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Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We argue that embryological morphogenesis provides a model of how massive swarms of microscopic agents can be coordinated to assemble complex, multiscale hierarchical structures. This is accomplished by understanding natural morphogenetic…
We present a general model allowing static analysis based on abstract interpretation for systems of communicating processes. Our technique, inspired by Regular Model Checking, represents set of program states as lattice automata and…
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to…
We introduce stochastic and quantum finite-state transducers as computation-theoretic models of classical stochastic and quantum finitary processes. Formal process languages, representing the distribution over a process's behaviors, are…
This thesis investigates how the sub-structure of words can be accounted for in probabilistic models of language. Such models play an important role in natural language processing tasks such as translation or speech recognition, but often…
After just a few hundred training updates, a standard probabilistic model for language generation has likely not yet learnt many semantic or syntactic rules of natural language, making it difficult to estimate the probability distribution…
We introduce the notion of a stochastic probabilistic program and present a reference implementation of a probabilistic programming facility supporting specification of stochastic probabilistic programs and inference in them. Stochastic…
To understand changes in physical systems and facilitate decisions, explaining how model predictions are made is crucial. We use model-based interpretability, where models of physical systems are constructed by composing basic constructs…
Recent advancements in large language models (LLMs) provide a more effective pathway for upgrading brain-computer interface (BCI) technology in terms of user interaction. The widespread adoption of BCIs in daily application scenarios is…
Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…
The pi-calculus is a widely used process calculus, which models communications between processes and allows the passing of communication links. Various operational semantics of the pi-calculus have been proposed, which can be classified…
The evolution of Large Language Models (LLMs) has showcased remarkable capacities for logical reasoning and natural language comprehension. These capabilities can be leveraged in solutions that semantically and textually model complex…
Applied process calculi include advanced programming constructs such as type systems, communication with pattern matching, encryption primitives, concurrent constraints, nondeterminism, process creation, and dynamic connection topologies.…
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate,…
In natural-language discourse, related events tend to appear near each other to describe a larger scenario. Such structures can be formalized by the notion of a frame (a.k.a. template), which comprises a set of related events and…
Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the complexity, heterogeneity and multi-scale nature of cancer pose significant computational challenges. Coupling discrete cell-based models…