Onur Küçüktunç

Bio: Onur Küçüktunç is an academic researcher from Ohio State University. The author has contributed to research in topics: Citation graph & Citation. The author has an hindex of 14, co-authored 21 publications receiving 827 citations. Previous affiliations of Onur Küçüktunç include Google & Bilkent University.

A comparative analysis of biclustering algorithms for gene expression data

Abstract: The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters.

A large-scale sentiment analysis for Yahoo! answers

Abstract: Sentiment extraction from online web documents has recently been an active research topic due to its potential use in commercial applications. By sentiment analysis, we refer to the problem of assigning a quantitative positive/negative mood to a short bit of text. Most studies in this area are limited to the identification of sentiments and do not investigate the interplay between sentiments and other factors. In this work, we use a sentiment extraction tool to investigate the influence of factors such as gender, age, education level, the topic at hand, or even the time of the day on sentiments in the context of a large online question answering site. We start our analysis by looking at direct correlations, e.g., we observe more positive sentiments on weekends, very neutral ones in the Science & Mathematics topic, a trend for younger people to express stronger sentiments, or people in military bases to ask the most neutral questions. We then extend this basic analysis by investigating how properties of the (asker, answerer) pair affect the sentiment present in the answer. Among other things, we observe a dependence on the pairing of some inferred attributes estimated by a user's ZIP code. We also show that the best answers differ in their sentiments from other answers, e.g., in the Business & Finance topic, best answers tend to have a more neutral sentiment than other answers. Finally, we report results for the task of predicting the attitude that a question will provoke in answers. We believe that understanding factors influencing the mood of users is not only interesting from a sociological point of view, but also has applications in advertising, recommendation, and search.

Hierarchical organization of urban mobility and its connection with city livability

Abstract: The recent trend of rapid urbanization makes it imperative to understand urban characteristics such as infrastructure, population distribution, jobs, and services that play a key role in urban livability and sustainability. A healthy debate exists on what constitutes optimal structure regarding livability in cities, interpolating, for instance, between mono- and poly-centric organization. Here anonymous and aggregated flows generated from three hundred million users, opted-in to Location History, are used to extract global Intra-urban trips. We develop a metric that allows us to classify cities and to establish a connection between mobility organization and key urban indicators. We demonstrate that cities with strong hierarchical mobility structure display an extensive use of public transport, higher levels of walkability, lower pollutant emissions per capita and better health indicators. Our framework outperforms previous metrics, is highly scalable and can be deployed with little cost, even in areas without resources for traditional data collection. The growing availability of human mobility data can help assess the structure and dynamics of urban environments and their relation to the performance of cities. Here the authors introduce a metric of hierarchy in urban travel and find correlations between levels of hierarchy and other urban indicators.

Fuzzy color histogram-based video segmentation

Abstract: We present a fuzzy color histogram-based shot-boundary detection algorithm specialized for content-based copy detection applications The proposed method aims to detect both cuts and gradual transitions (fade, dissolve) effectively in videos where heavy transformations (such as cam-cording, insertions of patterns, strong re-encoding) occur Along with the color histogram generated with the fuzzy linking method on L*a*b* color space, the system extracts a mask for still regions and the window of picture-in-picture transformation for each detected shot, which will be useful in a content-based copy detection system Experimental results show that our method effectively detects shot boundaries and reduces false alarms as compared to the state-of-the-art shot-boundary detection algorithms

Diversifying Citation Recommendations

Abstract: Literature search is one of the most important steps of academic research. With more than 100,000 papers published each year just in computer science, performing a complete literature search becomes a Herculean task. Some of the existing approaches and tools for literature search cannot compete with the characteristics of today’s literature, and they suffer from ambiguity and homonymy. Techniques based on citation information are more robust to the mentioned issues. Thus, we recently built a Web service called the advisor, which provides personalized recommendations to researchers based on their papers of interest. Since most recommendation methods may return redundant results, diversifying the results of the search process is necessary to increase the amount of information that one can reach via an automated search. This article targets the problem of result diversification in citation-based bibliographic search, assuming that the citation graph itself is the only information available and no categories or intents are known. The contribution of this work is threefold. We survey various random walk--based diversification methods and enhance them with the direction awareness property to allow users to reach either old, foundational (possibly well-cited and well-known) research papers or recent (most likely less-known) ones. Next, we propose a set of novel algorithms based on vertex selection and query refinement. A set of experiments with various evaluation criteria shows that the proposed γ-RLM algorithm performs better than the existing approaches and is suitable for real-time bibliographic search in practice.

国际刊物《Scientometrics》文献计量研究

Abstract: 本文对国际科学计量学杂志《Ｓｃｉｅｎｔｏｍｅｔｒｉｃｓ》１９７９－１９９１年的研究论文内容、栏目、作者及国别和编委及国别作了计量分析，揭示出科学计量学研究的重点、活动的中心及发展趋势，说明了学科带头人在发展科学计量学这门新兴学科中的作用。

Collaborative Deep Learning for Recommender Systems

Abstract: Collaborative filtering (CF) is a successful approach commonly used by many recommender systems. Conventional CF-based methods use the ratings given to items by users as the sole source of information for learning to make recommendation. However, the ratings are often very sparse in many applications, causing CF-based methods to degrade significantly in their recommendation performance. To address this sparsity problem, auxiliary information such as item content information may be utilized. Collaborative topic regression (CTR) is an appealing recent method taking this approach which tightly couples the two components that learn from two different sources of information. Nevertheless, the latent representation learned by CTR may not be very effective when the auxiliary information is very sparse. To address this problem, we generalize recently advances in deep learning from i.i.d. input to non-i.i.d. (CF-based) input and propose in this paper a hierarchical Bayesian model called collaborative deep learning (CDL), which jointly performs deep representation learning for the content information and collaborative filtering for the ratings (feedback) matrix. Extensive experiments on three real-world datasets from different domains show that CDL can significantly advance the state of the art.

Research-paper recommender systems: a literature survey

Abstract: In the last 16 years, more than 200 research articles were published about research-paper recommender systems. We reviewed these articles and present some descriptive statistics in this paper, as well as a discussion about the major advancements and shortcomings and an overview of the most common recommendation concepts and approaches. We found that more than half of the recommendation approaches applied content-based filtering (55 %). Collaborative filtering was applied by only 18 % of the reviewed approaches, and graph-based recommendations by 16 %. Other recommendation concepts included stereotyping, item-centric recommendations, and hybrid recommendations. The content-based filtering approaches mainly utilized papers that the users had authored, tagged, browsed, or downloaded. TF-IDF was the most frequently applied weighting scheme. In addition to simple terms, n-grams, topics, and citations were utilized to model users' information needs. Our review revealed some shortcomings of the current research. First, it remains unclear which recommendation concepts and approaches are the most promising. For instance, researchers reported different results on the performance of content-based and collaborative filtering. Sometimes content-based filtering performed better than collaborative filtering and sometimes it performed worse. We identified three potential reasons for the ambiguity of the results. (A) Several evaluations had limitations. They were based on strongly pruned datasets, few participants in user studies, or did not use appropriate baselines. (B) Some authors provided little information about their algorithms, which makes it difficult to re-implement the approaches. Consequently, researchers use different implementations of the same recommendations approaches, which might lead to variations in the results. (C) We speculated that minor variations in datasets, algorithms, or user populations inevitably lead to strong variations in the performance of the approaches. Hence, finding the most promising approaches is a challenge. As a second limitation, we noted that many authors neglected to take into account factors other than accuracy, for example overall user satisfaction. In addition, most approaches (81 %) neglected the user-modeling process and did not infer information automatically but let users provide keywords, text snippets, or a single paper as input. Information on runtime was provided for 10 % of the approaches. Finally, few research papers had an impact on research-paper recommender systems in practice. We also identified a lack of authority and long-term research interest in the field: 73 % of the authors published no more than one paper on research-paper recommender systems, and there was little cooperation among different co-author groups. We concluded that several actions could improve the research landscape: developing a common evaluation framework, agreement on the information to include in research papers, a stronger focus on non-accuracy aspects and user modeling, a platform for researchers to exchange information, and an open-source framework that bundles the available recommendation approaches.

How Do Users Like This Feature? A Fine Grained Sentiment Analysis of App Reviews

Abstract: App stores allow users to submit feedback for downloaded apps in form of star ratings and text reviews. Recent studies analyzed this feedback and found that it includes information useful for app developers, such as user requirements, ideas for improvements, user sentiments about specific features, and descriptions of experiences with these features. However, for many apps, the amount of reviews is too large to be processed manually and their quality varies largely. The star ratings are given to the whole app and developers do not have a mean to analyze the feedback for the single features. In this paper we propose an automated approach that helps developers filter, aggregate, and analyze user reviews. We use natural language processing techniques to identify fine-grained app features in the reviews. We then extract the user sentiments about the identified features and give them a general score across all reviews. Finally, we use topic modeling techniques to group fine-grained features into more meaningful high-level features. We evaluated our approach with 7 apps from the Apple App Store and Google Play Store and compared its results with a manually, peer-conducted analysis of the reviews. On average, our approach has a precision of 0.59 and a recall of 0.51. The extracted features were coherent and relevant to requirements evolution tasks. Our approach can help app developers to systematically analyze user opinions about single features and filter irrelevant reviews.

How can i improve my app? Classifying user reviews for software maintenance and evolution

Abstract: App Stores, such as Google Play or the Apple Store, allow users to provide feedback on apps by posting review comments and giving star ratings. These platforms constitute a useful electronic mean in which application developers and users can productively exchange information about apps. Previous research showed that users feedback contains usage scenarios, bug reports and feature requests, that can help app developers to accomplish software maintenance and evolution tasks. However, in the case of the most popular apps, the large amount of received feedback, its unstructured nature and varying quality can make the identification of useful user feedback a very challenging task. In this paper we present a taxonomy to classify app reviews into categories relevant to software maintenance and evolution, as well as an approach that merges three techniques: (1) Natural Language Processing, (2) Text Analysis and (3) Sentiment Analysis to automatically classify app reviews into the proposed categories. We show that the combined use of these techniques allows to achieve better results (a precision of 75% and a recall of 74%) than results obtained using each technique individually (precision of 70% and a recall of 67%).