3,057 research outputs found
Towards Cancer Hybrid Automata
This paper introduces Cancer Hybrid Automata (CHAs), a formalism to model the
progression of cancers through discrete phenotypes. The classification of
cancer progression using discrete states like stages and hallmarks has become
common in the biology literature, but primarily as an organizing principle, and
not as an executable formalism. The precise computational model developed here
aims to exploit this untapped potential, namely, through automatic verification
of progression models (e.g., consistency, causal connections, etc.),
classification of unreachable or unstable states and computer-generated
(individualized or universal) therapy plans. The paper builds on a
phenomenological approach, and as such does not need to assume a model for the
biochemistry of the underlying natural progression. Rather, it abstractly
models transition timings between states as well as the effects of drugs and
clinical tests, and thus allows formalization of temporal statements about the
progression as well as notions of timed therapies. The model proposed here is
ultimately based on hybrid automata, and we show how existing controller
synthesis algorithms can be generalized to CHA models, so that therapies can be
generated automatically. Throughout this paper we use cancer hallmarks to
represent the discrete states through which cancer progresses, but other
notions of discretely or continuously varying state formalisms could also be
used to derive similar therapies.Comment: In Proceedings HSB 2012, arXiv:1208.315
Towards Personalized Prostate Cancer Therapy Using Delta-Reachability Analysis
Recent clinical studies suggest that the efficacy of hormone therapy for
prostate cancer depends on the characteristics of individual patients. In this
paper, we develop a computational framework for identifying patient-specific
androgen ablation therapy schedules for postponing the potential cancer
relapse. We model the population dynamics of heterogeneous prostate cancer
cells in response to androgen suppression as a nonlinear hybrid automaton. We
estimate personalized kinetic parameters to characterize patients and employ
-reachability analysis to predict patient-specific therapeutic
strategies. The results show that our methods are promising and may lead to a
prognostic tool for personalized cancer therapy.Comment: HSCC 201
Under-approximating Cut Sets for Reachability in Large Scale Automata Networks
In the scope of discrete finite-state models of interacting components, we
present a novel algorithm for identifying sets of local states of components
whose activity is necessary for the reachability of a given local state. If all
the local states from such a set are disabled in the model, the concerned
reachability is impossible. Those sets are referred to as cut sets and are
computed from a particular abstract causality structure, so-called Graph of
Local Causality, inspired from previous work and generalised here to finite
automata networks. The extracted sets of local states form an
under-approximation of the complete minimal cut sets of the dynamics: there may
exist smaller or additional cut sets for the given reachability. Applied to
qualitative models of biological systems, such cut sets provide potential
therapeutic targets that are proven to prevent molecules of interest to become
active, up to the correctness of the model. Our new method makes tractable the
formal analysis of very large scale networks, as illustrated by the computation
of cut sets within a Boolean model of biological pathways interactions
gathering more than 9000 components
Statistical Model Checking for Stochastic Hybrid Systems
This paper presents novel extensions and applications of the UPPAAL-SMC model
checker. The extensions allow for statistical model checking of stochastic
hybrid systems. We show how our race-based stochastic semantics extends to
networks of hybrid systems, and indicate the integration technique applied for
implementing this semantics in the UPPAAL-SMC simulation engine. We report on
two applications of the resulting tool-set coming from systems biology and
energy aware buildings.Comment: In Proceedings HSB 2012, arXiv:1208.315
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
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The detection and classification of blast cell in Leukaemia Acute Promyelocytic Leukaemia (AML M3) blood using simulated annealing and neural networks
This paper was delivered at AIME 2011: 13th Conference on Artifical Intelligence in Medicine.This paper presents a method for the detection and classification of blast cells in M3 with others sub-types using simulated annealing and neural networks. In this paper, we increased our test result from 10 images to 20 images. We performed Hill Climbing, Simulated Annealing and Genetic Algorithms for detecting the blast cells. As a result, simulated annealing is the “best” heuristic search for detecting the leukaemia cells. From the detection, we performed features extraction on the blast cells and we classifying based on M3 and other sub-types using neural networks. We received convincing result which has targeting around 97% in classifying of M3 with other sub-types. Our results are based on real world image data from a Haematology Department.Universiti Sains Islam Malaysia and the Ministry of Higher Education, Malaysi
Comparison of Timed Automata with Discrete Event Simulation for Modeling Personalized Treatment Decisions:the Case of Metastatic Castration Resistant Prostate Cancer
Objectives: The aim of this study is to compare the usefulness of two promising alternative modeling techniques, Timed Automata (TA) originating from informatics, and Discrete Event Simulation (DES) known in operations research, for modeling todays complex and personalized treatment decisions over time, involving multiple interactions and decision gates. Methods: The usefulness of both modeling techniques was assessed in a case study on the treatment of metastatic Castration Resistant Prostate Cancer (mCRPC) in which Circulating Tumor Cells (CTC) may be used as a response marker for switching first to second line treatment. Techniques were compared on user-friendliness, input requirements, input possibilities, model checking facilities, and results. Input parameters were similar for both models, consisting of costs, QoL, treatment effectiveness, diagnostic performance, physicians’ behavior and survival. Primary outcome measures were health outcomes, expressed in QALYs, and costs. Results: Modelling was considered easier using TA, as this approach allows independent modeling of the actors and elements comprising the treatment process, such as patients, physicians, tests and treatments, and their mutual interaction and communication. Furthermore, the statistical model checking feature in the TA software was found to be a powerful tool for validation. Input requirements and possibilities were similar for both modelling approaches in this case study. Both modelling approaches yield comparable results. Using TA, CTC reduced first and second line treatment by, on average, 108.9 and 107.6 days, respectively. Using DES, treatment was reduced by 83.6 and 85.0 days. CTC therefore reduced healthcare costs by €28,998 and €21,992 according to TA and DES, respectively. Conclusions: Both Timed Automata and Discrete Event Simulation seem to be suitable for modeling complex and personalized treatment processes like that of mCRPC. Timed Automata is a new and interesting alternative modeling technique, as it allows explicit separation of model components and supports statistical model checking to validate models
Multiple verification in computational modeling of bone pathologies
We introduce a model checking approach to diagnose the emerging of bone
pathologies. The implementation of a new model of bone remodeling in PRISM has
led to an interesting characterization of osteoporosis as a defective bone
remodeling dynamics with respect to other bone pathologies. Our approach allows
to derive three types of model checking-based diagnostic estimators. The first
diagnostic measure focuses on the level of bone mineral density, which is
currently used in medical practice. In addition, we have introduced a novel
diagnostic estimator which uses the full patient clinical record, here
simulated using the modeling framework. This estimator detects rapid (months)
negative changes in bone mineral density. Independently of the actual bone
mineral density, when the decrease occurs rapidly it is important to alarm the
patient and monitor him/her more closely to detect insurgence of other bone
co-morbidities. A third estimator takes into account the variance of the bone
density, which could address the investigation of metabolic syndromes, diabetes
and cancer. Our implementation could make use of different logical combinations
of these statistical estimators and could incorporate other biomarkers for
other systemic co-morbidities (for example diabetes and thalassemia). We are
delighted to report that the combination of stochastic modeling with formal
methods motivate new diagnostic framework for complex pathologies. In
particular our approach takes into consideration important properties of
biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could
be further expanded, inching towards the complexity of human diseases. Finally,
we briefly introduce self-adaptiveness in formal methods which is a key
property in the regulative mechanisms of biological systems and well known in
other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104
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