Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.Comment: 11 pages, 7 figure

Fast and scalable inference of multi-sample cancer lineages.

Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee

Graph Partitioning-Based Coordination Methods for Large-Scale Multidisciplinary Design Optimization Problems

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97127/1/AIAA2012-5522.pd

EPICURE: A partitioning and co-design framework for reconfigurable computing

This paper presents a new design methodology able to bridge the gap between an abstract specification and a heterogeneous reconfigurable architecture. The EPICURE contribution is the result of a joint study on abstraction/refinement methods and a smart reconfigurable architecture within the formal Esterel design tools suite. The original points of this work are: (i) a generic HW/SW interface model, (ii) a specification methodology that handles the control, and includes efficient verification and HW/SW synthesis capabilities, (iii) a method for parallelism exploration based on abstract resources/performance estimation expressed in terms of area/delay tradeoffs, (iv) a HW/SW partitioning approach that refines the specification into explicit HW configurations and the associated SW control. The EPICURE framework shows how a cooperation of complementary methodologies and CAD tools associated with a relevant architecture can signficantly improve the designer productivity, especially in the context of reconfigurable architectures