Link-Prediction Enhanced Consensus Clustering for Complex Networks

Many real networks that are inferred or collected from data are incomplete due to missing edges. Missing edges can be inherent to the dataset (Facebook friend links will never be complete) or the result of sampling (one may only have access to a portion of the data). The consequence is that downstream analyses that consume the network will often yield less accurate results than if the edges were complete. Community detection algorithms, in particular, often suffer when critical intra-community edges are missing. We propose a novel consensus clustering algorithm to enhance community detection on incomplete networks. Our framework utilizes existing community detection algorithms that process networks imputed by our link prediction based algorithm. The framework then merges their multiple outputs into a final consensus output. On average our method boosts performance of existing algorithms by 7% on artificial data and 17% on ego networks collected from Facebook

icet - A Python library for constructing and sampling alloy cluster expansions

Alloy cluster expansions (CEs) provide an accurate and computationally efficient mapping of the potential energy surface of multi-component systems that enables comprehensive sampling of the many-dimensional configuration space. Here, we introduce \textsc{icet}, a flexible, extensible, and computationally efficient software package for the construction and sampling of CEs. \textsc{icet} is largely written in Python for easy integration in comprehensive workflows, including first-principles calculations for the generation of reference data and machine learning libraries for training and validation. The package enables training using a variety of linear regression algorithms with and without regularization, Bayesian regression, feature selection, and cross-validation. It also provides complementary functionality for structure enumeration and mapping as well as data management and analysis. Potential applications are illustrated by two examples, including the computation of the phase diagram of a prototypical metallic alloy and the analysis of chemical ordering in an inorganic semiconductor.Comment: 10 page

Unsupervised learning as a complement to convolutional neural network classification in the analysis of saccadic eye movement in spino-cerebellar ataxia type 2

IWANN es un congreso internacional que se celebra bienalmente desde 1991. Su campo de estudio se centra en la fundamentación y aplicación de las distintas técnicas de Inteligencia Computacional : Redes Neuronales Artificiales, Algoritmos Genéticos, Lógica Borrosa, Aprendizaje Automático. En esta edición han participado 150 investigadores.This paper aims at assessing spino-cerebellar type 2 ataxiaby classifying electrooculography records into registers corresponding to healthy, presymptomatic and ill individuals. The primary used technique is the convolutional neural network applied to the time series of eye movements, called saccades. The problem is exceptionally hard, though, because the recorded saccadic movements for presymptomatic cases often do not substantially di er from those of healthy individuals. Precisely this distinction is of the utmost clinical importance, since early intervention on presymptomatic patients can ameliorate symptoms or at least slow their progression. Yet, each register contains a number of saccades that, although not consistent with the current label, have not been considered indicative of another class by the examining physicians. As a consequence, an unsupervised learning mechanism may be more suitable to handle this form of misclassi cation. Thus, our proposal introduces the k-means approach and the SOM method, as complementary techniques to analyse the time series. The three techniques operating in tandem lead to a well performing solution to this diagnosis problem.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Universidad de Granada, Universitat Politècnica de Catalunya, Universidad de Las Palmas de Gran Canaria, Springe

Microbial community pattern detection in human body habitats via ensemble clustering framework

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural patterns. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.Comment: BMC Systems Biology 201

Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond

In this and a set of companion whitepapers, the USQCD Collaboration lays out a program of science and computing for lattice gauge theory. These whitepapers describe how calculation using lattice QCD (and other gauge theories) can aid the interpretation of ongoing and upcoming experiments in particle and nuclear physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers

Towards Operator-less Data Centers Through Data-Driven, Predictive, Proactive Autonomics

Continued reliance on human operators for managing data centers is a major impediment for them from ever reaching extreme dimensions. Large computer systems in general, and data centers in particular, will ultimately be managed using predictive computational and executable models obtained through data-science tools, and at that point, the intervention of humans will be limited to setting high-level goals and policies rather than performing low-level operations. Data-driven autonomics, where management and control are based on holistic predictive models that are built and updated using live data, opens one possible path towards limiting the role of operators in data centers. In this paper, we present a data-science study of a public Google dataset collected in a 12K-node cluster with the goal of building and evaluating predictive models for node failures. Our results support the practicality of a data-driven approach by showing the effectiveness of predictive models based on data found in typical data center logs. We use BigQuery, the big data SQL platform from the Google Cloud suite, to process massive amounts of data and generate a rich feature set characterizing node state over time. We describe how an ensemble classifier can be built out of many Random Forest classifiers each trained on these features, to predict if nodes will fail in a future 24-hour window. Our evaluation reveals that if we limit false positive rates to 5%, we can achieve true positive rates between 27% and 88% with precision varying between 50% and 72%.This level of performance allows us to recover large fraction of jobs' executions (by redirecting them to other nodes when a failure of the present node is predicted) that would otherwise have been wasted due to failures. [...

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin