Minimal Proof Search for Modal Logic K Model Checking

Most modal logics such as S5, LTL, or ATL are extensions of Modal Logic K. While the model checking problems for LTL and to a lesser extent ATL have been very active research areas for the past decades, the model checking problem for the more basic Multi-agent Modal Logic K (MMLK) has important applications as a formal framework for perfect information multi-player games on its own. We present Minimal Proof Search (MPS), an effort number based algorithm solving the model checking problem for MMLK. We prove two important properties for MPS beyond its correctness. The (dis)proof exhibited by MPS is of minimal cost for a general definition of cost, and MPS is an optimal algorithm for finding (dis)proofs of minimal cost. Optimality means that any comparable algorithm either needs to explore a bigger or equal state space than MPS, or is not guaranteed to find a (dis)proof of minimal cost on every input. As such, our work relates to A* and AO* in heuristic search, to Proof Number Search and DFPN+ in two-player games, and to counterexample minimization in software model checking.Comment: Extended version of the JELIA 2012 paper with the same titl

Coupled Reversible and Irreversible Bistable Switches Underlying TGF-\beta-induced Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) plays important roles in embryonic development, tissue regeneration and cancer metastasis. While several feedback loops have been shown to regulate EMT, it remains elusive how they coordinately modulate EMT response to TGF-\beta treatment. We construct a mathematical model for the core regulatory network controlling TGF-\beta-induced EMT. Through deterministic analyses and stochastic simulations, we show that EMT is a sequential two-step program that an epithelial cell first transits to partial EMT then to the mesenchymal state, depending on the strength and duration of TGF-\beta stimulation. Mechanistically the system is governed by coupled reversible and irreversible bistable switches. The SNAIL1/miR-34 double negative feedback loop is responsible for the reversible switch and regulates the initiation of EMT, while the ZEB/miR-200 feedback loop is accountable for the irreversible switch and controls the establishment of the mesenchymal state. Furthermore, an autocrine TGF-\beta/miR-200 feedback loop makes the second switch irreversible, modulating the maintenance of EMT. Such coupled bistable switches are robust to parameter variation and molecular noise. We provide a mechanistic explanation on multiple experimental observations. The model makes several explicit predictions on hysteretic dynamic behaviors, system response to pulsed stimulation and various perturbations, which can be straightforwardly tested.Comment: 32 pages, 8 figures, accepted by Biophysical Journa

Propagators and Solvers for the Algebra of Modular Systems

To appear in the proceedings of LPAR 21. Solving complex problems can involve non-trivial combinations of distinct knowledge bases and problem solvers. The Algebra of Modular Systems is a knowledge representation framework that provides a method for formally specifying such systems in purely semantic terms. Formally, an expression of the algebra defines a class of structures. Many expressive formalism used in practice solve the model expansion task, where a structure is given on the input and an expansion of this structure in the defined class of structures is searched (this practice overcomes the common undecidability problem for expressive logics). In this paper, we construct a solver for the model expansion task for a complex modular systems from an expression in the algebra and black-box propagators or solvers for the primitive modules. To this end, we define a general notion of propagators equipped with an explanation mechanism, an extension of the alge- bra to propagators, and a lazy conflict-driven learning algorithm. The result is a framework for seamlessly combining solving technology from different domains to produce a solver for a combined system.Comment: To appear in the proceedings of LPAR 2

Ackermannian and Primitive-Recursive Bounds with Dickson's Lemma

Dickson's Lemma is a simple yet powerful tool widely used in termination proofs, especially when dealing with counters or related data structures. However, most computer scientists do not know how to derive complexity upper bounds from such termination proofs, and the existing literature is not very helpful in these matters. We propose a new analysis of the length of bad sequences over (N^k,\leq) and explain how one may derive complexity upper bounds from termination proofs. Our upper bounds improve earlier results and are essentially tight