Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

An Introduction to MultiAgent Systems.

Many ``real-world'' networks are clearly defined while most ``social'' networks are to some extent subjective. Indeed, the accuracy of empirically-determined social networks is a question of some concern because individuals may have distinct perceptions of what constitutes a social link. One unambiguous type of connection is sexual contact. Here we analyze data on the sexual behavior of a random sample of individuals, and find that the cumulative distributions of the number of sexual partners during the twelve months prior to the survey decays as a power law with similar exponents $\alpha \approx 2.4$ for females and males. The scale-free nature of the web of human sexual contacts suggests that strategic interventions aimed at preventing the spread of sexually-transmitted diseases may be the most efficient approach.

The Web of Human Sexual Contacts

Motivation The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-ligand interactions assume a continuum of binding strength values, also called binding affinity and predicting this value still remains a challenge. The increase in the affinity data available in DT knowledge-bases allows the use of advanced learning techniques such as deep learning architectures in the prediction of binding affinities. In this study, we propose a deep-learning based model that uses only sequence information of both targets and drugs to predict DT interaction binding affinities. The few studies that focus on DT binding affinity prediction use either 3D structures of protein-ligand complexes or 2D features of compounds. One novel approach used in this work is the modeling of protein sequences and compound 1D representations with convolutional neural networks (CNNs). Results The results show that the proposed deep learning based model that uses the 1D representations of targets and drugs is an effective approach for drug target binding affinity prediction. The model in which high-level representations of a drug and a target are constructed via CNNs achieved the best Concordance Index (CI) performance in one of our larger benchmark datasets, outperforming the KronRLS algorithm and SimBoost, a state-of-the-art method for DT binding affinity prediction. Availability and implementation https://github.com/hkmztrk/DeepDTA. Supplementary information Supplementary data are available at Bioinformatics online.

DeepDTA: deep drug–target binding affinity prediction

Motivation: Understanding the role of genetics in diseases is one of the most important aims of the biological sciences. The completion of the Human Genome Project has led to a rapid increase in the number of publications in this area. However, the coverage of curated databases that provide information manually extracted from the literature is limited. Another challenge is that determining disease-related genes requires laborious experiments. Therefore, predicting good candidate genes before experimental analysis will save time and effort. We introduce an automatic approach based on text mining and network analysis to predict gene-disease associations. We collected an initial set of known disease-related genes and built an interaction network by automatic literature mining based on dependency parsing and support vector machines. Our hypothesis is that the central genes in this disease-specific network are likely to be related to the disease. We used the degree, eigenvector, betweenness and closeness centrality metrics to rank the genes in the network.

Results: The proposed approach can be used to extract known and to infer unknown gene-disease associations. We evaluated the approach for prostate cancer. Eigenvector and degree centrality achieved high accuracy. A total of 95% of the top 20 genes ranked by these methods are confirmed to be related to prostate cancer. On the other hand, betweenness and closeness centrality predicted more genes whose relation to the disease is currently unknown and are candidates for experimental study.

Availability: A web-based system for browsing the disease-specific gene-interaction networks is available at: http://gin.ncibi.org

Contact: [email protected]

/pdf/identifying-gene-disease-associations-using-centrality-on-a-4dx999viyo.pdf

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

We introduce a relation extraction method to identify the sentences in biomedical text that indicate an interaction among the protein names mentioned. Our approach is based on the analysis of the paths between two protein names in the dependency parse trees of the sentences. Given two dependency trees, we define two separate similarity functions (kernels) based on cosine similarity and edit distance among the paths between the protein names. Using these similarity functions, we investigate the performances of two classes of learning algorithms, Support Vector Machines and k-nearest-neighbor, and the semisupervised counterparts of these algorithms, transductive SVMs and harmonic functions, respectively. Significant improvement over the previous results in the literature is reported as well as a new benchmark dataset is introduced. Semi-supervised algorithms perform better than their supervised version by a wide margin especially when the amount of labeled data is limited.

/pdf/semi-supervised-classification-for-extracting-protein-n93mtz29mw.pdf

Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing

In this paper, we examine the use of keywords in text categorization with SVM. In contrast to the usual belief, we reveal that using keywords instead of all words yields better performance both in terms of accuracy and time. Unlike the previous studies that focus on keyword selection metrics, we compare the two approaches for keyword selection. In corpus-based approach, a single set of keywords is selected for all classes. In class-based approach, a distinct set of keywords is selected for each class. We perform the experiments with the standard Reuters-21578 dataset, with both boolean and tf-idf weighting. Our results show that although tf-idf weighting performs better, boolean weighting can be used where time and space resources are limited. Corpus-based approach with 2000 keywords performs the best. However, for small number of keywords, class-based approach outperforms the corpus-based approach with the same number of keywords.

https://cmpe.boun.edu.tr/~gungort/papers/text categorization with class-based and corpus-based keyword selection.pdf

Text categorization with class-based and corpus-based keyword selection

Summary: Knowledge of pathogen–host protein interactions is required to better understand infection mechanisms. The pathogen– host interaction search tool (PHISTO) is a web-accessible platform that provides relevant information about pathogen–host interactions (PHIs). It enables access to the most up-to-date PHI data for all pathogen types for which experimentally verified protein interactions with human are available. The platform also offers integrated tools for visualization of PHI networks, graph–theoretical analysis of targeted human proteins, BLAST search and text mining for detecting missing experimental methods. PHISTO will facilitate PHI studies that provide potential therapeutic targets for infectious diseases. Availability: http://www.phisto.org.

/pdf/phisto-pathogen-host-interaction-search-tool-3up70881od.pdf

Arzucan Özgür

Papers

DeepDTA: deep drug–target binding affinity prediction

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing

Text categorization with class-based and corpus-based keyword selection

PHISTO: pathogen–host interaction search tool