Statically bounded-memory delayed sampling for probabilistic streams

Probabilistic programming languages aid developers performing Bayesian inference. These languages provide programming constructs and tools for probabilistic modeling and automated inference. Prior work introduced a probabilistic programming language, ProbZelus, to extend probabilistic programming functionality to unbounded streams of data. This work demonstrated that the delayed sampling inference algorithm could be extended to work in a streaming context. ProbZelus showed that while delayed sampling could be effectively deployed on some programs, depending on the probabilistic model under consideration, delayed sampling is not guaranteed to use a bounded amount of memory over the course of the execution of the program. In this paper, we the present conditions on a probabilistic program’s execution under which delayed sampling will execute in bounded memory. The two conditions are dataflow properties of the core operations of delayed sampling: the m -consumed property and the unseparated paths property . A program executes in bounded memory under delayed sampling if, and only if, it satisfies the m -consumed and unseparated paths properties. We propose a static analysis that abstracts over these properties to soundly ensure that any program that passes the analysis satisfies these properties, and thus executes in bounded memory under delayed sampling.

Automated inference of Boolean models from molecular interaction maps using CaSQ

Motivation Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap between static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner. Results We developed CaSQ by defining conversion rules and logical formulas for inferred Boolean models according to the topology and the annotations of the starting molecular interaction maps. We used CaSQ to produce executable files of existing molecular maps that differ in size, complexity and the use of Systems Biology Graphical Notation (SBGN) standards. We also compared, where possible, the manually built logical models corresponding to a molecular map to the ones inferred by CaSQ. The tool is able to process large and complex maps built with CellDesigner (either following SBGN standards or not) and produce Boolean models in a standard output format, Systems Biology Marked Up Language-qualitative (SBML-qual), that can be further analyzed using popular modelling tools. References, annotations and layout of the CellDesigner molecular map are retained in the obtained model, facilitating interoperability and model reusability. Availability and implementation The present tool is available online: https://lifeware.inria.fr/∼soliman/post/casq/ and distributed as a Python package under the GNU GPLv3 license. The code can be accessed here: https://gitlab.inria.fr/soliman/casq. Supplementary information Supplementary data are available at Bioinformatics online.

ConSORT: Context- and Flow-Sensitive Ownership Refinement Types for Imperative Programs

We present ConSORT, a type system for safety verification in the presence of mutability and aliasing. Mutability requires strong updates to model changing invariants during program execution, but aliasing between pointers makes it difficult to determine which invariants must be updated in response to mutation. Our type system addresses this difficulty with a novel combination of refinement types and fractional ownership types. Fractional ownership types provide flow-sensitive and precise aliasing information for reference variables. ConSORT interprets this ownership information to soundly handle strong updates of potentially aliased references. We have proved ConSORT sound and implemented a prototype, fully automated inference tool. We evaluated our tool and found it verifies non-trivial programs including data structure implementations.

Semantic Enrichment of Streaming Healthcare Data

In the past decade, the healthcare industry has made significant advances in the digitization of patient information. However, a lack of interoperability among healthcare systems still imposes a high cost to patients, hospitals, and insurers. Currently, most systems pass messages using idiosyncratic messaging standards that require specialized knowledge to interpret. This increases the cost of systems integration and often puts more advanced uses of data out of reach. In this project, we demonstrate how two open standards, FHIR and RDF, can be combined both to integrate data from disparate sources in real time and make that data queryable and susceptible to automated inference. To validate the effectiveness of the semantic engine, we perform simulations of real-time data feeds and demonstrate how they can be combined and used by client-side applications with no knowledge of the underlying sources.

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes

Motivation The evolution and role of gene clusters in eukaryotes is poorly understood. Currently, most studies and computational prediction programs limit their focus to specific types of clusters, such as those involved in secondary metabolism. Results We present EvolClust, a python-based tool for the inference of evolutionary conserved gene clusters from genome comparisons, independently of the function or gene composition of the cluster. EvolClust predicts conserved gene clusters from pairwise genome comparisons and infers families of related clusters from multiple (all versus all) genome comparisons. Availability and implementation https://github.com/Gabaldonlab/EvolClust/. Supplementary information Supplementary data are available at Bioinformatics online.