Automated Protein Structure Classification: A Survey

Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and semi-automatic classification is becoming ever more difficult and prohibitively slow. Therefore, there is a growing need for automated, accurate and efficient classification methods to generate classification databases or increase the speed and accuracy of semi-automatic techniques. Recognizing this need, several automated classification methods have been developed. In this survey, we overview recent developments in this area. We classify different methods based on their characteristics and compare their methodology, accuracy and efficiency. We then present a few open problems and explain future directions.Comment: 14 pages, Technical Report CSRG-589, University of Toront

I Know Why You Went to the Clinic: Risks and Realization of HTTPS Traffic Analysis

Revelations of large scale electronic surveillance and data mining by governments and corporations have fueled increased adoption of HTTPS. We present a traffic analysis attack against over 6000 webpages spanning the HTTPS deployments of 10 widely used, industry-leading websites in areas such as healthcare, finance, legal services and streaming video. Our attack identifies individual pages in the same website with 89% accuracy, exposing personal details including medical conditions, financial and legal affairs and sexual orientation. We examine evaluation methodology and reveal accuracy variations as large as 18% caused by assumptions affecting caching and cookies. We present a novel defense reducing attack accuracy to 27% with a 9% traffic increase, and demonstrate significantly increased effectiveness of prior defenses in our evaluation context, inclusive of enabled caching, user-specific cookies and pages within the same website

From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results

Entropy-based active learning for object recognition

Most methods for learning object categories require large amounts of labeled training data. However, obtaining such data can be a difficult and time-consuming endeavor. We have developed a novel, entropy-based ldquoactive learningrdquo approach which makes significant progress towards this problem. The main idea is to sequentially acquire labeled data by presenting an oracle (the user) with unlabeled images that will be particularly informative when labeled. Active learning adaptively prioritizes the order in which the training examples are acquired, which, as shown by our experiments, can significantly reduce the overall number of training examples required to reach near-optimal performance. At first glance this may seem counter-intuitive: how can the algorithm know whether a group of unlabeled images will be informative, when, by definition, there is no label directly associated with any of the images? Our approach is based on choosing an image to label that maximizes the expected amount of information we gain about the set of unlabeled images. The technique is demonstrated in several contexts, including improving the efficiency of Web image-search queries and open-world visual learning by an autonomous agent. Experiments on a large set of 140 visual object categories taken directly from text-based Web image searches show that our technique can provide large improvements (up to 10 x reduction in the number of training examples needed) over baseline techniques

Zero-Annotation Object Detection with Web Knowledge Transfer

Object detection is one of the major problems in computer vision, and has been extensively studied. Most of the existing detection works rely on labor-intensive supervision, such as ground truth bounding boxes of objects or at least image-level annotations. On the contrary, we propose an object detection method that does not require any form of human annotation on target tasks, by exploiting freely available web images. In order to facilitate effective knowledge transfer from web images, we introduce a multi-instance multi-label domain adaption learning framework with two key innovations. First of all, we propose an instance-level adversarial domain adaptation network with attention on foreground objects to transfer the object appearances from web domain to target domain. Second, to preserve the class-specific semantic structure of transferred object features, we propose a simultaneous transfer mechanism to transfer the supervision across domains through pseudo strong label generation. With our end-to-end framework that simultaneously learns a weakly supervised detector and transfers knowledge across domains, we achieved significant improvements over baseline methods on the benchmark datasets.Comment: Accepted in ECCV 201

A framework for interrogating social media images to reveal an emergent archive of war

The visual image has long been central to how war is seen, contested and legitimised, remembered and forgotten. Archives are pivotal to these ends as is their ownership and access, from state and other official repositories through to the countless photographs scattered and hidden from a collective understanding of what war looks like in individual collections and dusty attics. With the advent and rapid development of social media, however, the amateur and the professional, the illicit and the sanctioned, the personal and the official, and the past and the present, all seem to inhabit the same connected and chaotic space.However, to even begin to render intelligible the complexity, scale and volume of what war looks like in social media archives is a considerable task, given the limitations of any traditional human-based method of collection and analysis. We thus propose the production of a series of ‘snapshots’, using computer-aided extraction and identification techniques to try to offer an experimental way in to conceiving a new imaginary of war. We were particularly interested in testing to see if twentieth century wars, obviously initially captured via pre-digital means, had become more ‘settled’ over time in terms of their remediated presence today through their visual representations and connections on social media, compared with wars fought in digital media ecologies (i.e. those fought and initially represented amidst the volume and pervasiveness of social media images).To this end, we developed a framework for automatically extracting and analysing war images that appear in social media, using both the features of the images themselves, and the text and metadata associated with each image. The framework utilises a workflow comprising four core stages: (1) information retrieval, (2) data pre-processing, (3) feature extraction, and (4) machine learning. Our corpus was drawn from the social media platforms Facebook and Flickr