Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Learning to detect video events from zero or very few video examples

In this work we deal with the problem of high-level event detection in video. Specifically, we study the challenging problems of i) learning to detect video events from solely a textual description of the event, without using any positive video examples, and ii) additionally exploiting very few positive training samples together with a small number of ``related'' videos. For learning only from an event's textual description, we first identify a general learning framework and then study the impact of different design choices for various stages of this framework. For additionally learning from example videos, when true positive training samples are scarce, we employ an extension of the Support Vector Machine that allows us to exploit ``related'' event videos by automatically introducing different weights for subsets of the videos in the overall training set. Experimental evaluations performed on the large-scale TRECVID MED 2014 video dataset provide insight on the effectiveness of the proposed methods.Comment: Image and Vision Computing Journal, Elsevier, 2015, accepted for publicatio

Deep learning in remote sensing: a review

Standing at the paradigm shift towards data-intensive science, machine learning techniques are becoming increasingly important. In particular, as a major breakthrough in the field, deep learning has proven as an extremely powerful tool in many fields. Shall we embrace deep learning as the key to all? Or, should we resist a 'black-box' solution? There are controversial opinions in the remote sensing community. In this article, we analyze the challenges of using deep learning for remote sensing data analysis, review the recent advances, and provide resources to make deep learning in remote sensing ridiculously simple to start with. More importantly, we advocate remote sensing scientists to bring their expertise into deep learning, and use it as an implicit general model to tackle unprecedented large-scale influential challenges, such as climate change and urbanization.Comment: Accepted for publication IEEE Geoscience and Remote Sensing Magazin

3D FACE RECOGNITION USING LOCAL FEATURE BASED METHODS

Face recognition has attracted many researchers’ attention compared to other biometrics due to its non-intrusive and friendly nature. Although several methods for 2D face recognition have been proposed so far, there are still some challenges related to the 2D face including illumination, pose variation, and facial expression. In the last few decades, 3D face research area has become more interesting since shape and geometry information are used to handle challenges from 2D faces. Existing algorithms for face recognition are divided into three different categories: holistic feature-based, local feature-based, and hybrid methods. According to the literature, local features have shown better performance relative to holistic feature-based methods under expression and occlusion challenges. In this dissertation, local feature-based methods for 3D face recognition have been studied and surveyed. In the survey, local methods are classified into three broad categories which consist of keypoint-based, curve-based, and local surface-based methods. Inspired by keypoint-based methods which are effective to handle partial occlusion, structural context descriptor on pyramidal shape maps and texture image has been proposed in a multimodal scheme. Score-level fusion is used to combine keypoints’ matching score in both texture and shape modalities. The survey shows local surface-based methods are efficient to handle facial expression. Accordingly, a local derivative pattern is introduced to extract distinct features from depth map in this work. In addition, the local derivative pattern is applied on surface normals. Most 3D face recognition algorithms are focused to utilize the depth information to detect and extract features. Compared to depth maps, surface normals of each point can determine the facial surface orientation, which provides an efficient facial surface representation to extract distinct features for recognition task. An Extreme Learning Machine (ELM)-based auto-encoder is used to make the feature space more discriminative. Expression and occlusion robust analysis using the information from the normal maps are investigated by dividing the facial region into patches. A novel hybrid classifier is proposed to combine Sparse Representation Classifier (SRC) and ELM classifier in a weighted scheme. The proposed algorithms have been evaluated on four widely used 3D face databases; FRGC, Bosphorus, Bu-3DFE, and 3D-TEC. The experimental results illustrate the effectiveness of the proposed approaches. The main contribution of this work lies in identification and analysis of effective local features and a classification method for improving 3D face recognition performance