Counterexample Generation in Probabilistic Model Checking

Providing evidence for the refutation of a property is an essential, if not the most important, feature of model checking. This paper considers algorithms for counterexample generation for probabilistic CTL formulae in discrete-time Markov chains. Finding the strongest evidence (i.e., the most probable path) violating a (bounded) until-formula is shown to be reducible to a single-source (hop-constrained) shortest path problem. Counterexamples of smallest size that deviate most from the required probability bound can be obtained by applying (small amendments to) k-shortest (hop-constrained) paths algorithms. These results can be extended to Markov chains with rewards, to LTL model checking, and are useful for Markov decision processes. Experimental results show that typically the size of a counterexample is excessive. To obtain much more compact representations, we present a simple algorithm to generate (minimal) regular expressions that can act as counterexamples. The feasibility of our approach is illustrated by means of two communication protocols: leader election in an anonymous ring network and the Crowds protocol

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches

Identification of strategic molecules for future circular supply chains using large reaction networks

Networks of chemical reactions represent relationships between molecules within chemical supply chains and promise to enhance planning of multi-step synthesis routes from bio-renewable feedstocks.</p

Optimal Control of Distributed Computing Networks with Mixed-Cast Traffic Flows

Distributed computing networks, tasked with both packet transmission and processing, require the joint optimization of communication and computation resources. We develop a dynamic control policy that determines both routes and processing locations for packets upon their arrival at a distributed computing network. The proposed policy, referred to as Universal Computing Network Control (UCNC), guarantees that packets i) are processed by a specified chain of service functions, ii) follow cycle-free routes between consecutive functions, and iii) are delivered to their corresponding set of destinations via proper packet duplications. UCNC is shown to be throughput-optimal for any mix of unicast and multicast traffic, and is the first throughput-optimal policy for non-unicast traffic in distributed computing networks with both communication and computation constraints. Moreover, simulation results suggest that UCNC yields substantially lower average packet delay compared with existing control policies for unicast traffic