An improved memory management scheme for large scale graph computing engine GraphChi

GraphChi is the first reported disk-based graph engine that can handle billion-scale graphs on a single PC efficiently. GraphChi is able to execute several advanced data mining, graph mining and machine learning algorithms on very large graphs. With the novel technique of parallel sliding windows (PSW) to load subgraph from disk to memory for vertices and edges updating, it can achieve data processing performance close to and even better than those of mainstream distributed graph engines. GraphChi mentioned that its memory is not effectively utilized with large dataset, which leads to suboptimal computation performances. In this paper we are motivated by the concepts of 'pin ' from TurboGraph and 'ghost' from GraphLab to propose a new memory utilization mode for GraphChi, which is called Part-in-memory mode, to improve the GraphChi algorithm performance. The main idea is to pin a fixed part of data inside the memory during the whole computing process. Part-in-memory mode is successfully implemented with only about 40 additional lines of code to the original GraphChi engine. Extensive experiments are performed with large real datasets (including Twitter graph with 1.4 billion edges). The preliminary results show that Part-in-memory mode memory management approach effectively reduces the GraphChi running time by up to 60% in PageRank algorithm. Interestingly it is found that a larger portion of data pinned in memory does not always lead to better performance in the case that the whole dataset cannot be fitted in memory. There exists an optimal portion of data which should be kept in the memory to achieve the best computational performance.

EnDNA-Prot:identification of DNA-binding proteins by applying ensemble learning

DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97-9.52% in ACC and 0.08-0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83-16.63% in terms of ACC and 0.02-0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public. © 2014 Ruifeng Xu et al.

Learning user and product distributed representations using a sequence model for sentiment analysis

In product reviews, it is observed that the distribution of polarity ratings over reviews written by different users or evaluated based on different products are often skewed in the real world. As such, incorporating user and product information would be helpful for the task of sentiment classification of reviews. However, existing approaches ignored the temporal nature of reviews posted by the same user or evaluated on the same product. We argue that the temporal relations of reviews might be potentially useful for learning user and product embedding and thus propose employing a sequence model to embed these temporal relations into user and product representations so as to improve the performance of document-level sentiment analysis. Specifically, we first learn a distributed representation of each review by a one-dimensional convolutional neural network. Then, taking these representations as pretrained vectors, we use a recurrent neural network with gated recurrent units to learn distributed representations of users and products. Finally, we feed the user, product and review representations into a machine learning classifier for sentiment classification. Our approach has been evaluated on three large-scale review datasets from the IMDB and Yelp. Experimental results show that: (1) sequence modeling for the purposes of distributed user and product representation learning can improve the performance of document-level sentiment classification; (2) the proposed approach achieves state-of-The-Art results on these benchmark datasets.

Learning Data-Driven Models of Non-Verbal Behaviors for Building Rapport Using an Intelligent Virtual Agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness. Evidence-based patient-centered Brief Motivational Interviewing (BMI) interven- tions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary. Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems. To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14].

Experience with Learning Agents which Manage Internet-Based Information

Postprint

Exploiting Learning Technologies for World Wide Web Agents

Postprint

Learning Mechanisms for Information Filtering Agents

Postprint

Intelligent Agents = Learning Agents

Postprint

Learning Meta-Descriptions of the FOAF Network

Postprint

Distributed Learning: An Agent-Based Approach to Data-Mining

Peer reviewed

An Empirical Investigation of Learning From the Semantic Web

Peer reviewed

New Advancements of Scalable Statistical Methods for Learning Latent Structures in Big Data

Constant technology advances have caused data explosion in recent years. Accord- ingly modern statistical and machine learning methods must be adapted to deal with complex and heterogeneous data types. This phenomenon is particularly true for an- alyzing biological data. For example DNA sequence data can be viewed as categorical variables with each nucleotide taking four different categories. The gene expression data, depending on the quantitative technology, could be continuous numbers or counts. With the advancement of high-throughput technology, the abundance of such data becomes unprecedentedly rich. Therefore efficient statistical approaches are crucial in this big data era.

Previous statistical methods for big data often aim to find low dimensional struc- tures in the observed data. For example in a factor analysis model a latent Gaussian distributed multivariate vector is assumed. With this assumption a factor model produces a low rank estimation of the covariance of the observed variables. Another example is the latent Dirichlet allocation model for documents. The mixture pro- portions of topics, represented by a Dirichlet distributed variable, is assumed. This dissertation proposes several novel extensions to the previous statistical methods that are developed to address challenges in big data. Those novel methods are applied in multiple real world applications including construction of condition specific gene co-expression networks, estimating shared topics among newsgroups, analysis of pro- moter sequences, analysis of political-economics risk data and estimating population structure from genotype data.

Bayesian Learning with Dependency Structures via Latent Factors, Mixtures, and Copulas

Bayesian methods offer a flexible and convenient probabilistic learning framework to extract interpretable knowledge from complex and structured data. Such methods can characterize dependencies among multiple levels of hidden variables and share statistical strength across heterogeneous sources. In the first part of this dissertation, we develop two dependent variational inference methods for full posterior approximation in non-conjugate Bayesian models through hierarchical mixture- and copula-based variational proposals, respectively. The proposed methods move beyond the widely used factorized approximation to the posterior and provide generic applicability to a broad class of probabilistic models with minimal model-specific derivations. In the second part of this dissertation, we design probabilistic graphical models to accommodate multimodal data, describe dynamical behaviors and account for task heterogeneity. In particular, the sparse latent factor model is able to reveal common low-dimensional structures from high-dimensional data. We demonstrate the effectiveness of the proposed statistical learning methods on both synthetic and real-world data.

AR-based Technoself Enhanced Learning Approach to Improving Student Engagement

The emerging technologies have expanded a new dimension of self – ‘technoself’ driven by socio-technical innovations and taken an important step forward in pervasive learning. Technology Enhanced Learning (TEL) research has increasingly focused on emergent technologies such as Augmented Reality (AR) for augmented learning, mobile learning, and game-based learning in order to improve self-motivation and self-engagement of the learners in enriched multimodal learning environments. These researches take advantage of technological innovations in hardware and software across different platforms and devices including tablets, phoneblets and even game consoles and their increasing popularity for pervasive learning with the significant development of personalization processes which place the student at the center of the learning process. In particular, augmented reality (AR) research has matured to a level to facilitate augmented learning, which is defined as an on-demand learning technique where the learning environment adapts to the needs and inputs from learners. In this paper we firstly study the role of Technology Acceptance Model (TAM) which is one of the most influential theories applied in TEL on how learners come to accept and use a new technology. Then we present the design methodology of the technoself approach for pervasive learning and introduce technoself enhanced learning as a novel pedagogical model to improve student engagement by shaping personal learning focus and setting. Furthermore we describe the design and development of an AR-based interactive digital interpretation system for augmented learning and discuss key features. By incorporating mobiles, game simulation, voice recognition, and multimodal interaction through Augmented Reality, the learning contents can be geared toward learner's needs and learners can stimulate discovery and gain greater understanding. The system demonstrates that Augmented Reality can provide rich contextual learning environment and contents tailored for individuals. Augment learning via AR can bridge this gap between the theoretical learning and practical learning, and focus on how the real and virtual can be combined together to fulfill different learning objectives, requirements, and even environments. Finally, we validate and evaluate the AR-based technoself enhanced learning approach to enhancing the student motivation and engagement in the learning process through experimental learning practices. It shows that Augmented Reality is well aligned with constructive learning strategies, as learners can control their own learning and manipulate objects that are not real in augmented environment to derive and acquire understanding and knowledge in a broad diversity of learning practices including constructive activities and analytical activities.

Directed Selection using Reinforcement Learning for the Examination Timetabling Problem

Traditional heuristic approaches to the Examination Timetabling Problem normally utilize a stochastic method during Optimization for the selection of the next examination to be considered for timetabling within the neighbourhood search process. This paper presents a technique whereby the stochastic method has been augmented with information from a weighted list gathered during the initial adaptive construction phase, with the purpose of intelligently directing examination selection. In addition, a Reinforcement Learning technique has been adapted to identify the most effective portions of the weighted list in terms of facilitating the greatest potential for overall solution improvement. The technique is tested against the 2007 International Timetabling Competition datasets with solutions generated within a time frame specified by the competition organizers. The results generated are better than those of the competition winner in seven of the twelve examinations, while being competitive for the remaining five examinations. This paper also shows experimentally how using reinforcement learning has improved upon our previous technique.