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

Simultaneous Dempster-Shafer clustering and gradual determination of number of clusters using a neural network structure

In this paper we extend an earlier result within Dempster-Shafer theory ["Fast Dempster-Shafer Clustering Using a Neural Network Structure," in Proc. Seventh Int. Conf. Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU'98)] where several pieces of evidence were clustered into a fixed number of clusters using a neural structure. This was done by minimizing a metaconflict function. We now develop a method for simultaneous clustering and determination of number of clusters during iteration in the neural structure. We let the output signals of neurons represent the degree to which a pieces of evidence belong to a corresponding cluster. From these we derive a probability distribution regarding the number of clusters, which gradually during the iteration is transformed into a determination of number of clusters. This gradual determination is fed back into the neural structure at each iteration to influence the clustering process.Comment: 6 pages, 10 figure

SOM-based algorithms for qualitative variables

It is well known that the SOM algorithm achieves a clustering of data which can be interpreted as an extension of Principal Component Analysis, because of its topology-preserving property. But the SOM algorithm can only process real-valued data. In previous papers, we have proposed several methods based on the SOM algorithm to analyze categorical data, which is the case in survey data. In this paper, we present these methods in a unified manner. The first one (Kohonen Multiple Correspondence Analysis, KMCA) deals only with the modalities, while the two others (Kohonen Multiple Correspondence Analysis with individuals, KMCA\_ind, Kohonen algorithm on DISJonctive table, KDISJ) can take into account the individuals, and the modalities simultaneously.Comment: Special Issue apr\`{e}s WSOM 03 \`{a} Kitakiush

3D Object Reconstruction from Imperfect Depth Data Using Extended YOLOv3 Network

State-of-the-art intelligent versatile applications provoke the usage of full 3D, depth-based streams, especially in the scenarios of intelligent remote control and communications, where virtual and augmented reality will soon become outdated and are forecasted to be replaced by point cloud streams providing explorable 3D environments of communication and industrial data. One of the most novel approaches employed in modern object reconstruction methods is to use a priori knowledge of the objects that are being reconstructed. Our approach is different as we strive to reconstruct a 3D object within much more difficult scenarios of limited data availability. Data stream is often limited by insufficient depth camera coverage and, as a result, the objects are occluded and data is lost. Our proposed hybrid artificial neural network modifications have improved the reconstruction results by 8.53 which allows us for much more precise filling of occluded object sides and reduction of noise during the process. Furthermore, the addition of object segmentation masks and the individual object instance classification is a leap forward towards a general-purpose scene reconstruction as opposed to a single object reconstruction task due to the ability to mask out overlapping object instances and using only masked object area in the reconstruction process

Managing the unknown: a survey on Open Set Recognition and tangential areas

In real-world scenarios classification models are often required to perform robustly when predicting samples belonging to classes that have not appeared during its training stage. Open Set Recognition addresses this issue by devising models capable of detecting unknown classes from samples arriving during the testing phase, while maintaining a good level of performance in the classification of samples belonging to known classes. This review comprehensively overviews the recent literature related to Open Set Recognition, identifying common practices, limitations, and connections of this field with other machine learning research areas, such as continual learning, out-of-distribution detection, novelty detection, and uncertainty estimation. Our work also uncovers open problems and suggests several research directions that may motivate and articulate future efforts towards more safe Artificial Intelligence methods.Comment: 35 pages, 1 figure, 1 tabl

Galois lattice theory for probabilistic visual landmarks

This paper presents an original application of the Galois lattice theory, the visual landmark selection for topological localization of an autonomous mobile robot, equipped with a color camera. First, visual landmarks have to be selected in order to characterize a structural environment. Second, such landmarks have to be detected and updated for localization. These landmarks are combinations of attributes, and the selection process is done through a Galois lattice. This paper exposes the landmark selection process and focuses on probabilistic landmarks, which give the robot thorough information on how to locate itself. As a result, landmarks are no longer binary, but probabilistic. The full process of using such landmarks is described in this paper and validated through a robotics experiment