This paper introduces an open-source implementation of a non-monotonic learning method called XHAIL and shows how it can be applied to a whole-organism model of yeast metabolism. Unlike the previous XHAIL prototype, which could only handle networks of a few dozen reactions, our new system can accommodate networks with over a thousand. This scale–up was achieved though several implementation improvements which increase the method’s efficiency and support an enhanced language bias that further increases its usability. We test the system in a case study using real data collected by a Robot Scientist.
Shock is a common complication of severe febrile illness, and worldwide aggressive correction with intravenous bolus therapy is recommended as the initial treatment. Nevertheless, the evidence supporting this approach remains weak. The only controlled trial of fluid resuscitation, Fluid Expansion as Supportive Therapy (FEAST), involving 3141 African children with severe febrile illness, including large groups with sepsis and malaria, called into question aggressive fluid resuscitation, demonstrating excess mortality in both bolus arms (albumin and saline) compared to no-bolus control, relative risk of morality in bolus versus control was 1.45(1.13-1.86, p=0.003). Excess mortality was consistent across all subgroups, being greatest in those with the most severe forms of shock and acidosis. Remarkably, despite earlier shock reversal in those receiving fluid boluses the excess mortality in the FEAST trial was caused by subsequent cardiovascular collapse and was not secondary to fluid overload.
These observations are intriguing warranting an in-depth understanding of host responses including those of the myocardium to fluid resuscitation and at the microvasacular level since the two maybe synergistic. Current studies are underway in ovine models of sepsis (‘FEAST-in-Sheep’) in Professor John Fraser’s laboratory, Brisbane to understand the mechanism of harm, gain further insights in host responses to fluid management, and re-define the optimal fluid and supportive inotrope/vasopressor management of septic shock.
Four years have elapsed since the publication of FEAST, yet World Health Organization continues to recommend fluid boluses for children managed in resource-poor hospitals, where there is no access to intensive care. These are the precise settings where the FEAST trial was conducted in order to inform management guidelines. In Africa alone, where one in 10 febrile child admissions present with shock, we have estimated that the current guidelines, if fully implemented, will result in ~5,600 and 33,000 excess deaths each year per million hospital admissions treated for shock.
This web app by WP9 acts as an interface to the WP3 Global Optimiser to provide a mean for stakeholders and policy makers to interact with the tool and provide their feedback. The official ePolicy interface, however, will be provided by Fraunhofer IGD in WP7.
"ePolicy" is a European FP7-ICT-7-5.6 Project whose aim is to assist the policy maker when defining policies to assess whether they meet the requirements of both the policy maker and the domain expert before they are actually enforced.
In order to deliver such result, we model the features of the territory, we consider the feedback from citizens, we build appropriate incentive schemas and we test our results by means of a social simulator.
Our case study is the energy plan for the Emilia Romagna region in Italy and we have an advanced visualisation layer to present the results and help the user to understand them.
This poster presents the key aspects of the project: from the idea to the implementation, showcasing the main components and the visualisation.
For more information on the project, visit the web site: http://www.epolicy-project.eu
Total workflow solutions that cater every budget, performance or throughput requirement for confirmatory dioxin analysis were discussed in the Thermo Scientific Lunch Seminar at the Dioxin 2014 conference. D. Hope, CEO & Owner Pacific Rim Laboratoris, presented about the economies of POPs analysis from the point of view of a leading laboratory using the very latest dioxin method kits. C. Cojocariu, Thermo Fisher Scientific, discussed recent changes in EU regulations which bring new opportunities for more labs to participate in dioxin analysis and about validating methods using Gas Chromatography triple quadrupole for PCDD/Fs with reference to the new EU Commission Regulation No. 709/2014.
Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conserv...Kate Barlow
Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden
Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.
Shock is a common complication of severe febrile illness, and worldwide aggressive correction with intravenous bolus therapy is recommended as the initial treatment. Nevertheless, the evidence supporting this approach remains weak. The only controlled trial of fluid resuscitation, Fluid Expansion as Supportive Therapy (FEAST), involving 3141 African children with severe febrile illness, including large groups with sepsis and malaria, called into question aggressive fluid resuscitation, demonstrating excess mortality in both bolus arms (albumin and saline) compared to no-bolus control, relative risk of morality in bolus versus control was 1.45(1.13-1.86, p=0.003). Excess mortality was consistent across all subgroups, being greatest in those with the most severe forms of shock and acidosis. Remarkably, despite earlier shock reversal in those receiving fluid boluses the excess mortality in the FEAST trial was caused by subsequent cardiovascular collapse and was not secondary to fluid overload.
These observations are intriguing warranting an in-depth understanding of host responses including those of the myocardium to fluid resuscitation and at the microvasacular level since the two maybe synergistic. Current studies are underway in ovine models of sepsis (‘FEAST-in-Sheep’) in Professor John Fraser’s laboratory, Brisbane to understand the mechanism of harm, gain further insights in host responses to fluid management, and re-define the optimal fluid and supportive inotrope/vasopressor management of septic shock.
Four years have elapsed since the publication of FEAST, yet World Health Organization continues to recommend fluid boluses for children managed in resource-poor hospitals, where there is no access to intensive care. These are the precise settings where the FEAST trial was conducted in order to inform management guidelines. In Africa alone, where one in 10 febrile child admissions present with shock, we have estimated that the current guidelines, if fully implemented, will result in ~5,600 and 33,000 excess deaths each year per million hospital admissions treated for shock.
This web app by WP9 acts as an interface to the WP3 Global Optimiser to provide a mean for stakeholders and policy makers to interact with the tool and provide their feedback. The official ePolicy interface, however, will be provided by Fraunhofer IGD in WP7.
"ePolicy" is a European FP7-ICT-7-5.6 Project whose aim is to assist the policy maker when defining policies to assess whether they meet the requirements of both the policy maker and the domain expert before they are actually enforced.
In order to deliver such result, we model the features of the territory, we consider the feedback from citizens, we build appropriate incentive schemas and we test our results by means of a social simulator.
Our case study is the energy plan for the Emilia Romagna region in Italy and we have an advanced visualisation layer to present the results and help the user to understand them.
This poster presents the key aspects of the project: from the idea to the implementation, showcasing the main components and the visualisation.
For more information on the project, visit the web site: http://www.epolicy-project.eu
Total workflow solutions that cater every budget, performance or throughput requirement for confirmatory dioxin analysis were discussed in the Thermo Scientific Lunch Seminar at the Dioxin 2014 conference. D. Hope, CEO & Owner Pacific Rim Laboratoris, presented about the economies of POPs analysis from the point of view of a leading laboratory using the very latest dioxin method kits. C. Cojocariu, Thermo Fisher Scientific, discussed recent changes in EU regulations which bring new opportunities for more labs to participate in dioxin analysis and about validating methods using Gas Chromatography triple quadrupole for PCDD/Fs with reference to the new EU Commission Regulation No. 709/2014.
Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conserv...Kate Barlow
Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden
Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.
Computational tools for drug discoveryEszter Szabó
Discovery of a novel drug is an optimizing challenge against an array of chemical and biological attributes to reach the desired efficacy and safety profile. The immense complexity of the human body combined with the astronomically large druggable chemical space hinders the selection of molecules with such a balanced profile. Therefore, the medicinal chemistry toolbox embraces all computational techniques with predictive power to focus the chemical space to the most promising candidates for synthesis and testing. The diversity includes data analysis tools, physics-based simulations, biological target structure driven or ligand structure based approaches [1-3]. While the size of the compound collections vary from a couple of close analogues up to billions of virtual compounds to process[4]. This presentation will highlight general concepts and techniques applied in computer aided drug design, focusing on data and ligand based computational chemistry approaches and showcase solutions developed by ChemAxon.
[1] Gisbert Schneider, David E Clark, Angew Chem Int Ed Engl. 2019, 5;58(32):10792-10803.
[2] John G Cumming, Andrew M Davis, Sorel Muresan, Markus Haeberlein, Hongming Chen, Nat Rev Drug Discov, 2013, 12(12):948-62.
[3] Yu-Chen Lo, Stefano E Rensi, Wen Torng, Russ B Altman, Drug Discov Today 2018, 23(8):1538-1546
[4] Torsten Hoffmanm, Marcus Gastreich, Drug Discov Today, 2019, 24(5):1148-1156.
A Statistical Approach to Optimize Parameters for Electrodeposition of Indium...Arkansas State University
A Statistical Approach to Optimize Parameters for Electrodeposition of Indium (III) Sulfide Films, Potential Low-Hazard Buffer Layers for Photovoltaic Applications
On preemptive resume versus non preemtive disciplines relevant to monopoly se...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
A Distributed System Using MS Kinect and Event Calculus for Adaptive Physioth...Stefano Bragaglia
In many countries of the world, the life expectancy increases but the population ages so rapidly that it is expected that soon it will be difficult to ensure a good life quality to the elder people when health issues arise. In this paper, we consider this problem from the point of view of the physiotherapy rehabili- tation which nowadays is perceived as costly and inconvenient for the elder patients. In order to lessen these problems, we propose a distributed architecture to allow the physiotherapists to remotely assist their patients while they comfortably do exercises from home. As in other proposals, the Human Pose Recognition is delegated to a computer equipped with MS Kinect and neural networks. Our approach, however, differs from others because it includes a logical framework based on Event Calculus augmented with Expectations which provides a higher-level description of the exercises and a mean to measure how well they were done.
It often happens during conferences and other visits that after a while people informally asks me things about food because I am Italian.
In particular, they are curious to know about 'spaghetti bolognese' because I am precisely from Bologna.
They barely believe me when I explain that it is not at all typical dish and the real one - tagliatelle al ragù - is quite different.
I ended up putting together these slides to support my explanations and they are always greatly appreciated.
So if you are curious to know how is the original recipe, take a look at this!
More Related Content
Similar to ILP 2014 - Nonmonotonic Learning in Large Biological Network
Computational tools for drug discoveryEszter Szabó
Discovery of a novel drug is an optimizing challenge against an array of chemical and biological attributes to reach the desired efficacy and safety profile. The immense complexity of the human body combined with the astronomically large druggable chemical space hinders the selection of molecules with such a balanced profile. Therefore, the medicinal chemistry toolbox embraces all computational techniques with predictive power to focus the chemical space to the most promising candidates for synthesis and testing. The diversity includes data analysis tools, physics-based simulations, biological target structure driven or ligand structure based approaches [1-3]. While the size of the compound collections vary from a couple of close analogues up to billions of virtual compounds to process[4]. This presentation will highlight general concepts and techniques applied in computer aided drug design, focusing on data and ligand based computational chemistry approaches and showcase solutions developed by ChemAxon.
[1] Gisbert Schneider, David E Clark, Angew Chem Int Ed Engl. 2019, 5;58(32):10792-10803.
[2] John G Cumming, Andrew M Davis, Sorel Muresan, Markus Haeberlein, Hongming Chen, Nat Rev Drug Discov, 2013, 12(12):948-62.
[3] Yu-Chen Lo, Stefano E Rensi, Wen Torng, Russ B Altman, Drug Discov Today 2018, 23(8):1538-1546
[4] Torsten Hoffmanm, Marcus Gastreich, Drug Discov Today, 2019, 24(5):1148-1156.
A Statistical Approach to Optimize Parameters for Electrodeposition of Indium...Arkansas State University
A Statistical Approach to Optimize Parameters for Electrodeposition of Indium (III) Sulfide Films, Potential Low-Hazard Buffer Layers for Photovoltaic Applications
On preemptive resume versus non preemtive disciplines relevant to monopoly se...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Similar to ILP 2014 - Nonmonotonic Learning in Large Biological Network (18)
A Distributed System Using MS Kinect and Event Calculus for Adaptive Physioth...Stefano Bragaglia
In many countries of the world, the life expectancy increases but the population ages so rapidly that it is expected that soon it will be difficult to ensure a good life quality to the elder people when health issues arise. In this paper, we consider this problem from the point of view of the physiotherapy rehabili- tation which nowadays is perceived as costly and inconvenient for the elder patients. In order to lessen these problems, we propose a distributed architecture to allow the physiotherapists to remotely assist their patients while they comfortably do exercises from home. As in other proposals, the Human Pose Recognition is delegated to a computer equipped with MS Kinect and neural networks. Our approach, however, differs from others because it includes a logical framework based on Event Calculus augmented with Expectations which provides a higher-level description of the exercises and a mean to measure how well they were done.
It often happens during conferences and other visits that after a while people informally asks me things about food because I am Italian.
In particular, they are curious to know about 'spaghetti bolognese' because I am precisely from Bologna.
They barely believe me when I explain that it is not at all typical dish and the real one - tagliatelle al ragù - is quite different.
I ended up putting together these slides to support my explanations and they are always greatly appreciated.
So if you are curious to know how is the original recipe, take a look at this!
I used these slides last year to introduce RTAI and Earliest Deadline First for the course "Real-Time Operating Systems" (in English), here at University of Bologna. They include an architectural overview of RTAI, some scheduling algorithms including EDF, and instructions to install and use RTAI.
Approximate Inference for Logic Programs with Annotated Disjunctions (RCRA 2009)Stefano Bragaglia
These slides, presented at RCRA 2009, summarises my work for the MSc thesis.
They introduce some fundamentals on LPADs, the standard inference mechanisms, two approximate algorithms and the graphs documenting our findings.
Stefano Bragaglia MSc Thesis, awarded as Best Italian thesis in AI 2009/2010Stefano Bragaglia
My MSc Thesis (only in Italian) introduces Logic Programs with Annotated Disjunction (LPADs) a Prolog's probabilistic extension, and my work on CPLINT (https://sites.google.com/a/unife.it/ml/cplint) to reason on them. My goal was to implement and test several approximated algorithms to balance speed and accuracy when solving probabilistic problems. It was awarded by the Italian Association for Artificial Intelligence (AIxIA) as the best Italian thesis in Artificial Intelligence of 2009/2010.
I presented these slides introducing Description Logic, Semantic Web and Ontology Development since May 2010 to the students of the 'Fondamenti di Intelligenza Artificiale' course of the University of Bologna, Italy. The last part of the presentation is about some best practices to develop good ontologies.
I presented these slides introducing Production Rules Systems in June 2013 to the students of the 'Fondamenti di Intelligenza Artificiale' course of the University of Bologna, Italy. I pass from the theory to the practice, showing the architecture and the components of PRSs. In the final part, an intuition of the operating principles are also given.
Collapsing Narratives: Exploring Non-Linearity • a micro report by Rosie WellsRosie Wells
Insight: In a landscape where traditional narrative structures are giving way to fragmented and non-linear forms of storytelling, there lies immense potential for creativity and exploration.
'Collapsing Narratives: Exploring Non-Linearity' is a micro report from Rosie Wells.
Rosie Wells is an Arts & Cultural Strategist uniquely positioned at the intersection of grassroots and mainstream storytelling.
Their work is focused on developing meaningful and lasting connections that can drive social change.
Please download this presentation to enjoy the hyperlinks!
This presentation, created by Syed Faiz ul Hassan, explores the profound influence of media on public perception and behavior. It delves into the evolution of media from oral traditions to modern digital and social media platforms. Key topics include the role of media in information propagation, socialization, crisis awareness, globalization, and education. The presentation also examines media influence through agenda setting, propaganda, and manipulative techniques used by advertisers and marketers. Furthermore, it highlights the impact of surveillance enabled by media technologies on personal behavior and preferences. Through this comprehensive overview, the presentation aims to shed light on how media shapes collective consciousness and public opinion.
Announcement of 18th IEEE International Conference on Software Testing, Verif...
ILP 2014 - Nonmonotonic Learning in Large Biological Network
1. Nonmonotonic Learning
in Large Biological Networks
Stefano Bragaglia, Oliver Ray
stefano.bragaglia@bristol.ac.uk, oray@cs.bris.ac.uk
Department of Computer Science
University of Bristol
14-17/09/2014 ILP '14, Nancy 1
2. • New open source XHAIL implementation
• Study of scalability on Biological Networks
• Found mistake in genome-scale network
14-17/09/2014 ILP '14, Nancy 2
3. XHAIL
• Nonmonotonic ILP
– normal (extended) logic programs
– abductive, deductive, inductive
• Prototype (2006)
– ASP-based (lparse/smodels)
– Prolog wrapper (SWI-Prolog)
– Not defeasible
– Not
• Metabolic Network Revision (ILP 09)
– AAA model (~30 reactions)
– Pathway-specific model
• Non
– normal
– Abductive
• Current application
– ASP-based (gringo/clasp)
– Java wrapper (Java 8)
– Defeasible (language bias)
– Open source
• Metabolic Network Revision
– ABER model (1100+ reactions)
– Whole-organism model
14-17/09/2014 ILP '14, Nancy 3
4. XHAIL
• Nonmonotonic ILP
– normal (extended) logic programs
– abductive, deductive, inductive
• Prototype (2006)
– ASP-based (lparse/smodels)
– Prolog wrapper (SWI-Prolog)
– Not defeasible
– Not
• Metabolic Network Revision (ILP 09)
– AAA model (~30 reactions)
– Pathway-specific model
• Non
– normal
– Abductive
• Current application
– ASP-based (gringo/clasp)
– Java wrapper (Java 8)
– Defeasible (language bias)
– Open source
http://github.com/cathexis-bris-ac-uk/XHAIL
• Metabolic Network Revision
– ABER model (1100+ reactions)
– Whole-organism model
14-17/09/2014 ILP '14, Nancy 4
12. Scalability Analysis
on Validation Experiments
standard
expressions
14-17/09/2014 ILP '14, Nancy 12
biased
expressions
# reactions hypotheses time (s) - means "out of memory"
14. NONMONOTONIC LEARNING
IN LARGE BIOLOGICAL NETWORKS
Stefano Bragaglia, Oliver Ray
stefano.bragaglia@bristol.ac.uk, oray@cs.bris.ac.uk
• Thanks for your attention
• Any questions?
14-17/09/2014 ILP '14, Nancy 14
Editor's Notes
Requirements Engineering (FLTL, ILP’06)
Deals with negation
Completion
Ross King
Fluent Linear Temporal Logic
Requirements Engineering (FLTL, ILP’06)
Deals with negation
Completion
Ross King
Fluent Linear Temporal Logic
Help the user to explore the part of the search space they want to focus on
We prepared a first set of tests to validate and revise the portion of ABER relating to AAA. These tests are divided into tasks.
Task A consists of two experiments that allow XHAIL to infer that YER090W is required in all enzyme complexes catalysing reaction 4.1.3.27.
Experiment 1 simply knocks out YER090W. ABER observes growth as it thinks YKL211C can catalyse 4.1.3.27 alone.
We prepared a first set of tests to validate and revise the portion of ABER relating to AAA. These tests are divided into tasks.
Task A consists of two experiments that allow XHAIL to infer that YER090W is required in all enzyme complexes catalysing reaction 4.1.3.27.
Experiment 1 simply knocks out YER090W. ABER observes growth as it thinks YKL211C can catalyse 4.1.3.27 alone.
We prepared a first set of tests to validate and revise the portion of ABER relating to AAA. These tests are divided into tasks.
Task A consists of two experiments that allow XHAIL to infer that YER090W is required in all enzyme complexes catalysing reaction 4.1.3.27.
Experiment 1 simply knocks out YER090W. ABER observes growth as it thinks YKL211C can catalyse 4.1.3.27 alone.
We prepared a first set of tests to validate and revise the portion of ABER relating to AAA. These tests are divided into tasks.
Task A consists of two experiments that allow XHAIL to infer that YER090W is required in all enzyme complexes catalysing reaction 4.1.3.27.
Experiment 1 simply knocks out YER090W. ABER observes growth as it thinks YKL211C can catalyse 4.1.3.27 alone.
We prepared a first set of tests to validate and revise the portion of ABER relating to AAA. These tests are divided into tasks.
Task A consists of two experiments that allow XHAIL to infer that YER090W is required in all enzyme complexes catalysing reaction 4.1.3.27.
Experiment 1 simply knocks out YER090W. ABER observes growth as it thinks YKL211C can catalyse 4.1.3.27 alone.
We have also prepared a second batch of 40 experiments using real data provided by a robot scientist.
The conventions are the same as before but we only compare the results in the case of the hardest problems.
We observe a gain in performance of about 30%.