Related papers: Simulating and model checking membrane systems usi…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g.,…
When humans conceive how to perform a particular task, they do so hierarchically: splitting higher-level tasks into smaller sub-tasks. However, in the literature on natural language (NL) command of situated agents, most works have treated…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
Scenario-Based Programming is a methodology for modeling and constructing complex reactive systems from simple, stand-alone building blocks, called scenarios. These scenarios are designed to model different traits of the system, and can be…
The interpretability of machine learning, particularly for deep neural networks, is crucial for decision making in real-world applications. One approach is replacing the un-interpretable machine learning model with a surrogate model, which…
Swarm protocols are a recently introduced formalism for specifying, implementing, and verifying peer-to-peer systems called swarms. A swarm consists of distributed agents called machines that communicate by asynchronous event propagation.…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
A unified mathematical language for medicine and science will be presented. Using this language, models for DNA replication, protein synthesis, chemical reactions, neurons and a cardiac cycle of a heart have been built. Models for Turing…
With the increasing importance of distributed systems as a computing paradigm, a systematic approach to their design is needed. Although the area of formal verification has made enormous advances towards this goal, the resulting…
Language model intelligence is revolutionizing the way we program materials simulations. However, the diversity of simulation scenarios renders it challenging to precisely transform human language into a tailored simulator. Here, using…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Complex software-driven systems often interleave distributed, concurrent computation processes with physical interactions with the environment. Developing these systems more efficiently and safely can be achieved by employing actionable,…
The operations drip and mate considered in (mem)brane computing resemble the operations cut and recombination well known from DNA computing. We here consider sets of vesicles with multisets of objects on their outside membrane interacting…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Organizations use data lakes to store and analyze sensitive data. But hackers may compromise data lake storage to bypass access controls and access sensitive data. To address this, we propose Membrane, a system that (1) cryptographically…
A logic is presented for reasoning on iterated sequences of formulae over some given base language. The considered sequences, or "schemata", are defined inductively, on some algebraic structure (for instance the natural numbers, the lists,…
We describe here our perception of complex systems, of how we feel the different layers of description are important part of a correct complex system simulation. We describe a rough models categorization between rules based and law based,…