On optimizing over lift-and-project closures

The lift-and-project closure is the relaxation obtained by computing all lift-and-project cuts from the initial formulation of a mixed integer linear program or equivalently by computing all mixed integer Gomory cuts read from all tableau's corresponding to feasible and infeasible bases. In this paper, we present an algorithm for approximating the value of the lift-and-project closure. The originality of our method is that it is based on a very simple cut generation linear programming problem which is obtained from the original linear relaxation by simply modifying the bounds on the variables and constraints. This separation LP can also be seen as the dual of the cut generation LP used in disjunctive programming procedures with a particular normalization. We study some properties of this separation LP in particular relating it to the equivalence between lift-and-project cuts and Gomory cuts shown by Balas and Perregaard. Finally, we present some computational experiments and comparisons with recent related works

First-Class Functions for First-Order Database Engines

We describe Query Defunctionalization which enables off-the-shelf first-order database engines to process queries over first-class functions. Support for first-class functions is characterized by the ability to treat functions like regular data items that can be constructed at query runtime, passed to or returned from other (higher-order) functions, assigned to variables, and stored in persistent data structures. Query defunctionalization is a non-invasive approach that transforms such function-centric queries into the data-centric operations implemented by common query processors. Experiments with XQuery and PL/SQL database systems demonstrate that first-order database engines can faithfully and efficiently support the expressive "functions as data" paradigm.Comment: Proceedings of the 14th International Symposium on Database Programming Languages (DBPL 2013), August 30, 2013, Riva del Garda, Trento, Ital

In silico generation of novel, drug-like chemical matter using the LSTM neural network

The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de novo approaches or various other machine-learning techniques for generating novel drug-like molecules. In this article we present a method to generate molecules using a long short-term memory (LSTM) neural network and provide an analysis of the results, including a virtual screening test. Using the network one million drug-like molecules were generated in 2 hours. The molecules are novel, diverse (contain numerous novel chemotypes), have good physicochemical properties and have good synthetic accessibility, even though these qualities were not specific constraints. Although novel, their structural features and functional groups remain closely within the drug-like space defined by the bioactive molecules from ChEMBL. Virtual screening using the profile QSAR approach confirms that the potential of these novel molecules to show bioactivity is comparable to the ChEMBL set from which they were derived. The molecule generator written in Python used in this study is available on request.Comment: in this version fixed some reference number