GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into consideration. Deep learning, an emerging machine learning technique in computational biology, can be used to generate an unbiased combination of gene set, and to determine the biological relevance and analysis consistency of these combining gene sets by leveraging large genomic data sets. In this study, we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model with the incorporation of a priori defined gene sets that retain the crucial biological features in the latent layer. We introduced the concept of the gene superset, an unbiased combination of gene sets with weights trained by the autoencoder, where each node in the latent layer is a superset. Trained with genomic data from TCGA and evaluated with their accompanying clinical parameters, we showed gene supersets' ability of discriminating tumor subtypes and their prognostic capability. We further demonstrated the biological relevance of the top component gene sets in the significant supersets. Using autoencoder model and gene superset at its latent layer, we demonstrated that gene supersets retain sufficient biological information with respect to tumor subtypes and clinical prognostic significance. Superset also provides high reproducibility on survival analysis and accurate prediction for cancer subtypes.Comment: Presented in the International Conference on Intelligent Biology and Medicine (ICIBM 2018) at Los Angeles, CA, USA and published in BMC Systems Biology 2018, 12(Suppl 8):14

Hypertext and the Docuverse: A Research Memo

The term docuverse was first developed by Apple Computer guru Allen Kay in the late 1960’s. The underlying idea can be traced back decades earlier, to the visionary Vannevar Bush and the Memex (Bush, 1945). According to Kay, a docuverse is a set of related documents together with the linkages between them. In this paper, a docuverse is conceived as a collection of related scholarly documents together with the links, ties and bonds that can bring them together into an integrated logical and conceptual whole. Kay who also coined the term hypertext, which refers to an electronic document with existing and anticipated hypermedia technology. have already made possible the construction of an electronic web of all the related documents of social science (and any other academic discipline, professional field or interdiscipline) like third sector studies

Games on interval and permutation graph representations

We describe combinatorial games on graphs in which two players antagonistically build a representation of a subgraph of a given graph. We show that for a large class of these games, determining whether a given instance is a winning position for the next player is PSPACE-hard. In contrast, we give polynomial time algorithms for solving some versions of the games on trees

DimLift: Interactive Hierarchical Data Exploration through Dimensional Bundling

The identification of interesting patterns and relationships is essential to exploratory data analysis. This becomes increasingly difficult in high dimensional datasets. While dimensionality reduction techniques can be utilized to reduce the analysis space, these may unintentionally bury key dimensions within a larger grouping and obfuscate meaningful patterns. With this work we introduce DimLift , a novel visual analysis method for creating and interacting with dimensional bundles . Generated through an iterative dimensionality reduction or user-driven approach, dimensional bundles are expressive groups of dimensions that contribute similarly to the variance of a dataset. Interactive exploration and reconstruction methods via a layered parallel coordinates plot allow users to lift interesting and subtle relationships to the surface, even in complex scenarios of missing and mixed data types. We exemplify the power of this technique in an expert case study on clinical cohort data alongside two additional case examples from nutrition and ecology.acceptedVersio

Plurals and Mereology

International audienceIn linguistics, the dominant approach to the semantics of plurals appeals to mere-ology. However, this approach has received strong criticisms from philosophical logicians who subscribe to an alternative framework based on plural logic. In the first part of the article, we offer a precise characterization of the mereological approach and the semantic background in which the debate can be meaningfully reconstructed. In the second part, we deal with the criticisms and assess their logical, linguistic, and philosophical significance. We identify four main objections and show how each can be addressed. Finally, we compare the strengths and shortcomings of the mereologi-cal approach and plural logic. Our conclusion is that the former remains a viable and well-motivated framework for the analysis of plurals

An exploratory study of the relationship between communication apprehension and personal construct theory in the context of a public speaking fundamentals course

Many psychologists, philosophers, and educators agree that individual self-concepts develop, in large part, through perceptions gained from communicative transactions. If the nature of the transaction changes, perceptions can change, and self-concept can be altered. Self-concept combines with many influences including cultural heritage, environment, and past experiences to form the basis of an individual’s unique communicative and behavior patterns

Numbers without aggregation

Suppose we can save either a larger group of persons or a distinct, smaller group from some harm. Many people think that, all else equal, we ought to save the greater number. This article defends this view (with qualifications). But unlike earlier theories, it does not rely on the idea that several people's interests or claims receive greater aggregate weight. The argument starts from the idea that due to their stakes, the affected people have claims to have a say in the rescue decision. As rescuers, our primary duty is to respect these procedural claims, which we must do by doing what these people would decide, in a process where each is given an equal vote on the matter. So in cases where each votes in their own self-interest, respect for their equal right to decide, or their autonomy, will lead us to save the greater number. The argument is explained in detail, with special attention to the questions of how, exactly, it avoids aggregation, and of why majority rule is superior to lottery procedures. The view has further advantages. Especially, it explains the “partial” relevance of numbers in cases involving unequal harms, and it does so in a way that dissolves the appearance of paradox that besets theories of “partial aggregation.

Plurals and Mereology

International audienceIn linguistics, the dominant approach to the semantics of plurals appeals to mere-ology. However, this approach has received strong criticisms from philosophical logicians who subscribe to an alternative framework based on plural logic. In the first part of the article, we offer a precise characterization of the mereological approach and the semantic background in which the debate can be meaningfully reconstructed. In the second part, we deal with the criticisms and assess their logical, linguistic, and philosophical significance. We identify four main objections and show how each can be addressed. Finally, we compare the strengths and shortcomings of the mereologi-cal approach and plural logic. Our conclusion is that the former remains a viable and well-motivated framework for the analysis of plurals