SDLS: a Matlab package for solving conic least-squares problems

This document is an introduction to the Matlab package SDLS (Semi-Definite Least-Squares) for solving least-squares problems over convex symmetric cones. The package is shortly presented through the addressed problem, a sketch of the implemented algorithm, the syntax and calling sequences, a simple numerical example and some more advanced features. The implemented method consists in solving the dual problem with a quasi-Newton algorithm. We note that SDLS is not the most competitive implementation of this algorithm: efficient, robust, commercial implementations are available (contact the authors). Our main goal with this Matlab SDLS package is to provide a simple, user-friendly software for solving and experimenting with semidefinite least-squares problems. Up to our knowledge, no such freeware exists at this date

SIFTER search: a web server for accurate phylogeny-based protein function prediction.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded

A Bi-Directional Refinement Algorithm for the Calculus of (Co)Inductive Constructions

The paper describes the refinement algorithm for the Calculus of (Co)Inductive Constructions (CIC) implemented in the interactive theorem prover Matita. The refinement algorithm is in charge of giving a meaning to the terms, types and proof terms directly written by the user or generated by using tactics, decision procedures or general automation. The terms are written in an "external syntax" meant to be user friendly that allows omission of information, untyped binders and a certain liberal use of user defined sub-typing. The refiner modifies the terms to obtain related well typed terms in the internal syntax understood by the kernel of the ITP. In particular, it acts as a type inference algorithm when all the binders are untyped. The proposed algorithm is bi-directional: given a term in external syntax and a type expected for the term, it propagates as much typing information as possible towards the leaves of the term. Traditional mono-directional algorithms, instead, proceed in a bottom-up way by inferring the type of a sub-term and comparing (unifying) it with the type expected by its context only at the end. We propose some novel bi-directional rules for CIC that are particularly effective. Among the benefits of bi-directionality we have better error message reporting and better inference of dependent types. Moreover, thanks to bi-directionality, the coercion system for sub-typing is more effective and type inference generates simpler unification problems that are more likely to be solved by the inherently incomplete higher order unification algorithms implemented. Finally we introduce in the external syntax the notion of vector of placeholders that enables to omit at once an arbitrary number of arguments. Vectors of placeholders allow a trivial implementation of implicit arguments and greatly simplify the implementation of primitive and simple tactics