相关论文: A Model of Colonic Crypts using SBML Spatial
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
The preliminary analyses on a multiscale model of intestinal crypt dynamics are here presented. The model combines a morphological model, based on the Cellular Potts Model (CPM), and a gene regulatory network model, based on Noisy Random…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
In this paper, we present a statistical framework for modeling conditional quantiles of spatial processes assumed to be strongly mixing in space. We establish the $L_1$ consistency and the asymptotic normality of the kernel conditional…
Membrane computing is a well-established and successful research field which belongs to the more general area of molecular computing. Membrane computing aims at defining parallel and non-deterministic computing models, called membrane…
This paper introduces a model that identifies spatial relationships for a structural analysis based on the concept of simplicial complex. The spatial relationships are identified through overlapping two map layers, namely a primary layer…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
The definition of complexity through Statistical Complexity Measures (SCM) has recently seen major improvements. Mostly, effort is concentrated in measures on time series. We propose a SCM definition for spatial dynamical systems. Our…
This thesis introduces "Embodied Spatial Intelligence" to address the challenge of creating robots that can perceive and act in the real world based on natural language instructions. To bridge the gap between Large Language Models (LLMs)…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
SpatialLM is a large language model designed to process 3D point cloud data and generate structured 3D scene understanding outputs. These outputs include architectural elements like walls, doors, windows, and oriented object boxes with…
Large language models (LLMs) have demonstrated emergent abilities across diverse tasks, raising the question of whether they acquire internal world models. In this work, we investigate whether LLMs implicitly encode linear spatial world…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in…
The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based…
The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: a) We distinguish different classes of cells: stem cells, 6 generations of transit…