Investigation of commuting Hamiltonian in quantum Markov network

Graphical Models have various applications in science and engineering which include physics, bioinformatics, telecommunication and etc. Usage of graphical models needs complex computations in order to evaluation of marginal functions,so there are some powerful methods including mean field approximation, belief propagation algorithm and etc. Quantum graphical models have been recently developed in context of quantum information and computation, and quantum statistical physics, which is possible by generalization of classical probability theory to quantum theory. The main goal of this paper is preparing a primary generalization of Markov network, as a type of graphical models, to quantum case and applying in quantum statistical physics.We have investigated the Markov network and the role of commuting Hamiltonian terms in conditional independence with simple examples of quantum statistical physics.Comment: 11 pages, 8 figure

Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data

In domains like bioinformatics, information retrieval and social network analysis, one can find learning tasks where the goal consists of inferring a ranking of objects, conditioned on a particular target object. We present a general kernel framework for learning conditional rankings from various types of relational data, where rankings can be conditioned on unseen data objects. We propose efficient algorithms for conditional ranking by optimizing squared regression and ranking loss functions. We show theoretically, that learning with the ranking loss is likely to generalize better than with the regression loss. Further, we prove that symmetry or reciprocity properties of relations can be efficiently enforced in the learned models. Experiments on synthetic and real-world data illustrate that the proposed methods deliver state-of-the-art performance in terms of predictive power and computational efficiency. Moreover, we also show empirically that incorporating symmetry or reciprocity properties can improve the generalization performance

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.ResultsWe performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.Availability and implementationDatasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.Supplementary informationSupplementary data are available at Bioinformatics online

Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries. Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.Comment: Pacific Symposium on Biocomputing, 201

Integrated Inference and Learning of Neural Factors in Structural Support Vector Machines

Tackling pattern recognition problems in areas such as computer vision, bioinformatics, speech or text recognition is often done best by taking into account task-specific statistical relations between output variables. In structured prediction, this internal structure is used to predict multiple outputs simultaneously, leading to more accurate and coherent predictions. Structural support vector machines (SSVMs) are nonprobabilistic models that optimize a joint input-output function through margin-based learning. Because SSVMs generally disregard the interplay between unary and interaction factors during the training phase, final parameters are suboptimal. Moreover, its factors are often restricted to linear combinations of input features, limiting its generalization power. To improve prediction accuracy, this paper proposes: (i) Joint inference and learning by integration of back-propagation and loss-augmented inference in SSVM subgradient descent; (ii) Extending SSVM factors to neural networks that form highly nonlinear functions of input features. Image segmentation benchmark results demonstrate improvements over conventional SSVM training methods in terms of accuracy, highlighting the feasibility of end-to-end SSVM training with neural factors

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Because of the intrinsic complexity of natural language, automatically extracting accurate information from text remains a challenge. We have applied rich featurevectors derived from dependency graphs to predict protein-protein interactions using machine learning techniques. We present the first extensive analysis of applyingfeature selection in this domain, and show that it can produce more cost-effective models. For the first time, our technique was also evaluated on several large-scalecross-dataset experiments, which offers a more realistic view on model performance. During benchmarking, we encountered several fundamental problems hindering comparability with other methods. We present a set of practical guidelines to set up ameaningful evaluation. Finally, we have analysed the feature sets from our experiments before and after feature selection, and evaluated the contribution of both lexical and syntacticinformation to our method. The gained insight will be useful to develop better performing methods in this domain