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Among the most compelling applications of Augmented Reality are spatially registered tutorials. The effort of creating such instructions remains one of the obstacles precluding a wider use. We propose a system that is capable of extracting 3D instructions in a completely model-free manner from demonstrations, based on volumetric changes. The instructions are visualised later in an interactive Augmented Reality guidance application, on a mobile head-mounted display. We enable a technology that can be used by anyone in an ad-hoc tabletop setup for assemblies with rigid components.

One of the promising opportunities of digital health is its potential to lead to more holistic understandings of diseases by interacting with the daily life of patients and through the collection of large amounts of real world data. Validating and benchmarking indicators of disease severity in the home setting is difficult, however, given the large number of confounders present in the real world and the challenges in collecting ground truth data in the home. Here we leverage two datasets with continuous wrist-worn accelerometer data coupled with frequent symptom reports in the home setting, to develop digital biomarkers of symptom severity. Using these data, we performed a public benchmarking challenge in which participants were asked to build measures of severity across 3 symptoms (on/off medication, dyskinesia, and tremor). 42 teams participated and performance was improved over baseline models for each subchallenge. Additional ensemble modeling across submissions further improved performance, and the top models validated in a subset of patients whose symptoms were observed and rated by trained clinicians.

We present a system for generating and visualizing interactive 3D Augmented Reality tutorials based on 2D video input, which allows viewpoint control at runtime. Inspired by assembly planning, we analyze the input video using a 3D CAD model of the object to determine an assembly graph that encodes blocking relationships between parts. Using an assembly graph enables us to detect assembly steps that are otherwise difficult to extract from the video, and generally improves object detection and tracking by providing prior knowledge about movable parts. To avoid information loss, we combine the 3D animation with relevant parts of the 2D video so that we can show detailed manipulations and tool usage that cannot be easily extracted from the video. To further support user orientation, we visually align the 3D animation with the real-world object by using texture information from the input video. We developed a presentation system that uses commonly available hardware to make our results accessible for home use and demonstrate the effectiveness of our approach by comparing it to traditional video tutorials.

A new algorithm is presented to find clusters in a dataset of points in Rn with no prior knowledge of possible clustering. The algorithm detects clusters in a top down fashion by testing modality of density functions generated from the dataset and splitting the set accordingly. Results on synthetic and text datasets demonstrate that the method is comparable to other established unsupervised learning algorithms, which do in fact require the number of clusters ab initio. The method proves to be particularly suitable for certain distributions and offers a valid alternative in situations where most of the well-known algorithms do not produce consistent results.

Exams are an integral assessment component in CS1 courses. However, little research exists concerning the impact of the exam format on student performance. To address this deficit, we conducted a year-long study to investigate student performance across two test formats, paper and IDE, with the goal of identifying any differences attributable to the format. Data was collected from the second and third exams over the course of two semesters, with five sections per semester. Each exam, whether paper or IDE, was constructed from a common list of concepts to ensure comparability across formats and sections. To assess the impact of exam format, we considered three points of concern. The first factor, grade received, provides a direct indication of student performance. Next, we examined the type of error committed by students (either syntax or logic) to determine influence of exam format (e.g., Does an IDE reduce the occurrence of syntax errors?). Finally, we considered exam completion rates to address concerns such as if the additional feedback might be overwhelming students in an already stressful environment (exam-taking) leading to lower completion rates.

The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses., The response to respiratory virus exposure can currently not be predicted by pre- or early post-exposure molecular signatures. Here, the authors conduct a community-based analysis of blood gene expression from healthy individuals exposed to respiratory viruses and provide predictive models and biological insight into the physiological response.

Respiratory viruses are highly infectious; however, the variation of individuals’ physiologic responses to viral exposure is poorly understood. Most studies examining molecular predictors of response focus on late stage predictors, typically near the time of peak symptoms. To determine whether pre- or early post-exposure factors could predict response, we conducted a community-based analysis to identify predictors of resilience or susceptibility to several respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV) using peripheral blood gene expression profiles collected from healthy subjects prior to viral exposure, as well as up to 24 hours following exposure. This analysis revealed that it is possible to construct models predictive of symptoms using profiles even prior to viral exposure. Analysis of predictive gene features revealed little overlap among models; however, in aggregate, these genes were enriched for common pathways. Heme Metabolism, the most significantly enriched pathway, was associated with higher risk of developing symptoms following viral exposure.

Objective To describe the activities performed by people involved in clinical decision support (CDS) at leading sites. Materials and methods We conducted ethnographic observations at seven diverse sites with a history of excellence in CDS using the Rapid Assessment Process and analyzed the data using a series of card sorts, informed by Linstone's Multiple Perspectives Model. Results We identified 18 activities and grouped them into four areas. Area 1: Fostering relationships across the organization, with activities (a) training and support, (b) visibility/presence on the floor, (c) liaising between people, (d) administration and leadership, (e) project management, (f) cheerleading/buy-in/sponsorship, (g) preparing for CDS implementation. Area 2: Assembling the system with activities (a) providing technical support, (b) CDS content development, (c) purchasing products from vendors (d) knowledge management, (e) system integration. Area 3: Using CDS to achieve the organization's goals with activities (a) reporting, (b) requirements-gathering/specifications, (c) monitoring CDS, (d) linking CDS to goals, (e) managing data. Area 4: Participation in external policy and standards activities (this area consists of only a single activity). We also identified a set of recommendations associated with these 18 activities. Discussion All 18 activities we identified were performed at all sites, although the way they were organized into roles differed substantially. We consider these activities critical to the success of a CDS program. Conclusions A series of activities are performed by sites strong in CDS, and sites adopting CDS should ensure they incorporate these activities into their efforts.

Prediction problems in biomedical sciences are generally quite difficult, partially due to incomplete knowledge of how the phenomenon of interest is influenced by the variables and measurements used for prediction, as well as a lack of consensus regarding the ideal predictor(s) for specific problems. In these situations, a powerful approach to improving prediction performance is to construct ensembles that combine the outputs of many individual base predictors, which have been successful for many biomedical prediction tasks. Moreover, selecting a parsimonious ensemble can be of even greater value for biomedical sciences, where it is not only important to learn an accurate predictor, but also to interpret what novel knowledge it can provide about the target problem. Ensemble selection is a promising approach for this task because of its ability to select a collectively predictive subset, often a relatively small one, of all input base predictors. One of the most well-known algorithms for ensemble selection, CES (Caruana et al.’s Ensemble Selection), generally performs well in practice, but faces several challenges due to the difficulty of choosing the right values of its various parameters. Since the choices made for these parameters are usually ad-hoc, good performance of CES is difficult to guarantee for a variety of problems or datasets. To address these challenges with CES and other such algorithms, we propose a novel heterogeneous ensemble selection approach based on the paradigm of reinforcement learning (RL), which offers a more systematic and mathematically sound methodology for exploring the many possible combinations of base predictors that can be selected into an ensemble. We develop three RL-based strategies for constructing ensembles and analyze their results on two unbalanced computational genomics problems, namely the prediction of protein function and splice sites in eukaryotic genomes. We show that the resultant ensembles are indeed substantially more parsimonious as compared to the full set of base predictors, yet still offer almost the same classification power, especially for larger datasets. The RL ensembles also yield a better combination of parsimony and predictive performance as compared to CES.

Recent advances in biotechnology have resulted in large volumes of genomic and proteomic data leading to the emergence of numerous in silico methods for annotation, such as supervised machine learning approaches. Such algorithms, however, require large amounts of labeled data for training. In practice, labeled data is oftentimes limited because it is difficult to obtain. Therefore, semi-supervised machine learning is preferable, in which classifiers trained on limited amounts of labeled data can be improved by exploiting the large amounts of unlabeled data. In this work, we focus on transductive learning, a special case of semi-supervised learning. A semi-supervised algorithm builds an inductive model that generalizes well to new, unseen (test) instances. In contrast, during the training phase, a transductive algorithm has access to the (test) instances that need to be classified, allowing advantageous utilization of these points in order to reach the best separation function. Compared to learning a classifier for use with future data, cassette exon identification is a suitable application for transductive learning, since the goal is to annotate a sequenced genome for which a limited amount of labeled data is available. We study the applicability of three popular transductive techniques and their compatibility with various kernels to the binary DNA classification problem of cassette exon identification. The results of our experiments suggest that transductive learning is a useful approach for assisting genome annotation.

Thanks to Next Generation Sequencing technologies, unlabelled data is now generated easily, while the annotation process remains expensive. Semi-supervised learning represents a cost-effective alternative to supervised learning, as it can improve supervised classifiers by making use of unlabelled data. However, semi-supervised learning has not been studied much for problems with highly skewed class distributions, which are prevalent in bioinformatics. To address this limitation, we carry out a study of a semi-supervised learning algorithm, specifically self-training based on Naive Bayes, with focus on data-level approaches for handling imbalanced class distributions. Our study is conducted on the problem of predicting splice sites and it is based on datasets for which the ratio of positive to negative examples is 1-to-99. Our results show that under certain conditions semi-supervised learning algorithms are a better choice than purely supervised classification algorithms.

Producing accurate classifiers depends on the quality and quantity of labeled data. The lack of labeled data, due to its expensive generation, critically affects the application of machine learning algorithms to biological problems. However, unlabeled data may be acquired relatively faster and in larger quantities thanks to current biochemical technologies, called Next Generation Sequencing. In such cases, when the number of labeled instances is overwhelmed by the number of unlabeled instances, semi-supervised learning represents a cost-effective alternative that can improve supervised classifiers by utilizing unlabeled data. In practice, data oftentimes exhibits imbalanced class distributions, which represents an obstacle for both supervised and semi-supervised learning. The problem of supervised learning from imbalanced datasets has been extensively studied, and various solutions have been proposed to produce classifiers with optimal performance on highly skewed class distributions. In the case of semi-supervised learning, there are not as many efforts aimed at the imbalance data problem. In this paper, we study several ensemble-based semi-supervised learning approaches for predicting splice sites, a problem for which the imbalance ratio is very high. We run experiments on five imbalanced datasets with the goal of identifying which variants are the most effective.

Over the last decade, user-generated content has grown continuously. Recommender systems that exploit user feedback are widely used in e-commerce and quite necessary for business enhancement. To make use of such user feedback, we propose a new content/collaborative hybrid approach, which is built on top of the recently released hetrec2011-movielens-2k dataset and is an extension of a previously proposed neighborhood based approach, called Weighted Tag Recommender (WTR). Our approach has two versions. Both versions make use of ratings to enable collaborative filtering and use either user tags, available in the hetrec2011-movielens-2k dataset, or movie keywords retrieved from IMDB, to capture movie content information. Experimental results show that the information from keywords can help build a movie recommender system competitive with other neighborhood based approaches and even with more sophisticated state-of-the-art approaches.

Cost-efficient next generation sequencers can now produce unprecedented volumes of raw DNA data, posing challenges for annotation. Supervised machine learning approaches have been traditionally used to analyse and annotate complex genomic information. However, such approaches require labelled data for training, which in practice is scarce or expensive, while the unlabelled data is abundant. For some problems, semi-supervised learning can help improve supervised classifiers by making use of large amounts of unlabelled data and the latent information within them. We evaluate the applicability of semi-supervised learning algorithms to the problem of DNA sequence annotation, specifically to the prediction of alternatively spliced exons. We employ Expectation Maximisation, Self-training, and Co-training algorithms in an effort to assess the strengths and limitations of these techniques in the context of alternative splicing.

Background Recent biochemical advances have led to inexpensive, time-efficient production of massive volumes of raw genomic data. Traditional machine learning approaches to genome annotation typically rely on large amounts of labeled data. The process of labeling data can be expensive, as it requires domain knowledge and expert involvement. Semi-supervised learning approaches that can make use of unlabeled data, in addition to small amounts of labeled data, can help reduce the costs associated with labeling. In this context, we focus on the problem of predicting splice sites in a genome using semi-supervised learning approaches. This is a challenging problem, due to the highly imbalanced distribution of the data, i.e., small number of splice sites as compared to the number of non-splice sites. To address this challenge, we propose to use ensembles of semi-supervised classifiers, specifically self-training and co-training classifiers. Results Our experiments on five highly imbalanced splice site datasets, with positive to negative ratios of 1-to-99, showed that the ensemble-based semi-supervised approaches represent a good choice, even when the amount of labeled data consists of less than 1% of all training data. In particular, we found that ensembles of co-training and self-training classifiers that dynamically balance the set of labeled instances during the semi-supervised iterations show improvements over the corresponding supervised ensemble baselines. Conclusions In the presence of limited amounts of labeled data, ensemble-based semi-supervised approaches can successfully leverage the unlabeled data to enhance supervised ensembles learned from highly imbalanced data distributions. Given that such distributions are common for many biological sequence classification problems, our work can be seen as a stepping stone towards more sophisticated ensemble-based approaches to biological sequence annotation in a semi-supervised framework.

This paper presents an approach to semantic segmentation and structural modeling from dense 3D point clouds. The core contribution is an efficient method for fitting of geometric primitives based on machine learning. First, the dense 3D point cloud is acquired together with RGB images on a mobile handheld device. Then, RANSAC is used to estimate the presence of geometric primitives, followed by an evaluation of their fit based on classification of the fitting parameters. Finally, the approach iterates over successive frames to optimize the fitting parameters or replace a detected primitive by a better fitting one. As a result, we obtain a semantic model of the scene consisting of a set of geometric primitives. We evaluate the approach on an extensive set of scenarios and show its plausibility in augmented reality applications.