Overview of Multiobjective Optimization Methods in in Silico Metabolic Engineering

Multiobjective optimization requires of finding a trade-off between multiple objectives. However, most of the objectives are contradict towards each other, thus makes it difficult for the traditional approaches to find a solution that satisfies all objectives. Fortunately, the problems are able to solve by the aid of Pareto methods. Meanwhile, in in silico Metabolic Engineering, the identification of reaction knockout strategies that produce mutant strains with a permissible growth rate and product rate of desired metabolites is still hindered. Previously, Evolutionary Algorithms (EAs) has been successfully used in determining the reaction knockout strategies. Nevertheless, most methods work by optimizing one objective function, which is growth rate or production rate. Furthermore, in bioprocesses, it involves multiple and conflicting objectives. In this review, we aim to show the different multiobjective evolutionary optimization methods developed for tackling the multiple and conflicting objectives in in silico metabolic engineering, as well as the approaches in multiobjective optimization

Designing Service-Oriented Chatbot Systems Using a Construction Grammar-Driven Natural Language Generation System

Service oriented chatbot systems are used to inform users in a conversational manner about a particular service or product on a website. Our research shows that current systems are time consuming to build and not very accurate or satisfying to users. We find that natural language understanding and natural language generation methods are central to creating an e�fficient and useful system. In this thesis we investigate current and past methods in this research area and place particular emphasis on Construction Grammar and its computational implementation. Our research shows that users have strong emotive reactions to how these systems behave, so we also investigate the human computer interaction component. We present three systems (KIA, John and KIA2), and carry out extensive user tests on all of them, as well as comparative tests. KIA is built using existing methods, John is built with the user in mind and KIA2 is built using the construction grammar method. We found that the construction grammar approach performs well in service oriented chatbots systems, and that users preferred it over other systems

Learning from Partially Labeled Data: Unsupervised and Semi-supervised Learning on Graphs and Learning with Distribution Shifting

This thesis focuses on two fundamental machine learning problems:unsupervised learning, where no label information is available, and semi-supervised learning, where a small amount of labels are given in addition to unlabeled data. These problems arise in many real word applications, such as Web analysis and bioinformatics,where a large amount of data is available, but no or only a small amount of labeled data exists. Obtaining classification labels in these domains is usually quite difficult because it involves either manual labeling or physical experimentation. This thesis approaches these problems from two perspectives: graph based and distribution based. First, I investigate a series of graph based learning algorithms that are able to exploit information embedded in different types of graph structures. These algorithms allow label information to be shared between nodes in the graph---ultimately communicating information globally to yield effective unsupervised and semi-supervised learning. In particular, I extend existing graph based learning algorithms, currently based on undirected graphs, to more general graph types, including directed graphs, hypergraphs and complex networks. These richer graph representations allow one to more naturally capture the intrinsic data relationships that exist, for example, in Web data, relational data, bioinformatics and social networks. For each of these generalized graph structures I show how information propagation can be characterized by distinct random walk models, and then use this characterization to develop new unsupervised and semi-supervised learning algorithms. Second, I investigate a more statistically oriented approach that explicitly models a learning scenario where the training and test examples come from different distributions. This is a difficult situation for standard statistical learning approaches, since they typically incorporate an assumption that the distributions for training and test sets are similar, if not identical. To achieve good performance in this scenario, I utilize unlabeled data to correct the bias between the training and test distributions. A key idea is to produce resampling weights for bias correction by working directly in a feature space and bypassing the problem of explicit density estimation. The technique can be easily applied to many different supervised learning algorithms, automatically adapting their behavior to cope with distribution shifting between training and test data

BMC Bioinformatics (Volume 6 Suppl 4) Italian Society of Bioinformatics (BITS): Annual Meeting 2005

The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17\u201319 2005, in Milan. This Editorial provides a brief overview of the Conference topics and introduces the peer-reviewed manuscripts accepted for publication in this Supplement