Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Investigating biocomplexity through the agent-based paradigm.

Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex

Working Notes from the 1992 AAAI Workshop on Automating Software Design. Theme: Domain Specific Software Design

The goal of this workshop is to identify different architectural approaches to building domain-specific software design systems and to explore issues unique to domain-specific (vs. general-purpose) software design. Some general issues that cut across the particular software design domain include: (1) knowledge representation, acquisition, and maintenance; (2) specialized software design techniques; and (3) user interaction and user interface

Special Session on Industry 4.0

No abstract available

Social based adaptation in multi-agent systems

This work presents a new agent model based in three main topics: emotional psychology (OCC list of emotions), sociology and cognitive psychology (KAI index) and the concept of "opinion" given by the agents. The new model is suitable for implementing adaptation in changing environments, as well as for static ones which are highly unpredictable.García-Pardo Giménez De Los Galanes, JÁ. (2010). Social based adaptation in multi-agent systems. http://hdl.handle.net/10251/13702Archivo delegad

Learning Personalized User Preference from Cold Start in Multi-turn Conversations

This paper presents a novel teachable conversation interaction system that is capable of learning users preferences from cold start by gradually adapting to personal preferences. In particular, the TAI system is able to automatically identify and label user preference in live interactions, manage dialogue flows for interactive teaching sessions, and reuse learned preference for preference elicitation. We develop the TAI system by leveraging BERT encoder models to encode both dialogue and relevant context information, and build action prediction (AP), argument filling (AF) and named entity recognition (NER) models to understand the teaching session. We adopt a seeker-provider interaction loop mechanism to generate diverse dialogues from cold-start. TAI is capable of learning user preference, which achieves 0.9122 turn level accuracy on out-of-sample dataset, and has been successfully adopted in production.Comment: preference, personalization, cold-start, dialogue, LLM. embeddin

Towards a knowledge structuring framework for decision making within industry 4.0 paradigm

International audienceThis article discusses the importance of data and knowledge structuring to allow their exploitation in emergent context of industry of the future. The complexity of integrating knowledge into decision support systems is particularly due to the heterogeneity of knowledge sources and the large volume of data to be analyzed. This problematic is challenging in the context of high-speed machining of aeronautical mechanical parts because of the high quality and safety constraints requested in this business area. To answer the above problem, this paper proposes a new semantic modeling framework covering both generic business knowledge and real time data. The application to the proposed semantic models for decision aid perspective within the SmartEmma project is also discussed