QSAR modeling of antitubercular activity of diverse organic compounds

Tuberculosis (TB) is a worldwide infectious disease that has shown over time extremely high mortality levels. The urgent need to develop new antitubercular drugs is due to the increasing rate of appearance of multi-drug resistant strains to the commonly used drugs, and the longer durations of therapy and recovery, particularly in immuno-compromised patients. The major goal of the present study is the exploration of data from different families of compounds through the use of a variety of machine learning techniques so that robust QSAR-based models can be developed to further guide in the quest for new potent anti-TB compounds. Eight QSAR models were built using various types of descriptors (from ADRIANA.Code and Dragon software) with two publicly available structurally diverse data sets, including recent data deposited in PubChem. QSAR methodologies used Random Forests and Associative Neural Networks. Predictions for the external evaluation sets obtained accuracies in the range of 0.76-0.88 (for active/inactive classifications) and Q(2)=0.66-0.89 for regressions. Models developed in this study can be used to estimate the anti-TB activity of drug candidates at early stages of drug development (C) 2011 Elsevier B.V. All rights reserved.

Nonlinear mixture model for hyperspectral unmixing

Proceedings of International Conference - SPIE 7477, Image and Signal Processing for Remote Sensing XV - 28 September 2009

Arrow plot and CA maps on microarray preprocessing methods

Microarray allow to monitoring simultaneously thousands of genes, where the abundance of the transcripts under a same experimental condition at the same time can be quantified. Among various available array technologies, double channel cDNA microarray experiments have arisen in numerous technical protocols associated to genomic studies, which is the focus of this work. Microarray experiments involve many steps and each one can affect the quality of raw data. Background correction and normalization are preprocessing techniques to clean and correct the raw data when undesirable fluctuations arise from technical factors. Several recent studies showed that there is no preprocessing strategy that outperforms others in all circumstances and thus it seems difficult to provide general recommendations. In this work, it is proposed to use exploratory techniques to visualize the effects of preprocessing methods on statistical analysis of cancer two-channel microarray data sets, where the cancer types (classes) are known. For selecting differential expressed genes the arrow plot was used and the graph of profiles resultant from the correspondence analysis for visualizing the results. It was used 6 background methods and 6 normalization methods, performing 36 pre-processing methods and it was analyzed in a published cDNA microarray database (Liver) available at http://genome-www5.stanford.edu/ which microarrays were already classified by cancer type. All statistical analyses were performed using the R statistical software.

Radioterapia adaptativa: utilização do cone-beam computed tomography para o cálculo de dose em radioterapia

Mestrado em Radiações Aplicadas às Tecnologias da Saúde - Ramo de especialização: Terapia com Radiações

A web-based platform for biosignal visualization and annotation

With the advent of wearable sensing and mobile technologies, biosignals have seen an increasingly growing number of application areas, leading to the collection of large volumes of data. One of the difficulties in dealing with these data sets, and in the development of automated machine learning systems which use them as input, is the lack of reliable ground truth information. In this paper we present a new web-based platform for visualization, retrieval and annotation of biosignals by non-technical users, aimed at improving the process of ground truth collection for biomedical applications. Moreover, a novel extendable and scalable data representation model and persistency framework is presented. The results of the experimental evaluation with possible users has further confirmed the potential of the presented framework.

Enabling Global Experiments With Interactive Reconfiguration And Steering By Multiple Users

In global scientific experiments with collaborative scenarios involving multinational teams there are big challenges related to data access, namely data movements are precluded to other regions or Clouds due to the constraints on latency costs, data privacy and data ownership. Furthermore, each site is processing local data sets using specialized algorithms and producing intermediate results that are helpful as inputs to applications running on remote sites. This paper shows how to model such collaborative scenarios as a scientific workflow implemented with AWARD (Autonomic Workflow Activities Reconfigurable and Dynamic), a decentralized framework offering a feasible solution to run the workflow activities on distributed data centers in different regions without the need of large data movements. The AWARD workflow activities are independently monitored and dynamically reconfigured and steering by different users, namely by hot-swapping the algorithms to enhance the computation results or by changing the workflow structure to support feedback dependencies where an activity receives feedback output from a successor activity. A real implementation of one practical scenario and its execution on multiple data centers of the Amazon Cloud is presented including experimental results with steering by multiple users.

Parallel hyperspectral unmixing on GPUs

This letter presents a new parallel method for hyperspectral unmixing composed by the efficient combination of two popular methods: vertex component analysis (VCA) and sparse unmixing by variable splitting and augmented Lagrangian (SUNSAL). First, VCA extracts the endmember signatures, and then, SUNSAL is used to estimate the abundance fractions. Both techniques are highly parallelizable, which significantly reduces the computing time. A design for the commodity graphics processing units of the two methods is presented and evaluated. Experimental results obtained for simulated and real hyperspectral data sets reveal speedups up to 100 times, which grants real-time response required by many remotely sensed hyperspectral applications.

Optimization of structures modeled with a Meshfree approach

Radial basis functions are being used in different scientific areas in order to reproduce the geometrical modeling of an object/structure, as well as to predict its behavior. Due to its characteristics, these functions are well suited for meshfree modeling of physical quantities, which for instances can be associated to the data sets of 3D laser scanning point clouds. In the present work the geometry of a structure is modeled by using multiquadric radial basis functions, and its configuration is further optimized in order to obtain better performances concerning to its static and dynamic behavior. For this purpose the authors consider the particle swarm optimization technique. A set of case studies is presented to illustrate the adequacy of the meshfree model used, as well as its link to particle swarm optimization technique. © 2014 IEEE.

Tris(2-Ethylhexyl) trimellitate (TOTM) a potential reference fluid for high viscosity. Part I: viscosity measurements at temperatures from (303 to 373)K and pressures up to 65MPa, using a novel vibrating-wire instrument

No literature data above atmospheric pressure could be found for the viscosity of TOTIVI. As a consequence, the present viscosity results could only be compared upon extrapolation of the vibrating wire data to 0.1 MPa. Independent viscosity measurements were performed, at atmospheric pressure, using an Ubbelohde capillary in order to compare with the vibrating wire results, extrapolated by means of the above mentioned correlation. The two data sets agree within +/- 1%, which is commensurate with the mutual uncertainty of the experimental methods. Comparisons of the literature data obtained at atmospheric pressure with the present extrapolated vibrating-wire viscosity measurements have shown an agreement within +/- 2% for temperatures up to 339 K and within +/- 3.3% for temperatures up to 368 K. (C) 2014 Elsevier B.V. All rights reserved.

Hyperspectral unmixing based on mixtures of Dirichlet components

This paper introduces a new unsupervised hyperspectral unmixing method conceived to linear but highly mixed hyperspectral data sets, in which the simplex of minimum volume, usually estimated by the purely geometrically based algorithms, is far way from the true simplex associated with the endmembers. The proposed method, an extension of our previous studies, resorts to the statistical framework. The abundance fraction prior is a mixture of Dirichlet densities, thus automatically enforcing the constraints on the abundance fractions imposed by the acquisition process, namely, nonnegativity and sum-to-one. A cyclic minimization algorithm is developed where the following are observed: 1) The number of Dirichlet modes is inferred based on the minimum description length principle; 2) a generalized expectation maximization algorithm is derived to infer the model parameters; and 3) a sequence of augmented Lagrangian-based optimizations is used to compute the signatures of the endmembers. Experiments on simulated and real data are presented to show the effectiveness of the proposed algorithm in unmixing problems beyond the reach of the geometrically based state-of-the-art competitors.

Viscosity measurements of compressed liquid dipropyl and dibutyl adipates

The paper reports viscosity measurements of compressed liquid dipropyl (DPA) and dibutyl (DBA) adipates obtained with two vibrating wire sensors developed in our group. The vibrating wire instruments were operated in the forced oscillation, or steady-state mode. The viscosity measurements of DPA were carried out in a range of pressures up to 18. MPa and temperatures from (303 to 333). K, and DBA up to 65. MPa and temperature from (303 to 373). K, covering a total range of viscosities from (1.3 to 8.3). mPa. s. The required density data of the liquid samples were obtained in our laboratory using an Anton Paar vibrating tube densimeter and were reported in a previous paper. The viscosity results were correlated with density, using a modified hard-spheres scheme. The root mean square deviation of the data from the correlation is less than (0.21 and 0.32)% and the maximum absolute relative deviations are within (0.43 and 0.81)%, for DPA and DBA respectively. No data for the viscosity of both adipates could be found in the literature. Independent viscosity measurements were also performed, at atmospheric pressure, using an Ubbelohde capillary in order to compare with the vibrating wire results. The expanded uncertainty of these results is estimated as ±1.5% at a 95% confidence level. The two data sets agree within the uncertainty of both methods. © 2015 Published by Elsevier B.V.

Parallel GPU architecture for hyperspectral unmixing based on augmented Lagrangian method

Hyperspectral imaging has become one of the main topics in remote sensing applications, which comprise hundreds of spectral bands at different (almost contiguous) wavelength channels over the same area generating large data volumes comprising several GBs per flight. This high spectral resolution can be used for object detection and for discriminate between different objects based on their spectral characteristics. One of the main problems involved in hyperspectral analysis is the presence of mixed pixels, which arise when the spacial resolution of the sensor is not able to separate spectrally distinct materials. Spectral unmixing is one of the most important task for hyperspectral data exploitation. However, the unmixing algorithms can be computationally very expensive, and even high power consuming, which compromises the use in applications under on-board constraints. In recent years, graphics processing units (GPUs) have evolved into highly parallel and programmable systems. Specifically, several hyperspectral imaging algorithms have shown to be able to benefit from this hardware taking advantage of the extremely high floating-point processing performance, compact size, huge memory bandwidth, and relatively low cost of these units, which make them appealing for onboard data processing. In this paper, we propose a parallel implementation of an augmented Lagragian based method for unsupervised hyperspectral linear unmixing on GPUs using CUDA. The method called simplex identification via split augmented Lagrangian (SISAL) aims to identify the endmembers of a scene, i.e., is able to unmix hyperspectral data sets in which the pure pixel assumption is violated. The efficient implementation of SISAL method presented in this work exploits the GPU architecture at low level, using shared memory and coalesced accesses to memory.

Parallel hyperspectral coded aperture for compressive sensing on GPUs

The application of compressive sensing (CS) to hyperspectral images is an active area of research over the past few years, both in terms of the hardware and the signal processing algorithms. However, CS algorithms can be computationally very expensive due to the extremely large volumes of data collected by imaging spectrometers, a fact that compromises their use in applications under real-time constraints. This paper proposes four efficient implementations of hyperspectral coded aperture (HYCA) for CS, two of them termed P-HYCA and P-HYCA-FAST and two additional implementations for its constrained version (CHYCA), termed P-CHYCA and P-CHYCA-FAST on commodity graphics processing units (GPUs). HYCA algorithm exploits the high correlation existing among the spectral bands of the hyperspectral data sets and the generally low number of endmembers needed to explain the data, which largely reduces the number of measurements necessary to correctly reconstruct the original data. The proposed P-HYCA and P-CHYCA implementations have been developed using the compute unified device architecture (CUDA) and the cuFFT library. Moreover, this library has been replaced by a fast iterative method in the P-HYCA-FAST and P-CHYCA-FAST implementations that leads to very significant speedup factors in order to achieve real-time requirements. The proposed algorithms are evaluated not only in terms of reconstruction error for different compressions ratios but also in terms of computational performance using two different GPU architectures by NVIDIA: 1) GeForce GTX 590; and 2) GeForce GTX TITAN. Experiments are conducted using both simulated and real data revealing considerable acceleration factors and obtaining good results in the task of compressing remotely sensed hyperspectral data sets.

Parallel hyperspectral unmixing method via split augmented lagrangian on GPU

One of the main problems of hyperspectral data analysis is the presence of mixed pixels due to the low spatial resolution of such images. Linear spectral unmixing aims at inferring pure spectral signatures and their fractions at each pixel of the scene. The huge data volumes acquired by hyperspectral sensors put stringent requirements on processing and unmixing methods. This letter proposes an efficient implementation of the method called simplex identification via split augmented Lagrangian (SISAL) which exploits the graphics processing unit (GPU) architecture at low level using Compute Unified Device Architecture. SISAL aims to identify the endmembers of a scene, i.e., is able to unmix hyperspectral data sets in which the pure pixel assumption is violated. The proposed implementation is performed in a pixel-by-pixel fashion using coalesced accesses to memory and exploiting shared memory to store temporary data. Furthermore, the kernels have been optimized to minimize the threads divergence, therefore achieving high GPU occupancy. The experimental results obtained for the simulated and real hyperspectral data sets reveal speedups up to 49 times, which demonstrates that the GPU implementation can significantly accelerate the method's execution over big data sets while maintaining the methods accuracy.

Comparing clustering solutions: the use of adjusted paired indices

In the present paper we compare clustering solutions using indices of paired agreement. We propose a new method - IADJUST - to correct indices of paired agreement, excluding agreement by chance. This new method overcomes previous limitations known in the literature as it permits the correction of any index. We illustrate its use in external clustering validation, to measure the accordance between clusters and an a priori known structure. The adjusted indices are intended to provide a realistic measure of clustering performance that excludes agreement by chance with ground truth. We use simulated data sets, under a range of scenarios - considering diverse numbers of clusters, clusters overlaps and balances - to discuss the pertinence and the precision of our proposal. Precision is established based on comparisons with the analytical approach for correction specific indices that can be corrected in this way are used for this purpose. The pertinence of the proposed correction is discussed when making a detailed comparison between the performance of two classical clustering approaches, namely Expectation-Maximization (EM) and K-Means (KM) algorithms. Eight indices of paired agreement are studied and new corrected indices are obtained.