Elephant Search with Deep Learning for Microarray Data Analysis

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, a novel elephant search (ES) based optimization is proposed to select best gene expressions from the large volume of microarray data. Further, a promising machine learning method is envisioned to leverage such high dimensional and complex microarray dataset for extracting hidden patterns inside to make a meaningful prediction and most accurate classification. In particular, stochastic gradient descent based Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on nine most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning (ESDL) approach are compared with most recent published article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl

Hierarchical social modularity in gorillas

Modern human societies show hierarchical social modularity (HSM) in which lower-order social units like nuclear families are nested inside increasingly larger units. It has been argued that this HSM evolved independently and after the chimpanzee–human split due to greater recognition of, and bonding between, dispersed kin. We used network modularity analysis and hierarchical clustering to quantify community structure within two western lowland gorilla populations. In both communities, we detected two hierarchically nested tiers of social structure which have not been previously quantified. Both tiers map closely to human social tiers. Genetic data from one population suggested that, as in humans, social unit membership was kin structured. The sizes of gorilla social units also showed the kind of consistent scaling ratio between social tiers observed in humans, baboons, toothed whales, and elephants. These results indicate that the hierarchical social organization observed in humans may have evolved far earlier than previously asserted and may not be a product of the social brain evolution unique to the hominin lineage

A Physiologically Based System Theory of Consciousness

A system which uses large numbers of devices to perform a complex functionality is forced to adopt a simple functional architecture by the needs to construct copies of, repair, and modify the system. A simple functional architecture means that functionality is partitioned into relatively equal sized components on many levels of detail down to device level, a mapping exists between the different levels, and exchange of information between components is minimized. In the instruction architecture functionality is partitioned on every level into instructions, which exchange unambiguous system information and therefore output system commands. The von Neumann architecture is a special case of the instruction architecture in which instructions are coded as unambiguous system information. In the recommendation (or pattern extraction) architecture functionality is partitioned on every level into repetition elements, which can freely exchange ambiguous information and therefore output only system action recommendations which must compete for control of system behavior. Partitioning is optimized to the best tradeoff between even partitioning and minimum cost of distributing data. Natural pressures deriving from the need to construct copies under DNA control, recover from errors, failures and damage, and add new functionality derived from random mutations has resulted in biological brains being constrained to adopt the recommendation architecture. The resultant hierarchy of functional separations can be the basis for understanding psychological phenomena in terms of physiology. A theory of consciousness is described based on the recommendation architecture model for biological brains. Consciousness is defined at a high level in terms of sensory independent image sequences including self images with the role of extending the search of records of individual experience for behavioral guidance in complex social situations. Functional components of this definition of consciousness are developed, and it is demonstrated that these components can be translated through subcomponents to descriptions in terms of known and postulated physiological mechanisms

A Convex Relaxation for Weakly Supervised Classifiers

This paper introduces a general multi-class approach to weakly supervised classification. Inferring the labels and learning the parameters of the model is usually done jointly through a block-coordinate descent algorithm such as expectation-maximization (EM), which may lead to local minima. To avoid this problem, we propose a cost function based on a convex relaxation of the soft-max loss. We then propose an algorithm specifically designed to efficiently solve the corresponding semidefinite program (SDP). Empirically, our method compares favorably to standard ones on different datasets for multiple instance learning and semi-supervised learning as well as on clustering tasks.Comment: Appears in Proceedings of the 29th International Conference on Machine Learning (ICML 2012

Multiple Instance Learning: A Survey of Problem Characteristics and Applications

Multiple instance learning (MIL) is a form of weakly supervised learning where training instances are arranged in sets, called bags, and a label is provided for the entire bag. This formulation is gaining interest because it naturally fits various problems and allows to leverage weakly labeled data. Consequently, it has been used in diverse application fields such as computer vision and document classification. However, learning from bags raises important challenges that are unique to MIL. This paper provides a comprehensive survey of the characteristics which define and differentiate the types of MIL problems. Until now, these problem characteristics have not been formally identified and described. As a result, the variations in performance of MIL algorithms from one data set to another are difficult to explain. In this paper, MIL problem characteristics are grouped into four broad categories: the composition of the bags, the types of data distribution, the ambiguity of instance labels, and the task to be performed. Methods specialized to address each category are reviewed. Then, the extent to which these characteristics manifest themselves in key MIL application areas are described. Finally, experiments are conducted to compare the performance of 16 state-of-the-art MIL methods on selected problem characteristics. This paper provides insight on how the problem characteristics affect MIL algorithms, recommendations for future benchmarking and promising avenues for research