Hisashi Kashima

The authors’ algorithm was favorably examined on two kinds of biological networks: a metabolic network and a protein interaction network. A statistical test confirmed that the weight that our algorithm assigned to each assay was meaningful.

The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered trees on the basis of their subpaths, which are vertical substructures of trees responsible for hierarchical information in them. Their kernel exhibits practically good performance in terms of accuracy and speed; however, linear-time computation is not guaranteed theoretically, unlike the case of the other unordered tree kernel proposed by Vishwanathan and Smola (2003). In this paper, we propose a theoretically guaranteed linear-time kernel computation algorithm that is practically fast, and we present an efficient prediction algorithm whose running time depends only on the size of the input tree. Experimental results show that the proposed algorithms are quite efficient in practice.

Most conventional Reinforcement Learning (RL) algorithms aim to optimize decision-making rules in terms of the expected returns. However, especially for risk management purposes, other risk-sensitive criteria such as the value-at-risk or the expected shortfall are sometimes preferred in real applications. Here, we describe a parametric method for estimating density of the returns, which allows us to handle various criteria in a unified manner. We first extend the Bellman equation for the conditional expected return to cover a conditional probability density of the returns. Then we derive an extension of the TD-learning algorithm for estimating the return densities in an unknown environment. As test instances, several parametric density estimation algorithms are presented for the Gaussian, Laplace, and skewed Laplace distributions. We show that these algorithms lead to risk-sensitive as well as robust RL paradigms through numerical experiments.

It has attracted considerable attention to use crowdsourcing services to collect a large amount of labeled data for machine learning, since crowdsourcing services allow one to ask the general public to label data at very low cost through the Internet. The use of crowdsourcing has introduced a new challenge in machine learning, that is, coping with low quality of crowd-generated data. There have been many recent attempts to address the quality problem of multiple labelers, however, there are two serious drawbacks in the existing approaches, that are, (i) non-convexity and (ii) task homogeneity. Most of the existing methods consider true labels as latent variables, which results in nonconvex optimization problems. Also, the existing models assume only single homogeneous tasks, while in realistic situations, clients can offer multiple tasks to crowds and crowd workers can work on different tasks in parallel. In this paper, we propose a convex optimization formulation of learning from crowds by introducing personal models of individual crowds without estimating true labels. We further extend the proposed model to multi-task learning based on the resemblance between the proposed formulation and that for an existing multi-task learning model. We also devise efficient iterative methods for solving the convex optimization problems by exploiting conditional independence structures in multiple classifiers.

Multi-task learning aims at transferring knowledge between similar tasks. The multi-task Gaussian process framework of Bonilla et al.models (incomplete) responses of C data points for R tasks (e.g., the responses are given by R × C matrix) by a Gaussian process; the covariance function is defined as the product of a covariance function on input-dependent features and the inter-task covariance matrix (which is empirically estimated as a model parameter). We extend this framework by incorporating a novel similarity measurement, which allows for the representation of much more complex data structures. The proposed framework also enables us to exploit additional information (e.g., the input-dependent features) by constructing the covariance matrices with combining them on the covariance function. We also derive an efficient learning algorithm to make prediction by using an iterative method. Finally, we apply our model to a real data set of recommender systems and show that the proposed method achieves the best prediction accuracy on the data set.

In this paper, we propose three approaches for the estimation of the Tucker decomposition of multi-way arrays (tensors) from partial observations. All approaches are formulated as convex minimization problems. Therefore, the minimum is guaranteed to be unique. The proposed approaches can automatically estimate the number of factors (rank) through the optimization. Thus, there is no need to specify the rank beforehand. The key technique we employ is the trace norm regularization, which is a popular approach for the estimation of low-rank matrices. In addition, we propose a simple heuristic to improve the interpretability of the obtained factorization. The advantages and disadvantages of three proposed approaches are demonstrated through numerical experiments on both synthetic and real world datasets. We show that the proposed convex optimization based approaches are more accurate in predictive performance, faster, and more reliable in recovering a known multilinear structure than conventional approaches.

Background: High-throughput methods for detecting protein-protein interactions enable us to obtain large interaction networks, and also allow us to computationally identify the associations of proteins as protein complexes. Although there are methods to extract protein complexes as sets of proteins from interaction networks, the extracted complexes may include false positives because they do not account for the structural limitations of the proteins and thus do not check that the proteins in the extracted complex can simultaneously bind to each other. In addition, there have been few searches for deeper insights into the protein complexes, such as of the topology of the protein-protein interactions or into the domain-domain interactions that mediate the protein interactions. Results: Here, we introduce a combinatorial approach for prediction of protein complexes focusing not only on determining member proteins in complexes but also on the DDI/PPI organization of the complexes. Our method analyzes complex candidates predicted by the existing methods. It searches for optimal combinations of domain-domain interactions in the candidates based on an assumption that the proteins in a candidate can form a true protein complex if each of the domains is used by a single protein interaction. This optimization problem was mathematically formulated and solved using binary integer linear programming. By using publicly available sets of yeast protein-protein interactions and domain-domain interactions, we succeeded in extracting protein complex candidates with an accuracy that is twice the average accuracy of the existing methods, MCL, MCODE, or clustering coefficient. Although the configuring parameters for each algorithm resulted in slightly improved precisions, our method always showed better precision for most values of the parameters. Conclusions: Our combinatorial approach can provide better accuracy for prediction of protein complexes and also enables to identify both direct PPIs and DDIs that mediate them in complexes.

Background: Understanding of secondary metabolic pathway in plant is essential for finding druggable candidate enzymes. However, there are many enzymes whose functions are not yet discovered in organism-specific metabolic pathways. Towards identifying the functions of those enzymes, assignment of EC numbers to the enzymatic reactions they catalyze plays a key role, since EC numbers represent the categorization of enzymes on one hand, and the categorization of enzymatic reactions on the other hand. Results: We propose reaction graph kernels for automatically assigning EC numbers to unknown enzymatic reactions in a metabolic network. Reaction graph kernels compute similarity between two chemical reactions considering the similarity of chemical compounds in reaction and their relationships. In computational experiments based on the KEGG/REACTION database, our method successfully predicted the first three digits of the EC number with 83% accuracy. We also exhaustively predicted missing EC numbers in plant's secondary metabolism pathway. The prediction results of reaction graph kernels on 36 unknown enzymatic reactions are compared with an expert's knowledge. Using the same data for evaluation, we compared our method with E-zyme, and showed its ability to assign more number of accurate EC numbers. Conclusion: Reaction graph kernels are a new metric for comparing enzymatic reactions.