497 research outputs found
Programmable models of growth and mutation of cancer-cell populations
In this paper we propose a systematic approach to construct mathematical
models describing populations of cancer-cells at different stages of disease
development. The methodology we propose is based on stochastic Concurrent
Constraint Programming, a flexible stochastic modelling language. The
methodology is tested on (and partially motivated by) the study of prostate
cancer. In particular, we prove how our method is suitable to systematically
reconstruct different mathematical models of prostate cancer growth - together
with interactions with different kinds of hormone therapy - at different levels
of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104
Mean-Field Limits Beyond Ordinary Differential Equations
16th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2016, Bertinoro, Italy, June 20-24, 2016, Advanced LecturesInternational audienceWe study the limiting behaviour of stochastic models of populations of interacting agents, as the number of agents goes to infinity. Classical mean-field results have established that this limiting behaviour is described by an ordinary differential equation (ODE) under two conditions: (1) that the dynamics is smooth; and (2) that the population is composed of a finite number of homogeneous sub-populations, each containing a large number of agents. This paper reviews recent work showing what happens if these conditions do not hold. In these cases, it is still possible to exhibit a limiting regime at the price of replacing the ODE by a more complex dynamical system. In the case of non-smooth or uncertain dynamics, the limiting regime is given by a differential inclusion. In the case of multiple population scales, the ODE is replaced by a stochastic hybrid automaton
Polarity assessment of reflection seismic data: a Deep Learning approach
We propose a procedure for the polarity assessment in reflection seismic data based on a Neural Network approach. The algorithm is based on a fully 1D approach, which does not require any input besides the seismic data since the necessary parameters are all automatically estimated. An added benefit is that the prediction has an associated probability, which automatically quantifies the reliability of the results. We tested the proposed procedure on synthetic and real reflection seismic data sets. The algorithm is able to correctly extract the seismic horizons also in case of complex conditions, such as along the flanks of salt domes, and is able to track polarity inversions
The Mean Drift: Tailoring the Mean Field Theory of Markov Processes for Real-World Applications
The statement of the mean field approximation theorem in the mean field
theory of Markov processes particularly targets the behaviour of population
processes with an unbounded number of agents. However, in most real-world
engineering applications one faces the problem of analysing middle-sized
systems in which the number of agents is bounded. In this paper we build on
previous work in this area and introduce the mean drift. We present the concept
of population processes and the conditions under which the approximation
theorems apply, and then show how the mean drift is derived through a
systematic application of the propagation of chaos. We then use the mean drift
to construct a new set of ordinary differential equations which address the
analysis of population processes with an arbitrary size
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
Experimental Biological Protocols with Formal Semantics
Both experimental and computational biology is becoming increasingly
automated. Laboratory experiments are now performed automatically on
high-throughput machinery, while computational models are synthesized or
inferred automatically from data. However, integration between automated tasks
in the process of biological discovery is still lacking, largely due to
incompatible or missing formal representations. While theories are expressed
formally as computational models, existing languages for encoding and
automating experimental protocols often lack formal semantics. This makes it
challenging to extract novel understanding by identifying when theory and
experimental evidence disagree due to errors in the models or the protocols
used to validate them. To address this, we formalize the syntax of a core
protocol language, which provides a unified description for the models of
biochemical systems being experimented on, together with the discrete events
representing the liquid-handling steps of biological protocols. We present both
a deterministic and a stochastic semantics to this language, both defined in
terms of hybrid processes. In particular, the stochastic semantics captures
uncertainties in equipment tolerances, making it a suitable tool for both
experimental and computational biologists. We illustrate how the proposed
protocol language can be used for automated verification and synthesis of
laboratory experiments on case studies from the fields of chemistry and
molecular programming
Probabilistic Model Checking for Continuous-Time Markov Chains via Sequential Bayesian Inference
Probabilistic model checking for systems with large or unbounded state space
is a challenging computational problem in formal modelling and its
applications. Numerical algorithms require an explicit representation of the
state space, while statistical approaches require a large number of samples to
estimate the desired properties with high confidence. Here, we show how model
checking of time-bounded path properties can be recast exactly as a Bayesian
inference problem. In this novel formulation the problem can be efficiently
approximated using techniques from machine learning. Our approach is inspired
by a recent result in statistical physics which derived closed form
differential equations for the first-passage time distribution of stochastic
processes. We show on a number of non-trivial case studies that our method
achieves both high accuracy and significant computational gains compared to
statistical model checking
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