Underapproximation of Procedure Summaries for Integer Programs

We show how to underapproximate the procedure summaries of recursive programs over the integers using off-the-shelf analyzers for non-recursive programs. The novelty of our approach is that the non-recursive program we compute may capture unboundedly many behaviors of the original recursive program for which stack usage cannot be bounded. Moreover, we identify a class of recursive programs on which our method terminates and returns the precise summary relations without underapproximation. Doing so, we generalize a similar result for non-recursive programs to the recursive case. Finally, we present experimental results of an implementation of our method applied on a number of examples.Comment: 35 pages, 3 figures (this report supersedes the STTT version which in turn supersedes the TACAS'13 version

Deciding Conditional Termination

We address the problem of conditional termination, which is that of defining the set of initial configurations from which a given program always terminates. First we define the dual set, of initial configurations from which a non-terminating execution exists, as the greatest fixpoint of the function that maps a set of states into its pre-image with respect to the transition relation. This definition allows to compute the weakest non-termination precondition if at least one of the following holds: (i) the transition relation is deterministic, (ii) the descending Kleene sequence overapproximating the greatest fixpoint converges in finitely many steps, or (iii) the transition relation is well founded. We show that this is the case for two classes of relations, namely octagonal and finite monoid affine relations. Moreover, since the closed forms of these relations can be defined in Presburger arithmetic, we obtain the decidability of the termination problem for such loops.Comment: 61 pages, 6 figures, 2 table

Snails as intermediate hosts for parasitic infections: host-parasite relationships and intervention strategies

A fundamental prerequisite in the fight against medically and veterinary important parasites transmitted by intermediate host snails is a good knowledge of their life cycles, host specificity and geographical distribution. With scientists around the world collecting material from the wild and generating vast amounts of sequencing data, there is a huge opportunity to expand our knowledge of host-parasite relationships from the comfort of an office chair. With these motivations in mind, a bioinformatics tool was developed that has proven to be time efficient and accurate for the rapid identification of hidden parasites in publicly available datasets. Several dozen hidden parasite infections were discovered from the 2150 gastropod datasets tested, and some of these relationships have not yet been described. With our better understanding and the rapid progress in development of molecular and genetic methods, new avenues are opening for the control and eradication of diseases caused by vector-borne parasites. To study crucial parasite-snail interactions and eventually try to interfere with the infection, it is desirable to edit the host genome. Thus, in the framework of this work, preliminary experiments for the development of the CRISPR/Cas9 protocol in Biomphalaria glabrata, the intermediate host of the dangerous blood fluke Schistosoma mansoni, were also performed. The most significant findings in this case are the proof-of-concept of cultivation of B. glabrata embryos in glass capillaries using natural egg fluid and the demonstration that dilution of this fluid or complete replacement by other culture media are not suitable for successful cultivation. I also show that the Diaphanous gene, which has been used in the past to optimize CRISPR/Cas9 in another snail model, is not suitable for our model. The ultimate goal of the development of this molecular-genetic toolbox is the eradication of schistosomiasis by replacing susceptible populations in nature with resistant populations using gene drive technology. Although disrupted by COVID-19 pandemic, this work’s contribution to progress in the fight against helminthic parasitic infections is considerable