonal shrinkage. The proposed strategies can be applied either separately or simultaneously, being complements to the method considered for reconciling the base forecasts and completely independent from each other. Their effect is evaluated using the monthly series of the M and M3 competitions. The results are very promising, displaying lots of potential for improving the performance of temporal hierarchies, both in terms of accuracy and bias. [ABSTRACT FROM AUTHOR]

Background and objective: To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment. Methods: The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data. In our prototypical implementation we use an OMOP common data model (OMOP-CDM) database. The architecture supports the entire research lifecycle from creating a data analysis environment, retrieving data, and training to final deployment in a hospital setting. Results: We evaluated the platform by establishing and deploying an analysis and end user application for hemoglobin reference intervals within the University Hospital Erlangen. To demonstrate the potential of the system to deploy arbitrary models, we loaded a colorectal cancer dataset into an OMOP database and built machine learning models to predict patient outcomes and made them available via a web service. We demonstrated both the integration with FHIR as well as an example end user application. Finally, we integrated the platform with the open source DataSHIELD architecture to allow for distributed privacy preserving data analysis and training across networks of hospitals. Conclusion: The KETOS platform takes a novel approach to data analysis, training and deploying decision support models in a hospital or healthcare setting. It does so in a secure and privacy-preserving manner, combining the flexibility of Docker virtualization with the advantages of standardized vocabularies, a widely applied database schema (OMOP-CDM), and a standardized way to exchange medical data (FHIR). [ABSTRACT FROM AUTHOR]

Purpose: Development of a supervised machine-learning model capable of predicting clinically relevant molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) from diffusion-weighted-imaging-derived radiomic features. Methods: The retrospective observational study assessed 55 surgical PDAC patients. Molecular subtypes were defined by immunohistochemical staining of KRT81. Tumors were manually segmented and 1606 radiomic features were extracted with PyRadiomics. A gradient-boosted-tree algorithm was trained on 70% of the patients (N = 28) and tested on 30% (N = 17) to predict KRT81+ vs. KRT81- tumor subtypes. A gradient-boosted survival regression model was fit to the disease-free and overall survival data. Chemotherapy response and survival were assessed stratified by subtype and radiomic signature. Radiomic feature importance was ranked. Results: The mean±STDEV sensitivity, specificity and ROC-AUC were 0.90±0.07, 0.92±0.11, and 0.93±0.07, respectively. The mean±STDEV concordance indices between the disease-free and overall survival predicted by the model based on the radiomic parameters and actual patient survival were 0.76±0.05 and 0.71±0.06, respectively. Patients with a KRT81+ subtype experienced significantly diminished median overall survival compared to KRT81- patients (7.0 vs. 22.6 months, HR 4.03, log-rank-test P = <0.001) and a significantly improved response to gemcitabine-based chemotherapy over FOLFIRINOX (10.14 vs. 3.8 months median overall survival, HR 2.33, P = 0.037) compared to KRT81- patients, who responded significantly better to FOLFIRINOX over gemcitabine-based treatment (30.8 vs. 13.4 months median overall survival, HR 2.41, P = 0.027). Entropy was ranked as the most important radiomic feature. Conclusions: The machine-learning based analysis of radiomic features enables the prediction of subtypes of PDAC, which are highly relevant for disease-free and overall patient survival and response to chemotherapy. [ABSTRACT FROM AUTHOR]

Most cetacean species are wide-ranging and highly mobile, creating significant challenges for researchers by limiting the scope of data that can be collected and leaving large areas un-surveyed. Aerial surveys have proven an effective way to locate and study cetacean movements but are costly and limited in spatial extent. Here we present a semi-automated pipeline for whale detection from very high-resolution (sub-meter) satellite imagery that makes use of a convolutional neural network (CNN). We trained ResNet, and DenseNet CNNs using down-scaled aerial imagery and tested each model on 31 cm-resolution imagery obtained from the WorldView-3 sensor. Satellite imagery was tiled and the trained algorithms were used to classify whether or not a tile was likely to contain a whale. Our best model correctly classified 100% of tiles with whales, and 94% of tiles containing only water. All model architectures performed well, with learning rate controlling performance more than architecture. While the resolution of commercially-available satellite imagery continues to make whale identification a challenging problem, our approach provides the means to efficiently eliminate areas without whales and, in doing so, greatly accelerates ocean surveys for large cetaceans. [ABSTRACT FROM AUTHOR]

Cancer driver genes, i.e., oncogenes and tumor suppressor genes, are involved in the acquisition of important functions in tumors, providing a selective growth advantage, allowing uncontrolled proliferation and avoiding apoptosis. It is therefore important to identify these driver genes, both for the fundamental understanding of cancer and to help finding new therapeutic targets or biomarkers. Although the most frequently mutated driver genes have been identified, it is believed that many more remain to be discovered, particularly for driver genes specific to some cancer types. In this paper, we propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types. We empirically show that LOTUS outperforms five other state-of-the-art driver gene prediction methods, both in terms of intrinsic consistency and prediction accuracy, and provide predictions of new cancer genes across many cancer types. [ABSTRACT FROM AUTHOR]

Background: The Sequential Organ Failure Assessment (SOFA) score is commonly used in ICUs around the world, designed to assess the severity of the patient's clinical state based on function/dysfunction of six major organ systems. The goal of this work is to build a computational model to predict mortality based on a series of SOFA scores. In addition, we examined the possibility of improving the prediction by incorporating a new component designed to measure the performance of the gastrointestinal system, added to the other six components. Methods: In this retrospective study, we used patients’ three latest SOFA scores recorded during an individual ICU stay as input to different machine learning models and ensemble learning models. We added three validated parameters representing gastrointestinal failure. Among others, we used classification models such as Support Vector Machines (SVMs), Neural Networks, Logistic Regression and a penalty function used to increase model robustness in regard to certain extreme cases, which may be found in ICU population. We used the Area under Curve (AUC) performance metric to examine performance. Results: We found an ensemble model of linear and logistic regression achieves a higher AUC compared related works in past years. After incorporating the gastrointestinal failure score along with the penalty function, our best performing ensemble model resulted in an additional improvement in terms of AUC metrics. We implemented and compared 36 different models that were built using both the information from the SOFA score as well as that of the gastrointestinal system. All compared models have approximately similar and relatively large AUC (between 0.8645 and 0.9146) with the best results are achieved by incorporating the gastrointestinal parameters into the prediction models. Conclusions: Our findings indicate that gastrointestinal parameters carry significant information as a mortality predictor in addition to the conventional SOFA score. This information improves the predictive power of machine learning models by extending the SOFA to include information related to gastrointestinal organ system. The described method improves mortality prediction by considering the dynamics of the extended SOFA score. Although tested on a limited data set, the results' stability across different models suggests robustness in real-time use. [ABSTRACT FROM AUTHOR]

Comprehensive information on the timing and location of gene expression is fundamental to our understanding of embryonic development and tissue formation. While high-throughput in situ hybridization projects provide invaluable information about developmental gene expression patterns for model organisms like Drosophila, the output of these experiments is primarily qualitative, and a high proportion of protein coding genes and most non-coding genes lack any annotation. Accurate data-centric predictions of spatio-temporal gene expression will therefore complement current in situ hybridization efforts. Here, we applied a machine learning approach by training models on all public gene expression and chromatin data, even from whole-organism experiments, to provide genome-wide, quantitative spatio-temporal predictions for all genes. We developed structured in silico nano-dissection, a computational approach that predicts gene expression in >200 tissue-developmental stages. The algorithm integrates expression signals from a compendium of 6,378 genome-wide expression and chromatin profiling experiments in a cell lineage-aware fashion. We systematically evaluated our performance via cross-validation and experimentally confirmed 22 new predictions for four different embryonic tissues. The model also predicts complex, multi-tissue expression and developmental regulation with high accuracy. We further show the potential of applying these genome-wide predictions to extract tissue specificity signals from non-tissue-dissected experiments, and to prioritize tissues and stages for disease modeling. This resource, together with the exploratory tools are freely available at our webserver , which provides a valuable tool for a range of applications, from predicting spatio-temporal expression patterns to recognizing tissue signatures from differential gene expression profiles. [ABSTRACT FROM AUTHOR]

The blood flow through the major vessels holds great diagnostic potential for the identification of cardiovascular complications and is therefore routinely assessed with current diagnostic modalities. Heart valves are subject to high hydrodynamic loads which render them prone to premature degradation. Failing native aortic valves are routinely replaced with bioprosthetic heart valves. This type of prosthesis is limited by a durability that is often less than the patient’s life expectancy. Frequent assessment of valvular function can therefore help to ensure good long-term outcomes and to plan reinterventions. In this article, we describe how unsupervised novelty detection algorithms can be used to automate the interpretation of blood flow data to improve outcomes through early detection of adverse cardiovascular events without requiring repeated check-ups in a clinical environment. The proposed method was tested in an in-vitro flow loop which allowed simulating a failing aortic valve in a laboratory setting. Aortic regurgitation of increasing severity was deliberately introduced with tube-shaped inserts, preventing complete valve closure during diastole. Blood flow recordings from a flow meter at the location of the ascending aorta were analyzed with the algorithms introduced in this article and a diagnostic index was defined that reflects the severity of valvular degradation. The results indicate that the proposed methodology offers a high sensitivity towards pathological changes of valvular function and that it is capable of automatically identifying valvular degradation. Such methods may be a step towards computer-assisted diagnostics and telemedicine that provide the clinician with novel tools to improve patient care. [ABSTRACT FROM AUTHOR]

Objective: The Centers for Disease Control and Prevention (CDC) coordinates a labor-intensive process to measure the prevalence of autism spectrum disorder (ASD) among children in the United States. Random forests methods have shown promise in speeding up this process, but they lag behind human classification accuracy by about 5%. We explore whether more recently available document classification algorithms can close this gap. Materials and methods: Using data gathered from a single surveillance site, we applied 8 supervised learning algorithms to predict whether children meet the case definition for ASD based solely on the words in their evaluations. We compared the algorithms’ performance across 10 random train-test splits of the data, using classification accuracy, F1 score, and number of positive calls to evaluate their potential use for surveillance. Results: Across the 10 train-test cycles, the random forest and support vector machine with Naive Bayes features (NB-SVM) each achieved slightly more than 87% mean accuracy. The NB-SVM produced significantly more false negatives than false positives (P = 0.027), but the random forest did not, making its prevalence estimates very close to the true prevalence in the data. The best-performing neural network performed similarly to the random forest on both measures. Discussion: The random forest performed as well as more recently available models like the NB-SVM and the neural network, and it also produced good prevalence estimates. NB-SVM may not be a good candidate for use in a fully-automated surveillance workflow due to increased false negatives. More sophisticated algorithms, like hierarchical convolutional neural networks, may not be feasible to train due to characteristics of the data. Current algorithms might perform better if the data are abstracted and processed differently and if they take into account information about the children in addition to their evaluations. Conclusion: Deep learning models performed similarly to traditional machine learning methods at predicting the clinician-assigned case status for CDC’s autism surveillance system. While deep learning methods had limited benefit in this task, they may have applications in other surveillance systems. [ABSTRACT FROM AUTHOR]

Linkage of medical databases, including insurer claims and electronic health records (EHRs), is increasingly common. However, few studies have investigated the behavior and output of linkage software. To determine how linkage quality is affected by different algorithms, blocking variables, methods for string matching and weight determination, and decision rules, we compared the performance of 4 nonproprietary linkage software packages linking patient identifiers from noninteroperable inpatient and outpatient EHRs. We linked datasets using first and last name, gender, and date of birth (DOB). We evaluated DOB and year of birth (YOB) as blocking variables and used exact and inexact matching methods. We compared the weights assigned to record pairs and evaluated how matching weights corresponded to a gold standard, medical record number. Deduplicated datasets contained 69,523 inpatient and 176,154 outpatient records, respectively. Linkage runs blocking on DOB produced weights ranging in number from 8 for exact matching to 64,273 for inexact matching. Linkage runs blocking on YOB produced 8 to 916,806 weights. Exact matching matched record pairs with identical test characteristics (sensitivity 90.48%, specificity 99.78%) for the highest ranked group, but algorithms differentially prioritized certain variables. Inexact matching behaved more variably, leading to dramatic differences in sensitivity (range 0.04–93.36%) and positive predictive value (PPV) (range 86.67–97.35%), even for the most highly ranked record pairs. Blocking on DOB led to higher PPV of highly ranked record pairs. An ensemble approach based on averaging scaled matching weights led to modestly improved accuracy. In summary, we found few differences in the rankings of record pairs with the highest matching weights across 4 linkage packages. Performance was more consistent for exact string matching than for inexact string matching. Most methods and software packages performed similarly when comparing matching accuracy with the gold standard. In some settings, an ensemble matching approach may outperform individual linkage algorithms. [ABSTRACT FROM AUTHOR]

High Content Analysis (HCA) has become a cornerstone of cellular analysis within the drug discovery industry. To expand the capabilities of HCA, we have applied the same analysis methods, validated in numerous mammalian cell models, to microbiology methodology. Image acquisition and analysis of various microbial samples, ranging from pure cultures to culture mixtures containing up to three different bacterial species, were quantified and identified using various machine learning processes. These HCA techniques allow for faster cell enumeration than standard agar-plating methods, identification of “viable but not plate culturable” microbe phenotype, classification of antibiotic treatment effects, and identification of individual microbial strains in mixed cultures. These methods greatly expand the utility of HCA methods and automate tedious and low-throughput standard microbiological methods. [ABSTRACT FROM AUTHOR]

Objectives: Cardiovascular disease (CVD) is one of the major causes of death worldwide. For improved accuracy of CVD prediction, risk classification was performed using national time-series health examination data. The data offers an opportunity to access deep learning (RNN-LSTM), which is widely known as an outstanding algorithm for analyzing time-series datasets. The objective of this study was to show the improved accuracy of deep learning by comparing the performance of a Cox hazard regression and RNN-LSTM based on survival analysis. Methods and findings: We selected 361,239 subjects (age 40 to 79 years) with more than two health examination records from 2002–2006 using the National Health Insurance System-National Health Screening Cohort (NHIS-HEALS). The average number of health screenings (from 2002–2013) used in the analysis was 2.9 ± 1.0. Two CVD prediction models were developed from the NHIS-HEALS data: a Cox hazard regression model and a deep learning model. In an internal validation of the NHIS-HEALS dataset, the Cox regression model showed a highest time-dependent area under the curve (AUC) of 0.79 (95% CI 0.70 to 0.87) for in females and 0.75 (95% CI 0.70 to 0.80) in males at 2 years. The deep learning model showed a highest time-dependent AUC of 0.94 (95% CI 0.91 to 0.97) for in females and 0.96 (95% CI 0.95 to 0.97) in males at 2 years. Layer-wise Relevance Propagation (LRP) revealed that age was the variable that had the greatest effect on CVD, followed by systolic blood pressure (SBP) and diastolic blood pressure (DBP), in that order. Conclusion: The performance of the deep learning model for predicting CVD occurrences was better than that of the Cox regression model. In addition, it was confirmed that the known risk factors shown to be important by previous clinical studies were extracted from the study results using LRP. [ABSTRACT FROM AUTHOR]

While most of the existing class stability assessors just rely on structural information retrieved from a desired source code snapshot. However, class stability is intrinsically characterized by the evolution of a number of dependencies and change propagation factors which aid to promote the ripple effect. Identification of classes prone to ripple effect (instable classes) through mining the version history of change propagation factors can aid developers to reduce the efforts needed to maintain and evolve the system. We propose Historical Information for Class Stability Prediction (HICSP), an approach to exploit change history information to predict the instable classes based on its correlation with change propagation factors. Subsequently, we performed two empirical studies. In the first study, we evaluate the HICSP on the version history of 10 open source projects. Subsequently, in the second replicated study, we evaluate the effectiveness of HICSP by tuning the parameters of its stability assessors. We observed the 4 to 16 percent improvement in term of F-measure value to predict the instable classes through HICSP as compared to existing class stability assessors. The promising results indicate that HICSP is able to identify instable classes and can aid developers in their decision making. [ABSTRACT FROM AUTHOR]

Neural correlates of mind wandering: The ability to detect mind wandering as it occurs is an important step towards improving our understanding of this phenomenon and studying its effects on learning and performance. Current detection methods typically rely on observable behaviour in laboratory settings, which do not capture the underlying neural processes and may not translate well into real-world settings. We address both of these issues by recording electroencephalography (EEG) simultaneously from 15 participants during live lectures on research in orthopedic surgery. We performed traditional group-level analysis and found neural correlates of mind wandering during live lectures that are similar to those found in some laboratory studies, including a decrease in occipitoparietal alpha power and frontal, temporal, and occipital beta power. However, individual-level analysis of these same data revealed that patterns of brain activity associated with mind wandering were more broadly distributed and highly individualized than revealed in the group-level analysis. Mind wandering detection: To apply these findings to mind wandering detection, we used a data-driven method known as common spatial patterns to discover scalp topologies for each individual that reflects their differences in brain activity when mind wandering versus attending to lectures. This approach avoids reliance on known neural correlates primarily established through group-level statistics. Using this method for individual-level machine learning of mind wandering from EEG, we were able to achieve an average detection accuracy of 80–83%. Conclusions: Modelling mind wandering at the individual level may reveal important details about its neural correlates that are not reflected when using traditional observational and statistical methods. Using machine learning techniques for this purpose can provide new insight into the varieties of neural activity involved in mind wandering, while also enabling real-time detection of mind wandering in naturalistic settings. [ABSTRACT FROM AUTHOR]

Filter or screening methods are often used as a preprocessing step for reducing the number of variables used by a learning algorithm in obtaining a classification or regression model. While there are many such filter methods, there is a need for an objective evaluation of these methods. Such an evaluation is needed to compare them with each other and also to answer whether they are at all useful, or a learning algorithm could do a better job without them. For this purpose, many popular screening methods are partnered in this paper with three regression learners and five classification learners and evaluated on ten real datasets to obtain accuracy criteria such as R-square and area under the ROC curve (AUC). The obtained results are compared through curve plots and comparison tables in order to find out whether screening methods help improve the performance of learning algorithms and how they fare with each other. Our findings revealed that the screening methods were useful in improving the prediction of the best learner on two regression and two classification datasets out of the ten datasets evaluated. [ABSTRACT FROM AUTHOR]

Due to the fast speed of data generation and collection from advanced equipment, the amount of data obviously overflows the limit of available memory space and causes difficulties achieving high learning accuracy. Several methods based on discard-after-learn concept have been proposed. Some methods were designed to cope with a single incoming datum but some were designed for a chunk of incoming data. Although the results of these approaches are rather impressive, most of them are based on temporally adding more neurons to learn new incoming data without any neuron merging process which can obviously increase the computational time and space complexities. Only online versatile elliptic basis function (VEBF) introduced neuron merging to reduce the space-time complexity of learning only a single incoming datum. This paper proposed a method for further enhancing the capability of discard-after-learn concept for streaming data-chunk environment in terms of low computational time and neural space complexities. A set of recursive functions for computing the relevant parameters of a new neuron, based on statistical confidence interval, was introduced. The newly proposed method, named streaming chunk incremental learning (SCIL), increases the plasticity and the adaptabilty of the network structure according to the distribution of incoming data and their classes. When being compared to the others in incremental-like manner, based on 11 benchmarked data sets of 150 to 581,012 samples with attributes ranging from 4 to 1,558 formed as streaming data, the proposed SCIL gave better accuracy and time in most data sets. [ABSTRACT FROM AUTHOR]

In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biological networks, six performance metrics and compared two types of input gene-disease association scores. The impact of the design factors in performance was quantified through additive explanatory models. Standard cross-validation led to over-optimistic performance estimates due to the presence of protein complexes. In order to obtain realistic estimates, we introduced two novel protein complex-aware cross-validation schemes. When seeding biological networks with known drug targets, machine learning and diffusion-based methods found around 2-4 true targets within the top 20 suggestions. Seeding the networks with genes associated to disease by genetics decreased performance below 1 true hit on average. The use of a larger network, although noisier, improved overall performance. We conclude that diffusion-based prioritisers and machine learning applied to diffusion-based features are suited for drug discovery in practice and improve over simpler neighbour-voting methods. We also demonstrate the large impact of choosing an adequate validation strategy and the definition of seed disease genes. [ABSTRACT FROM AUTHOR]

The mammalian neocortex is subdivided into a series of cortical areas that are functionally and anatomically distinct and are often distinguished in brain sections using histochemical stains and other markers of protein expression. We searched the Allen Mouse Brain Atlas, a database of gene expression, for novel markers of cortical areas. To screen for genes that change expression at area borders, we employed a random forest algorithm and binary region classification. Novel genetic markers were identified for 19 of 39 areas and provide code that quickly and efficiently searches the Allen Mouse Brain Atlas. Our results demonstrate the utility of the random forest algorithm for cortical area classification and we provide code that may be used to facilitate the identification of genetic markers of cortical and subcortical structures and perhaps changes in gene expression in disease states. [ABSTRACT FROM AUTHOR]

In transcriptomics, micro RNAs (miRNAs) has gained much interest especially as potential disease indicators. However, apart from holding a great promise related to their clinical application, a lot of inconsistent results have been published. Our aim was to compare the miRNA expression levels in ovarian cancer and healthy subjects using the Bayesian multilevel model and to assess their potential usefulness in diagnosis. We have analyzed a case-control observational data on expression profiling of 49 preselected miRNA-based ovarian cancer indicators in 119 controls and 59 patients. A Bayesian multilevel model was used to characterize the effect of disease on miRNA levels controlling for differences in age and body weight. The difference between the miRNA level and health status of the patient on the scale of the data variability were discussed in the context of their potential usefulness in diagnosis. Additionally, the cross-validated area under the ROC curve (AUC) was used to assess the expected out-of-sample discrimination index of a different sets of miRNAs. The proposed model allowed us to describe the set of miRNA levels in patients and controls. Three highly correlated miRNAs: miR-101-3p, miR-142-5p, miR-148a-3p rank the highest with almost identical effect sizes that ranges from 0.45 to 1.0. For those miRNAs the credible interval for AUC ranged from 0.63 to 0.67 indicating their limited discrimination potential. A little benefit in adding information from other miRNAs was observed. There were several miRNAs in the dataset (miR-604, hsa-miR-221-5p) for which inferences were uncertain. For those miRNAs more experimental effort is needed to fully assess their effect in the context of new hits discovery and usefulness as disease indicators. The proposed multilevel Bayesian model can be used to characterize the panel of miRNA profile and to assess the difference in expression levels between healthy and cancer individuals. [ABSTRACT FROM AUTHOR]

Caveolae are plasma membrane invaginations whose formation requires caveolin-1 (Cav1), the adaptor protein polymerase I, and the transcript release factor (PTRF or CAVIN1). Caveolae have an important role in cell functioning, signaling, and disease. In the absence of CAVIN1/PTRF, Cav1 forms non-caveolar membrane domains called scaffolds. In this work, we train machine learning models to automatically distinguish between caveolae and scaffolds from single molecule localization microscopy (SMLM) data. We apply machine learning algorithms to discriminate biological structures from SMLM data. Our work is the first that is leveraging machine learning approaches (including deep learning models) to automatically identifying biological structures from SMLM data. In particular, we develop and compare three binary classification methods to identify whether or not a given 3D cluster of Cav1 proteins is a caveolae. The first uses a random forest classifier applied to 28 hand-crafted/designed features, the second uses a convolutional neural net (CNN) applied to a projection of the point clouds onto three planes, and the third uses a PointNet model, a recent development that can directly take point clouds as its input. We validate our methods on a dataset of super-resolution microscopy images of PC3 prostate cancer cells labeled for Cav1. Specifically, we have images from two cell populations: 10 PC3 and 10 CAVIN1/PTRF-transfected PC3 cells (PC3-PTRF cells) that form caveolae. We obtained a balanced set of 1714 different cellular structures. Our results show that both the random forest on hand-designed features and the deep learning approach achieve high accuracy in distinguishing the intrinsic features of the caveolae and non-caveolae biological structures. More specifically, both random forest and deep CNN classifiers achieve classification accuracy reaching 94% on our test set, while the PointNet model only reached 83% accuracy. We also discuss the pros and cons of the different approaches. [ABSTRACT FROM AUTHOR]

Big web data from sources including online news and Twitter are good resources for investigating deep learning. However, collected news articles and tweets almost certainly contain data unnecessary for learning, and this disturbs accurate learning. This paper explores the performance of word2vec Convolutional Neural Networks (CNNs) to classify news articles and tweets into related and unrelated ones. Using two word embedding algorithms of word2vec, Continuous Bag-of-Word (CBOW) and Skip-gram, we constructed CNN with the CBOW model and CNN with the Skip-gram model. We measured the classification accuracy of CNN with CBOW, CNN with Skip-gram, and CNN without word2vec models for real news articles and tweets. The experimental results indicated that word2vec significantly improved the accuracy of the classification model. The accuracy of the CBOW model was higher and more stable when compared to that of the Skip-gram model. The CBOW model exhibited better performance on news articles, and the Skip-gram model exhibited better performance on tweets. Specifically, CNN with word2vec models was more effective on news articles when compared to that on tweets because news articles are typically more uniform when compared to tweets. [ABSTRACT FROM AUTHOR]

Purpose: To benchmark the human and machine performance of spectral-domain (SD) and swept-source (SS) optical coherence tomography (OCT) image segmentation, i.e., pixel-wise classification, for the compartments vitreous, retina, choroid, sclera. Methods: A convolutional neural network (CNN) was trained on OCT B-scan images annotated by a senior ground truth expert retina specialist to segment the posterior eye compartments. Independent benchmark data sets (30 SDOCT and 30 SSOCT) were manually segmented by three classes of graders with varying levels of ophthalmic proficiencies. Nine graders contributed to benchmark an additional 60 images in three consecutive runs. Inter-human and intra-human class agreement was measured and compared to the CNN results. Results: The CNN training data consisted of a total of 6210 manually segmented images derived from 2070 B-scans (1046 SDOCT and 1024 SSOCT; 630 C-Scans). The CNN segmentation revealed a high agreement with all grader groups. For all compartments and groups, the mean Intersection over Union (IOU) score of CNN compartmentalization versus group graders’ compartmentalization was higher than the mean score for intra-grader group comparison. Conclusion: The proposed deep learning segmentation algorithm (CNN) for automated eye compartment segmentation in OCT B-scans (SDOCT and SSOCT) is on par with manual segmentations by human graders. [ABSTRACT FROM AUTHOR]

Due to the characteristics of T-connection transmission lines, a new method for T-connection transmission lines fault identification based on current reverse travelling wave multi-scale S-transformation energy entropy and limit learning machine is proposed. S-transform are implemented on the faulty reverse traveling waves measured by each traveling wave protection unit of the T-connection transmission line, the reverse travelling wave energy entropies under eight different frequencies are respectively calculated, and a T-connection transmission line fault characteristic vector sample set are thus formed. Establish an intelligent fault identification model of extreme learning machines, and use the sample set for training and testing to identify the specific faulty branch of the T-connection transmission line. The simulation results show that the proposed algorithm can accurately and quickly identify the branch where the fault is located on the T-connection transmission line under various operation conditions. [ABSTRACT FROM AUTHOR]

Accurately predicting and testing the types of Pulmonary arterial hypertension (PAH) of each patient using cost-effective microarray-based expression data and machine learning algorithms could greatly help either identifying the most targeting medicine or adopting other therapeutic measures that could correct/restore defective genetic signaling at the early stage. Furthermore, the prediction model construction processes can also help identifying highly informative genes controlling PAH, leading to enhanced understanding of the disease etiology and molecular pathways. In this study, we used several different gene filtering methods based on microarray expression data obtained from a high-quality patient PAH dataset. Following that, we proposed a novel feature selection and refinement algorithm in conjunction with well-known machine learning methods to identify a small set of highly informative genes. Results indicated that clusters of small-expression genes could be extremely informative at predicting and differentiating different forms of PAH. Additionally, our proposed novel feature refinement algorithm could lead to significant enhancement in model performance. To summarize, integrated with state-of-the-art machine learning and novel feature refining algorithms, the most accurate models could provide near-perfect classification accuracies using very few (close to ten) low-expression genes. [ABSTRACT FROM AUTHOR]

While there have been many studies using machine learning (ML) algorithms to predict process outcomes and device performance in semiconductor manufacturing, the extensively developed technology computer-aided design (TCAD) physical models should play a more significant role in conjunction with ML. While TCAD models have been effective in predicting the trends of experiments, a machine learning statistical model is more capable of predicting the anomalous effects that can be dependent on the chambers, machines, fabrication environment, and specific layouts. In this paper, we use an analytics-statistics mixed training (ASMT) approach using TCAD. Under this method, the TCAD models are incorporated into the machine learning training procedure. The mixed dataset with the experimental and TCAD results improved the prediction in terms of accuracy. With the application of ASMT to the BOSCH process, we show that the mean square error (MSE) can be effectively decreased when the analytics-statistics mixed training (ASMT) scheme is used instead of the classic neural network (NN) used in the baseline study. In this method, statistical induction and analytical deduction can be combined to increase the prediction accuracy of future intelligent semiconductor manufacturing. [ABSTRACT FROM AUTHOR]

Over the last few decades, the Internet has experienced tremendous growth in data traffic. This continuous growth due to the increase in the number of connected devices and platforms has dramatically boosted content consumption. However, retrieving content from the servers of Content Providers (CPs) can increase network traffic and incur high network delay and congestion. To address these challenges, we propose a joint deep learning and auction-based approach for congestion-aware caching in Named Data Networking (NDN), which aims to prevent congestion and minimize the content downloading delays. First, using recorded network traffic data on the Internet Service Provider (ISP) network, we propose a deep learning model to predict future traffic over transit links. Second, to prevent congestion and avoid high latency on transit links, which may experience congestion in the future; we propose a caching model that helps the ISP to cache content that has a high predicted future demand. Paid-content requires payment to be downloaded and cached. Therefore, we propose an auction mechanism to obtain paid-content at an optimal price. The simulation results show that our proposal prevents congestion and increases the profits of both ISPs and CPs. [ABSTRACT FROM AUTHOR]

Gene co-expression networks (GCNs) are constructed from Gene Expression Matrices (GEMs) in a bottom up approach where all gene pairs are tested for correlation within the context of the input sample set. This approach is computationally intensive for many current GEMs and may not be scalable to millions of samples. Further, traditional GCNs do not detect non-linear relationships missed by correlation tests and do not place genetic relationships in a gene expression intensity context. In this report, we propose EdgeScaping, which constructs and analyzes the pairwise gene intensity network in a holistic, top down approach where no edges are filtered. EdgeScaping uses a novel technique to convert traditional pairwise gene expression data to an image based format. This conversion not only performs feature compression, making our algorithm highly scalable, but it also allows for exploring non-linear relationships between genes by leveraging deep learning image analysis algorithms. Using the learned embedded feature space we implement a fast, efficient algorithm to cluster the entire space of gene expression relationships while retaining gene expression intensity. Since EdgeScaping does not eliminate conventionally noisy edges, it extends the identification of co-expression relationships beyond classically correlated edges to facilitate the discovery of novel or unusual expression patterns within the network. We applied EdgeScaping to a human tumor GEM to identify sets of genes that exhibit conventional and non-conventional interdependent non-linear behavior associated with brain specific tumor sub-types that would be eliminated in conventional bottom-up construction of GCNs. Edgescaping source code is available at under the MIT license. [ABSTRACT FROM AUTHOR]