Agents for educational games and simulations

This book consists mainly of revised papers that were presented at the Agents for Educational Games and Simulation (AEGS) workshop held on May 2, 2011, as part of the Autonomous Agents and MultiAgent Systems (AAMAS) conference in Taipei, Taiwan. The 12 full papers presented were carefully reviewed and selected from various submissions. The papers are organized topical sections on middleware applications, dialogues and learning, adaption and convergence, and agent applications

UIPC-MF: User-Item Prototype Connection Matrix Factorization for Explainable Collaborative Filtering

Recommending items to potentially interested users has been an important commercial task that faces two main challenges: accuracy and explainability. While most collaborative filtering models rely on statistical computations on a large scale of interaction data between users and items and can achieve high performance, they often lack clear explanatory power. We propose UIPC-MF, a prototype-based matrix factorization method for explainable collaborative filtering recommendations. In UIPC-MF, both users and items are associated with sets of prototypes, capturing general collaborative attributes. To enhance explainability, UIPC-MF learns connection weights that reflect the associative relations between user and item prototypes for recommendations. UIPC-MF outperforms other prototype-based baseline methods in terms of Hit Ratio and Normalized Discounted Cumulative Gain on three datasets, while also providing better transparency

Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation

BACKGROUND: During the last few years, the knowledge of drug, disease phenotype and protein has been rapidly accumulated and more and more scientists have been drawn the attention to inferring drug-disease associations by computational method. Development of an integrated approach for systematic discovering drug-disease associations by those informational data is an important issue. METHODS: We combine three different networks of drug, genomic and disease phenotype and assign the weights to the edges from available experimental data and knowledge. Given a specific disease, we use our network propagation approach to infer the drug-disease associations. RESULTS: We apply prostate cancer and colorectal cancer as our test data. We use the manually curated drug-disease associations from comparative toxicogenomics database to be our benchmark. The ranked results show that our proposed method obtains higher specificity and sensitivity and clearly outperforms previous methods. Our result also show that our method with off-targets information gets higher performance than that with only primary drug targets in both test data. CONCLUSIONS: We clearly demonstrate the feasibility and benefits of using network-based analyses of chemical, genomic and phenotype data to reveal drug-disease associations. The potential associations inferred by our method provide new perspectives for toxicogenomics and drug reposition evaluation

Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF). The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well

Pathway Detection from Protein Interaction Networks and Gene Expression Data Using Color-Coding Methods and A∗ Search Algorithms

With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set. The comparisons of our method with other existing methods on known yeast MAPK pathways in terms of precision and recall show that we can find maximum number of the proteins and perform comparably well. On the other hand, our method is more efficient than previous ones and detects the paths of length 10 within 40 seconds using CPU Intel 1.73GHz and 1GB main memory running under windows operating system

Identifying co-targets to fight drug resistance based on a random walk model

Abstract- Drug resistance has now posed more severe and emergent threats to human health and infectious disease treatment. However, the wet-lab approaches alone to counter drug resistance have so far achieved limited success in understanding the underlying mechanisms and pathways of drug resistance. Our approach applied A * heuristic search algorithm in order to extract drug response pathways from protein-protein interaction networks and to identify the co-target for effective antibacterial drugs. In this paper, we chose one of the killer infectious diseases, Mycobacterium Tuberculosis as our test bed. The results showed that the acetyl-CoA carboxylase is believed to be involved in fatty acid and mycolic acid biosynthesis and is strongly associated with the drug resistance mechanisms. Our analysis are consistent with the recent experimental results and also found alanine and glycine rich membrane and cell wall-associated lipoproteins to be potential co-targets for countering drug resistance. keywords: Drug resistance, Co-target, Random walk, Mycobacterium Tuberculosi