Combination of Multiple Bipartite Ranking for Web Content Quality Evaluation

Web content quality estimation is crucial to various web content processing applications. Our previous work applied Bagging + C4.5 to achive the best results on the ECML/PKDD Discovery Challenge 2010, which is the comibination of many point-wise rankinig models. In this paper, we combine multiple pair-wise bipartite ranking learner to solve the multi-partite ranking problems for the web quality estimation. In encoding stage, we present the ternary encoding and the binary coding extending each rank value to $L - 1$ (L is the number of the different ranking value). For the decoding, we discuss the combination of multiple ranking results from multiple bipartite ranking models with the predefined weighting and the adaptive weighting. The experiments on ECML/PKDD 2010 Discovery Challenge datasets show that \textit{binary coding} + \textit{predefined weighting} yields the highest performance in all four combinations and furthermore it is better than the best results reported in ECML/PKDD 2010 Discovery Challenge competition.Comment: 17 pages, 8 figures, 2 table

An Email Attachment is Worth a Thousand Words, or Is It?

There is an extensive body of research on Social Network Analysis (SNA) based on the email archive. The network used in the analysis is generally extracted either by capturing the email communication in From, To, Cc and Bcc email header fields or by the entities contained in the email message. In the latter case, the entities could be, for instance, the bag of words, url's, names, phones, etc. It could also include the textual content of attachments, for instance Microsoft Word documents, excel spreadsheets, or Adobe pdfs. The nodes in this network represent users and entities. The edges represent communication between users and relations to the entities. We suggest taking a different approach to the network extraction and use attachments shared between users as the edges. The motivation for this is two-fold. First, attachments represent the "intimacy" manifestation of the relation's strength. Second, the statistical analysis of private email archives that we collected and Enron email corpus shows that the attachments contribute in average around 80-90% to the archive's disk-space usage, which means that most of the data is presently ignored in the SNA of email archives. Consequently, we hypothesize that this approach might provide more insight into the social structure of the email archive. We extract the communication and shared attachments networks from Enron email corpus. We further analyze degree, betweenness, closeness, and eigenvector centrality measures in both networks and review the differences and what can be learned from them. We use nearest neighbor algorithm to generate similarity groups for five Enron employees. The groups are consistent with Enron's organizational chart, which validates our approach.Comment: 12 pages, 4 figures, 7 tables, IML'17, Liverpool, U

Visual Scene Understanding by Deep Fisher Discriminant Learning

Modern deep learning has recently revolutionized several fields of classic machine learning and computer vision, such as, scene understanding, natural language processing and machine translation. The substitution of feature hand-crafting with automatic feature learning, provides an excellent opportunity for gaining an in-depth understanding of large-scale data statistics. Deep neural networks generally train models with huge numbers of parameters, facilitating efficient search for optimal and sub-optimal spaces of highly non-convex objective functions. On the other hand, Fisher discriminant analysis has been widely employed to impose class discrepancy, for the sake of segmentation, classification, and recognition tasks. This thesis bridges between contemporary deep learning and classic discriminant analysis, to accommodate some important challenges in visual scene understanding, i.e. semantic segmentation, texture classification, and object recognition. The aim is to accomplish specific tasks in some new high-dimensional spaces, covered by the statistical information of the datasets under study. Inspired by a new formulation of Fisher discriminant analysis, this thesis introduces some novel arrangements of well-known deep learning architectures, to achieve better performances on the targeted missions. The theoretical justifications are based upon a large body of experimental work, and consolidate the contribution of the proposed idea; Deep Fisher Discriminant Learning, to several challenges in visual scene understanding

RANDOM WALK APPLIED TO HETEROGENOUS DRUG-TARGET NETWORKS FOR PREDICTING BIOLOGICAL OUTCOMES

Thesis (Ph.D.) - Indiana University, Informatics and Computing, 2016Prediction of unknown drug target interactions from bioassay data is critical not only for the understanding of various interactions but also crucial for the development of new drugs and repurposing of old ones. Conventional methods for prediction of such interactions can be divided into 2D based and 3D based methods. 3D methods are more CPU expensive and require more manual interpretation whereas 2D methods are actually fast methods like machine learning and similarity search which use chemical fingerprints. One of the problems of using traditional machine learning based method to predict drug-target pairs is that it requires a labeled information of true and false interactions. One of the major problems of supervised learning methods is selection on negative samples. Unknown drug target interactions are regarded as false interactions, which may influence the predictive accuracy of the model. To overcome this problem network based methods has become an effective tool in predicting the drug target interactions overcoming the negative sampling problem. In this dissertation study, I will describe traditional machine learning methods and 3D methods of pharmacophore modeling for drug target prediction and will show how these methods work in a drug discovery scenario. I will then introduce a new framework for drug target prediction based on bipartite networks of drug target relations known as Random Walk with Restart (RWR). RWR integrates various networks including drug– drug similarity networks, protein-protein similarity networks and drug- target interaction networks into a heterogeneous network that is capable of predicting novel drug-target relations. I will describe how chemical features for measuring drug-drug similarity do not affect performance in predicting interactions and further show the performance of RWR using an external dataset from ChEMBL database. I will describe about further implementations of RWR approach into multilayered networks consisting of biological data like diseases, tissue based gene expression data, protein- complexes and metabolic pathways to predict associations between human diseases and metabolic pathways which are very crucial in drug discovery. I have further developed a software tool package netpredictor in R (standalone and the web) for unipartite and bipartite networks and implemented network-based predictive algorithms and network properties for drug-target prediction. This package will be described

Topic Distiller:distilling semantic topics from documents

Abstract. This thesis details the design and implementation of a system that can find relevant and latent semantic topics from textual documents. The design of this system, named Topic Distiller, is inspired by research conducted on automatic keyphrase extraction and automatic topic labeling, and it employs entity linking and knowledge bases to reduce text documents to their semantic topics. The Topic Distiller is evaluated using methods and datasets used in information retrieval and automatic keyphrase extraction. On top of the common datasets used in the literature three additional datasets are created to evaluate the system. The evaluation reveals that the Topic Distiller is able to find relevant and latent topics from textual documents, beating the state-of-the-art automatic keyphrase methods in performance when used on news articles and social media posts.Semanttisten aiheiden suodattaminen dokumenteista. Tiivistelmä. Tässä diplomityössä tarkastellaan järjestelmää, joka pystyy löytämään tekstistä relevantteja ja piileviä semanttisia aihealueita, sekä kyseisen järjestelmän suunnittelua ja implementaatiota. Tämän Topic Distiller -järjestelmän suunnittelu ammentaa inspiraatiota automaattisen termintunnistamisen ja automaattisen aiheiden nimeämisen tutkimuksesta sekä hyödyntää automaattista semanttista annotointia ja tietämyskantoja tekstin aihealueiden löytämisessä. Topic Distiller -järjestelmän suorituskykyä mitataan hyödyntämällä kirjallisuudessa paljon käytettyjä automaattisen termintunnistamisen evaluontimenetelmiä ja aineistoja. Näiden yleisten aineistojen lisäksi esittelemme kolme uutta aineistoa, jotka on luotu Topic Distiller -järjestelmän arviointia varten. Evaluointi tuo ilmi, että Topic Distiller kykenee löytämään relevantteja ja piileviä aiheita tekstistä. Se päihittää kirjallisuuden viimeisimmät automaattisen termintunnistamisen menetelmät suorituskyvyssä, kun sitä käytetään uutisartikkelien sekä sosiaalisen median julkaisujen analysointiin

A computational approach to the art of visual storytelling

For millennia, humanity as been using images to tell stories. In modern society, these visual narratives take the center stage in many different contexts, from illustrated children’s books to news media and comic books. They leverage the power of compounding various images in sequence to present compelling and informative narratives, in an immediate and impactful manner. In order to create them, many criteria are taken into account, from the quality of the individual images to how they synergize with one another. With the rise of the Internet, visual content with which to create these visual storylines is now in abundance. In areas such as news media, where visual storylines are regularly used to depict news stories, this has both advantages and disadvantages. Although content might be available online to create a visual storyline, filtering the massive amounts of existing images for high quality, relevant ones is a hard and time consuming task. Furthermore, combining these images into visually and semantically cohesive narratives is a highly skillful process and one that takes time. As a first step to help solve this problem, this thesis brings state of the art computational methodologies to the age old tradition of creating visual storylines. Leveraging these methodologies, we define a three part architecture to help with the creation of visual storylines in the context of news media, using social media content. To ensure the quality of the storylines from a human perception point of view, we deploy methods for filtering and raking images according to news quality standards, we resort to multimedia retrieval techniques to find relevant content and we propose a machine learning based approach to organize visual content into cohesive and appealing visual narratives