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The Gaussian Conditional Random Fields (GCRF) algorithm and its extensions are used for machine learning regression problems in which the attributes of objects and the correlation between objects should be considered when making predictions. These algorithms can be applied in different domains where problems can be seen as graphs, but their implementation requires complex calculations and good programming skills. This paper presents an open source software package that includes a tool with graphical user interface (GCRFs tool) and Java library (GCRFs library). GCRFs tool is software that integrates various GCRF-based algorithms and supports training and testing of those algorithms on real-world datasets. The main goal of GCRFs tool is to provide a straightforward and user-friendly graphical user interface that will simplify the use of GCRF-based algorithms. GCRFs Java library contains basic classes for GCRF concepts and can be used by researchers who have experience in Java programming. Also, this paper presents the results of a pilot usability evaluation of the GCRFs tool, where the software was evaluated with expert and non-expert users. This evaluation gave us detailed insight into the experiences and opinions of the users and helped us outline priorities for future development.

Medical outcomes are inexorably linked to patient illness and clinical interventions. Interventions change the course of disease, crucially determining outcome. Traditional outcome prediction models build a single classifier by augmenting interventions with disease information. Interventions, however, differentially affect prognosis, thus a single prediction rule may not suffice to capture variations. Interventions also evolve over time as more advanced interventions replace older ones. To this end, we propose a Bayesian nonparametric, supervised framework that models a set of intervention groups through a mixture distribution building a separate prediction rule for each group, and allows the mixture distribution to change with time. This is achieved by using a hierarchical Dirichlet process mixture model over the interventions. The outcome is then modeled as conditional on both the latent grouping and the disease information through a Bayesian logistic regression. Experiments on synthetic and medical cohorts for 30-day readmission prediction demonstrate the superiority of the proposed model over clinical and data mining baselines.

The analysis of social networks often assumes time invariant scenario, while in practice actor attributes and links in such networks often evolve over time and are inextricably dependent on each other. In this article, we propose a new method to predict actor attributes and links in temporal networks. Our approach takes into account the attributes corresponding to the participating actors together with topological and structural changes of the network over time. This is achieved by building two conditional predictors to jointly infer links and actor attributes. The proposed prediction method was significantly more accurate than alternatives when evaluated on synthetic data sets and two well-studied real-life temporal social networks. In addition, the new algorithm is computationally more efficient than a related alternative scaling up linearly with the number of temporal observations and quadratically with the number of actors considered.

Comparisons were made among four categories of protein flexibility: (1) low-13-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high-B-factors. This predictor achieved an accuracy of 70\% and a correlation of 0.43 with experimental data, outperforming the 64\% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81\% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.

Comparisons were made among four categories of protein flexibility: (1) low-13-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high-B-factors. This predictor achieved an accuracy of 70\% and a correlation of 0.43 with experimental data, outperforming the 64\% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81\% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.

Comparisons were made among four categories of protein flexibility: (1) low-13-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high-B-factor ordered and short disordered regions being the most similar pair. The high-B-factor (flexible) ordered regions are characterized by a higher average flexibility index, higher average hydrophilicity, higher average absolute net charge, and higher total charge than disordered regions. The low-B-factor regions are significantly enriched in hydrophobic residues and depleted in the total number of charged residues compared to the other three categories. We examined the predictability of the high-B-factor regions and developed a predictor that discriminates between regions of low and high-B-factors. This predictor achieved an accuracy of 70\% and a correlation of 0.43 with experimental data, outperforming the 64\% accuracy and 0.32 correlation of predictors based solely on flexibility indices. To further clarify the differences between short disordered regions and ordered regions, a predictor of short disordered regions was developed. Its relatively high accuracy of 81\% indicates considerable differences between ordered and disordered regions. The distinctive amino acid biases of high-B-factor ordered regions, short disordered regions, and long disordered regions indicate that the sequence determinants for these flexibility categories differ from one another, whereas the significantly-greater-than-chance predictability of these categories from sequence suggest that flexible ordered regions, short disorder, and long disorder are, to a significant degree, encoded at the primary structure level.

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.

Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures, with some segments showing little mobility while others may be so disordered as to be unresolvable by techniques such as X-ray crystallography. Atomic displacement parameters, or B-factors, from X-ray crystallographic studies give an experimentally determined indication of the degree of mobility in a protein structure. To provide better estimators of amino acid flexibility, we have examined B-factors from a large set of high-resolution crystal structures. Because of the differences among structures, it is necessary to normalize the B-factors. However, many proteins have segments of unusually high mobility, which must be accounted for before normalization can be performed. Accordingly, a median-based method from quality control studies was used to identify outliers. After removal of outliers from, and normalization of, each protein chain, the B-factors were collected for each amino acid in the set. It was found that the distribution of normalized B-factors followed a Gumbel, or extreme value distribution, and the location parameter, or mode, of this distribution was used as an estimator of flexibility for the amino acid. These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods.