Petr Sosík

dblp:89/7033 · DBLP profile ↗
← Back
39ranked-venue papers
16as first author
7since 2021 · last 2026
0000-0001-7624-3816ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Theory of computation · 26 · 9 first-author · 2 since 2021Artificial intelligence and machine learning · 7 · 4 first-author · 3 since 2021Databases, data management, data science and information retrieval · 3 · 2 first-author · 2 since 2021Applied, interdisciplinary, general and emerging computing · 3 · 1 first-author
YearPublicationVenuePosition
2026 BIPOLAR: Polarization-based granular framework for LLM bias evaluation
abstract
Large language models (LLMs) are known to exhibit biases in downstream tasks, especially when dealing with sensitive topics such as political discourse, gender identity, ethnic relations, or national stereotypes. Although significant progress has been made in bias detection and mitigation techniques, certain challenges remain underexplored. This study proposes a reusable, granular and topic-agnostic framework to evaluate polarisation-related biases in LLM (both open-source and closed-source). Our approach combines polarisation-sensitive sentiment metrics with a synthetically generated balanced dataset of conflict-related statements, using a predefined set of semantic categories. Using our synthetic dataset that focuses on the Russia-Ukraine war, we evaluated the entity-asymmetry in sentiment scoring in six LLMs: Llama-3.1-8B, Ministral-3-14B, Gemma-3-27B, Qwen3-30B-A3B, Claude Sonnet 4.6, and GPT-5.2. Beyond aggregate asymmetries scores, with a general trend for more positive sentiment toward Ukraine, the framework allowed fine-grained analysis with considerable variation between semantic categories, uncovering divergent behavioural patterns among models. Adaptation to prompt modifications showed further entity-asymmetry in sentiment scoring towards preconceived language and citizenship modification. Overall, the framework supports automated dataset generation and fine-grained entity-asymmetry in sentiment scoring assessment, is applicable to a variety of polarisation-driven scenarios and topics, and is complementary to embedding-based and probability-based bias-evaluation strategies.
Tomás Filip, Martin Pavlícek, Petr Sosík
Theor. Comput. Sci.3
2025 A survey on learning models of spiking neural membrane systems
abstract
Abstract Spiking neural P systems (SN P systems) are a mathematical model of neural networks, abstracting the way biological neurons communicate with spikes, developed within the framework of the membrane computing theory. Recently, driven by the boom of learning neural models, SN P systems have become a rapidly emerging research front. Consequently, many different variants of the learning models of SN P system prevail among the new research results. Although large proprietary deep learning models are still based on the continuous neural network paradigm, spiking neurons are attractive because of their low-energy demands. The purpose of this paper is to provide an up-to-date overview of learning paradigms and techniques for SN P systems. After a brief introduction of the structure and function of SN P systems, we summarise recent approaches to learning and adaptation in SN P systems, including Hebbian learning, Widrow-Hoff algorithm, fuzzy approaches, nonlinear SN P systems, gated and long short-term memory inspired SN P systems, convolutional SN P systems, and more.
Petr Sosík, Prithwineel Paul, Lucie Ciencialová
Nat. Comput.1
2023 Morphogenetic computing: computability and complexity results
Petr Sosík
Nat. Comput.1
2022 Computational Universality and Efficiency in Morphogenetic Systems
Petr Sosík, Jan Drastík
MCU1
2022 P colonies with agent division
Ludek Cienciala, Lucie Ciencialová, Petr Sosík
Inf. Sci.3
2021 Morphogenetic systems for resource bounded computation and modeling
Petr Sosík, Max H. Garzon, Vladimír Smolka, Jan Drastík
Inf. Sci.1
2021 Self-healing turing-universal computation in morphogenetic systems
Petr Sosík, Max H. Garzon, Jan Drastík
Nat. Comput.1
2018 Generalized P colonies with passive environment
Lucie Ciencialová, Ludek Cienciala, Petr Sosík
Theor. Comput. Sci.3
2017 Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments
David Benes, Alfonso Rodríguez-Patón, Petr Sosík
Nat. Comput.3
2016 Small (purely) catalytic P systems simulating register machines
Petr Sosík, Miroslav Langer
Theor. Comput. Sci.1
2015 An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits
abstract
Success in synthetic biology depends on the efficient construction of robust genetic circuitry. However, even the direct engineering of the simplest genetic elements (switches, logic gates) is a challenge and involves intense lab work. As the complexity of biological circuits grows, it becomes more complicated and less fruitful to rely on the rational design paradigm, because it demands many time-consuming trial-and-error cycles. One of the reasons is the context-dependent behavior of small assembly parts (like BioBricks), which in a complex environment often interact in an unpredictable way. Therefore, the idea of evolutionary engineering (artificial directed in vivo evolution) based on screening and selection of randomized combinatorial genetic circuit libraries became popular. In this article we build on the so-called dual selection technique. We propose a plasmid-based framework using toxin-antitoxin pairs together with the relaxase conjugative protein, enabling an efficient autonomous in vivo evolutionary selection of simple Boolean circuits in bacteria (E. coli was chosen for demonstration). Unlike previously reported protocols, both on and off selection steps can run simultaneously in various cells in the same environment without human intervention; and good circuits not only survive the selection process but are also horizontally transferred by conjugation to the neighbor cells to accelerate the convergence rate of the selection process. Our directed evolution strategy combines a new dual selection method with fluorescence-based screening to increase the robustness of the technique against mutations. As there are more orthogonal toxin-antitoxin pairs in E. coli, the approach is likely to be scalable to more complex functions. In silico experiments based on empirical data confirm the high search and selection capability of the protocol.
David Benes, Petr Sosík, Alfonso Rodríguez-Patón
Artif. Life2
2015 An Optimal Frontier of the Efficiency of Tissue P Systems with Cell Separation
abstract
A membrane system (P system) is a distributed computing model inspired by information processes in living cells. P systems previously provided new characterizations of a variety of complexity classes and their borderlines. Specifically, in tissue-like membrane systems, cell separation rules have been considered joint with communication rules of the form symport/antiport. On the one hand, only tractable problems can be efficiently solved by using cell separation and communication rules with length at most 2. On the other hand, an efficient and uniform solution to the SAT problem by using cell separation and communication rules with length at most 8 has been recently given. In this paper we improve the previous result by showing that the SAT problem can be solved by a family of tissue P systems with cell separation in linear time, by using communication rules with length at most 3. Thus, in the framework of tissue P systems with cell separation, we provide an optimal tractability borderline: passing from length 2 to 3 amounts to passing from non–efficiency to efficiency, assuming that P ≠ NP.
Mario J. Pérez-Jiménez, Petr Sosík
Fundam. Informaticae2
2015 A limitation of cell division in tissue P systems by PSPACE
Petr Sosík, Ludek Cienciala
J. Comput. Syst. Sci.1
2014 Three Universal Homogeneous Spiking Neural P Systems Using Max Spike
abstract
We improve and extend a recent result showing that spiking neural P systems with the same rules in all neurons of the system (homogenous) and working in the max sequential manner are universal. The previous work in this area reported by the group led
Andrei Paun, Petr Sosík
Fundam. Informaticae2
2014 Computational power of cell separation in tissue P systems
Petr Sosík, Ludek Cienciala
Inf. Sci.1
2013 P systems with proteins on membranes characterize PSPACE
Petr Sosík, Andrei Paun, Alfonso Rodríguez-Patón
Theor. Comput. Sci.1
2011 Autonomous Resolution Based on DNA Strand Displacement
Alfonso Rodríguez-Patón, Iñaki Sainz de Murieta, Petr Sosík
DNA3
2011 On the scalability of biocomputing algorithms: The case of the maximum clique problem
Daniel Manrique, Alfonso Rodríguez-Patón, Petr Sosík
Theor. Comput. Sci.3
2009 The Undecidability of the Infinite Ribbon Problem: Implications for Computing by Self-Assembly
abstract
Self-assembly, the process by which objects autonomously come together to form complex structures, is omnipresent in the physical world. Recent experiments in self-assembly demonstrate its potential for the parallel creation of a large number of nanostructures, including possibly computers. A systematic study of self-assembly as a mathematical process has been initiated by L. Adleman and E. Winfree. The individual components are modeled as square tiles on the infinite two-dimensional plane. Each side of a tile is covered by a specific “glue,” and two adjacent tiles will stick iff they have matching glues on their abutting edges. Tiles that stick to each other may form various two-dimensional “structures” such as squares and rectangles, or may cover the entire plane. In this paper we focus on a special type of structure, called a ribbon: a non-self-crossing rectilinear sequence of tiles on the plane, in which successive tiles are adjacent along an edge and abutting edges of consecutive tiles have matching glues. We prove that it is undecidable whether an arbitrary finite set of tiles with glues (infinite supply of each tile type available) can be used to assemble an infinite ribbon. While the problem can be proved undecidable using existing techniques if the ribbon is required to start with a given “seed” tile, our result settles the “unseeded” case, an open problem formerly known as the “unlimited infinite snake problem.” The proof is based on a construction, due to R. Robinson, of a special set of tiles that allow only aperiodic tilings of the plane. This construction is used to create a special set of directed tiles (tiles with arrows painted on the top) with the “strong plane-filling property”—a variation of the “plane-filling property” previously defined by J. Kari. A construction of “sandwich” tiles is then used in conjunction with this special tile set, to reduce the well-known undecidable tiling problem to the problem of the existence of an infinite directed zipper (a special kind of ribbon). A “motif” construction is then introduced that allows one tile system to simulate another by using geometry to represent glues. Using motifs, the infinite directed zipper problem is reduced to the infinite ribbon problem, proving the latter undecidable. An immediate consequence of our result is the undecidability of the existence of arbitrarily large structures self-assembled using tiles from a given tile set.
Leonard M. Adleman, Jarkko Kari 0001, Lila Kari, Dustin Reishus, Petr Sosík
SIAM J. Comput.5
2008 On the power of elementary features in spiking neural P systems
Marc García-Arnau, Alfonso Rodríguez-Patón, Petr Sosík
Nat. Comput.4
2008 On the weight of universal insertion grammars
Lila Kari, Petr Sosík
Theor. Comput. Sci.2
2007 Towards a Robust Biocomputing Solution of Intractable Problems
Marc García-Arnau, Daniel Manrique, Alfonso Rodríguez-Patón, Petr Sosík
DNA4
2007 Modelling Multiple Robots in Space: An Adaptive Eco-Grammar System
Peter Sebestyén, Petr Sosík
Fundam. Informaticae2
2007 Membrane computing and complexity theory: A characterization of PSPACE
Petr Sosík, Alfonso Rodríguez-Patón
J. Comput. Syst. Sci.1
2007 Normal forms for spiking neural P systems
Oscar H. Ibarra, Andrei Paun, Gheorghe Paun, Alfonso Rodríguez-Patón, Petr Sosík, Sara Woodworth
Theor. Comput. Sci.5
2006 P Systems with Active Membranes Characterize PSPACE
Petr Sosík, Alfonso Rodríguez-Patón
DNA1
2006 A Formal Language Analysis of DNA Hairpin Structures
Lila Kari, Elena Losseva, Stavros Konstantinidis, Petr Sosík, Gabriel Thierrin
Fundam. Informaticae4
2006 Algebraic properties of substitution on trajectories
Michael Domaratzki, Petr Sosík, Alfonso Rodríguez-Patón
Theor. Comput. Sci.2
2005 On Hairpin-Free Words and Languages
Lila Kari, Stavros Konstantinidis, Petr Sosík, Gabriel Thierrin
Developments in Language Theory3
2005 Computationally universal P systems without priorities: two catalysts are sufficient
Rudolf Freund, Lila Kari, Marion Oswald, Petr Sosík
Theor. Comput. Sci.4
2005 On properties of bond-free DNA languages
Lila Kari, Stavros Konstantinidis, Petr Sosík
Theor. Comput. Sci.3
2005 Aspects of shuffle and deletion on trajectories
Lila Kari, Petr Sosík
Theor. Comput. Sci.2
2004 Substitutions, Trajectories and Noisy Channels
Lila Kari, Stavros Konstantinidis, Petr Sosík
CIAA3
2003 The computational power of cell division in P systems: Beating down parallel computers?
Petr Sosík
Nat. Comput.1
2003 Watson-Crick D0L systems: the power of one transition
Arto Salomaa, Petr Sosík
Theor. Comput. Sci.2
2003 Watson-Crick D0L systems: generative power and undecidable problems
Petr Sosík
Theor. Comput. Sci.1
2002 Universal computation with Watson-Crick D0L systems
Petr Sosík
Theor. Comput. Sci.1
2001 String Rewriting Sequential P-Systems and Regulated Rewriting
Petr Sosík, Rudolf Freund
Developments in Language Theory1
2001 D0L System + Watson-Crick Complementarity = Universal Computation
Petr Sosík
MCU1