Wordlength Optimization for Custom Floating-point Systems

International audienceAlgorithm complexity and problem size explosion during the last few years brought new challenges for hardware implementation of data-oriented applications. In particular, they have caused a large increase in memory, execution time, and power needed. One solution to address those challenges is to reduce data sizes. Custom floating-point is a good candidate that brings a large dynamic range in a compact representation. Thanks to improvement in floating-point units, it is more and more explored as an alternative to fixed-point.This paper proposes an automatic optimization flow to optimize floating-point wordlength for a given quality metric. This flow is generic and can be used for any C or C++ algorithm. Different strategies are proposed to optimize the exponent and mantissa wordlengths. These strategies take advantages of analyzing the data dynamic range to reduce the optimization time. The obtained results show that better implementation costcan be obtained compared to 16-bit floating-point for a same quality

Wordlength Optimization for Custom Floating-point Systems

International audienceAlgorithm complexity and problem size explosion during the last few years brought new challenges for hardware implementation of data-oriented applications. In particular, they have caused a large increase in memory, execution time, and power needed. One solution to address those challenges is to reduce data sizes. Custom floating-point is a good candidate that brings a large dynamic range in a compact representation. Thanks to improvement in floating-point units, it is more and more explored as an alternative to fixed-point.This paper proposes an automatic optimization flow to optimize floating-point wordlength for a given quality metric. This flow is generic and can be used for any C or C++ algorithm. Different strategies are proposed to optimize the exponent and mantissa wordlengths. These strategies take advantages of analyzing the data dynamic range to reduce the optimization time. The obtained results show that better implementation costcan be obtained compared to 16-bit floating-point for a same quality

A Proposed Terminology of Convergent Evolution

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An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees

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ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

International audienceANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions , using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different viewpoint. A developmental browser summarizes the information in a gene-or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuteros-tome. This new release covers an extended taxo-nomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oiko-pleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally , gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

International audienceANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates