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Van-Giang Trinh

Publications and source records attributed to Van-Giang Trinh.

10 recordsLinked to original sources

Walk-In Multi-Stage Patient Flow Scheduling: An ASP Model with DES-Based Evaluation

An effective examination and test schedule for patients plays a crucial role in hospital resource management. In this work, we formulate a new reactive patient-flow scheduling problem in multi-department hospitals where walk-in patients arrive over time and each patient requires multiple examinations per visit. Upon each arrival, the scheduler computes a feasible examination pathway-both the sequence of examinations and the room assignment-for the incoming patient only, while previously scheduled assignments remain fixed. This process is subject to medical precedence constraints and room capacity limitations. We model the problem declaratively in Answer Set Programming (ASP) with clingo, and optimize a two-part cost: travel time between consecutive examination locations and queue-induced waiting time, weighted by the duration of the upcoming examination. To assess robustness under stochastic service times, we propose a Discrete-Event Simulation (DES) evaluation layer and a baseline greedy policy for comparison. On large-scale synthetic datasets across various capacity regimes and patient loads, the ASP approach reduces median stay time and increases the proportion of zero-wait patients compared to DES-based baselines. These improvements are most pronounced under heavy load, while the approach still outperforms baselines across all capacity settings, with smaller gains at higher capacities.

cs.LO

BAss: Symbolic Reasoning in Abstract Dialectical Frameworks

We present BAss (BDD-based ADF symbolic solver), a novel analysis tool for Abstract Dialectical Frameworks (ADFs) based on Binary Decision Diagrams (BDDs). It supports the fully symbolic computation of all admissible, complete, and preferred interpretations, as well as two-valued and stable models of an ADFs. Our approach is inspired by the recently discovered equivalence between Boolean Networks (BNs) and ADFs by Heyninck et al. (2024) and Azpeitia et al. (2024), significantly extending current BDD-based tools bioLQM, AEON, and adf-bdd. We conducted experiments on a large-scale collection of real-world models from both the BN and ADF communities. Our results show that BAss dramatically outperforms previous BDD-based tools and is competitive (even significantly better in some cases) with state-of-the-art SAT/ASP-based methods, particularly in scenarios involving large solution spaces. Notably, BAss is able to enumerate all fixed points or minimal trap spaces of certain biological networks beyond the reach of existing tools, thereby enabling new analysis and case studies in systems biology. These results highlight the practical relevance of symbolic reasoning for complex real-world applications, particularly in systems biology and formal argumentation.

cs.LO

Relating biomarkers and phenotypes using dynamical trap spaces

Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is committed to a certain dynamical outcome while otherwise being minimally constrained. We focus on Boolean models and define \emph{dynamical phenotypes} as complete trap spaces that maximally specify a chosen set of phenotype-determining nodes that correspond to biomarkers while keeping external inputs unconstrained. We show that dynamical phenotypes can be efficiently identified without full attractor enumeration. Using four published models, including a 70-node Boolean model of T cell differentiation, we show that dynamical phenotypes recover known cell types and activation states, and indicate the environmental conditions ensuring their existence. We also propose a method to identify informative phenotype-determining nodes based on the canalization of the Boolean functions. This method reveals biologically relevant cell state information that is complementary to the phenotypes manually defined by model creators and is validated by two attractor-based approaches. Our results demonstrate that dynamical phenotypes provide a scalable framework for linking model structure, external inputs, and phenotypic outcomes, and offer a principled tool for model-guided biomarker selection.

q-bio.MN

On the Trap Space Semantics of Normal Logic Programs

The logical semantics of normal logic programs has traditionally been based on the notions of Clark's completion and two-valued or three-valued canonical models, including supported, stable, regular, and well-founded models. Two-valued interpretations can also be seen as states evolving under a program's update operator, producing a transition graph whose fixed points and cycles capture stable and oscillatory behaviors, respectively. We refer to this view as dynamical semantics since it characterizes the program's meaning in terms of state-space trajectories, as first introduced in the stable (supported) class semantics. Recently, we have established a formal connection between Datalog^\neg programs (i.e., normal logic programs without function symbols) and Boolean networks, leading to the introduction of the trap space concept for Datalog^\neg programs. In this paper, we generalize the trap space concept to arbitrary normal logic programs, introducing trap space semantics as a new approach to their interpretation. This new semantics admits both model-theoretic and dynamical characterizations, providing a comprehensive approach to understanding program behavior. We establish the foundational properties of the trap space semantics and systematically relate it to the established model-theoretic semantics, including the stable (supported), stable (supported) partial, regular, and L-stable model semantics, as well as to the dynamical stable (supported) class semantics. Our results demonstrate that the trap space semantics offers a unified and precise framework for proving the existence of supported classes, strict stable (supported) classes, and regular models, in addition to uncovering and formalizing deeper relationships among the existing semantics of normal logic programs.

cs.LO

Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

Boolean Networks (BNs) serve as a fundamental modeling framework for capturing complex dynamical systems across various domains, including systems biology, computational logic, and artificial intelligence. A crucial property of BNs is the presence of trap spaces -- subspaces of the state space that, once entered, cannot be exited. Minimal trap spaces, in particular, play a significant role in analyzing the long-term behavior of BNs, making their efficient enumeration and counting essential. The fixed points in BNs are a special case of minimal trap spaces. In this work, we formulate several meaningful counting problems related to minimal trap spaces and fixed points in BNs. These problems provide valuable insights both within BN theory (e.g., in probabilistic reasoning and dynamical analysis) and in broader application areas, including systems biology, abstract argumentation, and logic programming. To address these computational challenges, we propose novel methods based on {\em approximate answer set counting}, leveraging techniques from answer set programming. Our approach efficiently approximates the number of minimal trap spaces and the number of fixed points without requiring exhaustive enumeration, making it particularly well-suited for large-scale BNs. Our experimental evaluation on an extensive and diverse set of benchmark instances shows that our methods significantly improve the feasibility of counting minimal trap spaces and fixed points, paving the way for new applications in BN analysis and beyond.

cs.LO

On the Boolean Network Theory of Datalog$^\neg$

Datalog$^\neg$ is a central formalism used in a variety of domains ranging from deductive databases and abstract argumentation frameworks to answer set programming. Its model theory is the finite counterpart of the logical semantics developed for normal logic programs, mainly based on the notions of Clark's completion and two-valued or three-valued canonical models including supported, stable, regular and well-founded models. In this paper we establish a formal link between Datalog$^\neg$ and Boolean network theory first introduced for gene regulatory networks. We show that in the absence of odd cycles in a Datalog$^\neg$ program, the regular models coincide with the stable models, which entails the existence of stable models, and in the absence of even cycles, we prove the uniqueness of stable partial models and regular models. This connection also gives new upper bounds on the numbers of stable partial, regular, and stable models of a Datalog$^\neg$ program using the cardinality of a feedback vertex set in its atom dependency graph. Interestingly, our connection to Boolean network theory also points us to the notion of trap spaces. In particular we show the equivalence between subset-minimal stable trap spaces and regular models.

cs.LO

On the number of asynchronous attractors in AND-NOT Boolean networks

Boolean Networks (BNs) describe the time evolution of binary states using logic functions on the nodes of a network. They are fundamental models for complex discrete dynamical systems, with applications in various areas of science and engineering, and especially in systems biology. A key aspect of the dynamical behavior of BNs is the number of attractors, which determines the diversity of long-term system trajectories. Due to the noisy nature and incomplete characterization of biological systems, a stochastic asynchronous update scheme is often more appropriate than the deterministic synchronous one. AND-NOT BNs, whose logic functions are the conjunction of literals, are an important subclass of BNs because of their structural simplicity and their usefulness in analyzing biological systems for which the only information available is a collection of interactions among components. In this paper, we establish new theoretical results regarding asynchronous attractors in AND-NOT BNs. We derive two new upper bounds for the number of asynchronous attractors in an AND-NOT BN based on structural properties (strong even cycles and dominating sets, respectively) of the AND-NOT BN. These findings contribute to a more comprehensive understanding of asynchronous dynamics in AND-NOT BNs, with implications for attractor enumeration and counting, as well as for network design and control.

cs.DM

Graphical Conditions for the Existence, Unicity and Number of Regular Models

The regular models of a normal logic program are a particular type of partial (i.e. 3-valued) models which correspond to stable partial models with minimal undefinedness. In this paper, we explore graphical conditions on the dependency graph of a finite ground normal logic program to analyze the existence, unicity and number of regular models for the program. We show three main results: 1) a necessary condition for the existence of non-trivial (i.e. non-2-valued) regular models, 2) a sufficient condition for the unicity of regular models, and 3) two upper bounds for the number of regular models based on positive feedback vertex sets. The first two conditions generalize the finite cases of the two existing results obtained by You and Yuan (1994) for normal logic programs with well-founded stratification. The third result is also new to the best of our knowledge. Key to our proofs is a connection that we establish between finite ground normal logic programs and Boolean network theory.

cs.LO

Static Analysis of Logic Programs via Boolean Networks

Answer Set Programming (ASP) is a declarative problem solving paradigm that can be used to encode a combinatorial problem as a logic program whose stable models correspond to the solutions of the considered problem. ASP has been widely applied to various domains in AI and beyond. The question "What can be said about stable models of a logic program from its static information?" has been investigated and proved useful in many circumstances. In this work, we dive into this direction more deeply by making the connection between a logic program and a Boolean network, which is a prominent modeling framework with applications to various areas. The proposed connection can bring the existing results in the rich history on static analysis of Boolean networks to explore and prove more theoretical results on ASP, making it become a unified and powerful tool to further study the static analysis of ASP. In particular, the newly obtained insights have the potential to benefit many problems in the field of ASP.

cs.LO

mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks

The tool mpbn offers a Python programming interface for an easy interactive editing of Boolean networks and the efficient computation of elementary properties of their dynamics, including fixed points, trap spaces, and reachability properties under the Most Permissive update mode. Relying on Answer-Set Programming logical framework, we show that mpbn is scalable to models with several thousands of nodes and is one of the best-performing tool for computing minimal and maximal trap spaces of Boolean networks, a key feature for understanding and controling their stable behaviors. The tool is available at https://github.com/bnediction/mpbn.

cs.LO