Jaime Gomez-Ramirez | The Hospital for Sick Children (original) (raw)
Papers by Jaime Gomez-Ramirez
Integral Biomathics, 2012
Leslie S. Smith, Neuroscience and Natural Computing, UK l.s.smith@cs.stir.ac.uk 2 _______________... more Leslie S. Smith, Neuroscience and Natural Computing, UK l.s.smith@cs.stir.ac.uk 2 ______________________________________________________________________________ Note: This White Paper is not a concise report on the research program we seek to elaborate in INBIOSA. It has been conceived as a 'living' document, progressively developed along the months by discussions among scientists with differing formations and states of mind. We have chosen to respect their personalities, at the risk of some lack of homogeneity and repetitions between different passages. Also, incompleteness, inconsistences and antagonisms could not be completely avoided.
By 2050 it is estimated that the number of worldwide Alzheimer’s disease (AD) patients will quadr... more By 2050 it is estimated that the number of worldwide Alzheimer’s disease (AD) patients
will quadruple from the current number of 36 million people. To date, no single test, prior
to postmortem examination, can confirm that a person suffers from AD.Therefore, there is
a strong need for accurate and sensitive tools for the early diagnoses of AD. The complex
etiology and multiple pathogenesis of AD call for a system-level understanding of the currently
available biomarkers and the study of new biomarkers via network-based modeling
of heterogeneous data types. In this review,we summarize recent research on the study of
AD as a connectivity syndrome.We argue that a network-based approach in biomarker discovery
will provide key insights to fully understand the network degeneration hypothesis
(disease starts in specific network areas and progressively spreads to connected areas of
the initial loci-networks) with a potential impact for early diagnosis and disease-modifying
treatments.We introduce a new framework for the quantitative study of biomarkers that
can help shorten the transition between academic research and clinical diagnosis in AD.
The paper discusses how neural and mental processes correlate for developing cognitive abilities ... more The paper discusses how neural and mental processes correlate for developing cognitive abilities like
memory or spatial representation and allowing the emergence of higher cognitive processes up to
embodied cognition, consciousness and creativity. It is done via the presentation of MENS (for Memory
Evolutive Neural System), a mathematical methodology, based on category theory, which encompasses
the neural and mental systems and analyzes their dynamics in the process of ‘becoming’. Using the
categorical notion of a colimit, it describes the generation of mental objects through the iterative
binding of distributed synchronous assemblies of neurons, and presents a new rationale of spatial
representation in the hippocampus (Gomez-Ramirez and Sanz, 2011). An important result is that the
degeneracy of the neural code (Edelman, 1989) is the property allowing for the formation of mental
objects and cognitive processes of increasing complexity order, with multiple neuronal realizabilities;
it is essential “to explain certain empirical phenomena like productivity and systematicity of thought
and thinking (Aydede 2010)”. Rather than restricting the discourse to linguistics or philosophy of
mind, the formal methods used in MENS lead to precise notions of Compositionality, Productivity and
Systematicity, which overcome the dichotomic debate of classicism vs. connectionism and their
multiple facets. It also allows developing the naturalized phenomenology approach asked for by
Varela (1996) which “seeks articulations by mutual constraints between phenomena present in
experience and the correlative field of phenomena established by the cognitive sciences”, while
avoiding their pitfalls.
The seriousness of the current crisis urgently demands new economic thinking that breaks the aust... more The seriousness of the current crisis urgently demands new economic thinking that breaks the austerity vs. deficit spending circle in economic policy. The core tenet of the paper is that the most important problems that natural and social science are facing today are inverse problems, and that a new approach that goes beyond optimization is necessary. The approach presented here is radical in the sense that it identifies the roots in key assumptions in economic theory such as optimal behavior and stability to provide an inverse thinking perspective to economic modeling, of use in economic and financial stability policy. The inverse problem provides a truly multidisciplinary platform where related problems from different disciplines can be studied under a common approach with comparable results.
From Brains to Systems, Jan 1, 2011
… ophthalmology & visual …, Jan 1, 1999
PURPOSE. TO investigate in vivo the survival of abducens motoneurons (AMNs) at different periods ... more PURPOSE. TO investigate in vivo the survival of abducens motoneurons (AMNs) at different periods of time after a single intramuscular injection of the neurotoxin botulinum toxin A (BTxA) or doxorubicin (DXR).
In this paper is presented the theoretical framework for the construction on a foundational ontol... more In this paper is presented the theoretical framework for the construction on a foundational ontology with cognitive bias and solid philosophical specifications, that relates how sensory robot information, is grounded and linked to internal a conceptual system symbols. We expect that from this starting point, semantic technologies will permit to access, share and enhance robot knowledge in a more performant and distributed way.
Complex Medical Engineering (CME) …, Jan 1, 2012
While it is widely recognised that, on the one hand, reductionistic approaches are inadequate to ... more While it is widely recognised that, on the one hand, reductionistic approaches are inadequate to deal with the multifactorial and complex nature of health and disease, and on the other hand, a system level understanding of the normal and pathological functioning of biological systems is sorely needed; no clear procedure have been put forth about the actual implementation of such a program. In this paper we review the tools and the mode of thinking that systems biology has set forward in the last twenty years, pinpointing its key methodological and epistemic aspects, together with the technical obstacles and conceptual limitations that it is faced with. A new approach conducive to a system level understanding of biomedical systems is thus proposed.
From Brains to Systems, Jan 1, 2011
It goes without saying that in science, experiments are essential; hypothesis need to be contrast... more It goes without saying that in science, experiments are essential; hypothesis need to be contrasted against empirical results in order to build scientific theories. In a system of overwhelming complexity like the brain, it is very likely that hidden variables, unknown by the experimentalist, are interacting with those few elements of which the values are expected and can be validated or rejected in the laboratory. Thus, at the end of the day, the experimentalist is refuting or validating tentative models that are somehow prisoners of the lack of knowledge about the structure of the system. The global picture being missing, a key is to look for the fundamental structure which must be found not in the objects, but in the relationships between the objects-their morphisms. How components at the same level interact (the objects here being neurons) and how superior levels constrain those levels below and emerge from those above is tackled here with a mathematical tooling. The mathematical theory of categories is proposed as a valid foundational framework for theoretical modeling in brain sciences.
Towards a Service- …, Jan 1, 2011
This paper discusses the rebirth of the old quest for the principles of biology along the discour... more This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization.
tierra.aslab.upm.es
Page 1. Universidad Politécnica de Madrid A New Foundation for Representation in Cognitive and Br... more Page 1. Universidad Politécnica de Madrid A New Foundation for Representation in Cognitive and Brain Science: Category Theory and the Hippocampus Jaime David Gómez Ram´ırez jd.gomez@upm.es 2010 Page 2. Page 3. To my wife and my son, with love. Page 4. Page 5. ...
… : Tracing the Road to Reality, P. …, Jan 1, 2012
The Escherichia coli is a bacterium that comfortingly lives in the human gut and one of the best ... more The Escherichia coli is a bacterium that comfortingly lives in the human gut and one of the best known living organisms. The sensitivity of this cell to environmental changes is reflected in two kind of movements that can be observed in a swimming bacterium: "run" towards an attractant, for example food, and "tumbling", in which a new direction is chosen randomly for the next "run".
Advances in experimental …, Jan 1, 2011
1. Adv Exp Med Biol. 2011;718:1-6. Introduction: from brains to the machines of the future. Sanz ... more 1. Adv Exp Med Biol. 2011;718:1-6. Introduction: from brains to the machines of the future. Sanz R, Hernández C, Gómez-Ramirez J. PMID: 21744205 [PubMed - indexed for MEDLINE]. Publication Types: Editorial; Introductory Journal Article. MeSH Terms. ...
Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineer... more Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineers who use analytic and synthetic methods both to understand the astonishing processing properties of biological systems and specifically of the brain, and to exploit such knowledge to advance engineering methods to build artificial systems with higher levels of cognitive competence. BICS is a meeting point of brain scientists and cognitive systems engineers where cross-domain ideas are fostered in the hope of getting emerging insights ...
Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineer... more Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineers who use analytic and synthetic methods both to understand the astonishing processing properties of biological systems and specifically of the brain, and to exploit such knowledge to advance engineering methods to build artificial systems with higher levels of cognitive competence. BICS is a meeting point of brain scientists and cognitive systems engineers where cross-domain ideas are fostered in the hope of getting emerging insights ...
Cognitive Computation, Jan 1, 2012
Abstract The stupendous technical development of brain measuring techniques, notably neuroimaging... more Abstract The stupendous technical development of brain measuring techniques, notably neuroimaging, have produced a massive amount of data about the brain at all levels. Nevertheless, the global picture of brain functioning is still missing. While an unified theory of cognition seems today unrealistic, the project of building an unified theory of the brain has already started. For example, Karl Friston[1], [2], is putting forward the free energy principle as a quantifiable framework, where several global brain theories can be merged. This integrative ...
arXiv preprint arXiv:1208.3460, Jan 1, 2012
Books by Jaime Gomez-Ramirez
The purpose of the book is to advance in the understanding of brain function by defining a genera... more The purpose of the book is to advance in the understanding of brain function by defining a general framework for representation based on category theory. The idea is to bring this mathematical formalism into the domain of neural representation of physical spaces, setting the basis for a theory of mental representation, able to relate empirical findings, uniting them into a sound theoretical corpus.
The innovative approach presented in the book provides a horizon of interdisciplinary collaboration that aims to set up a common agenda that synthesizes mathematical formalization and empirical procedures in a systemic way. Category theory has been successfully applied to qualitative analysis, mainly in theoretical computer science to deal with programming language semantics. Nevertheless, the potential of category theoretic tools for quantitative analysis of networks has not been tackled so far. Statistical methods to investigate graph structure typically rely on network parameters. Category theory can be seen as an abstraction of graph theory. Thus, new categorical properties can be added into network analysis and graph theoretic constructs can be accordingly extended in more fundamental basis. By generalizing networks using category theory we can address questions and elaborate answers in a more fundamental way without waiving graph theoretic tools. The vital issue is to establish a new framework for quantitative analysis of networks using the theory of categories, in which computational neuroscientists and network theorists may tackle in more efficient ways the dynamics of brain cognitive networks.
The intended audience of the book is researchers who wish to explore thevalidity of mathematical principles in the understanding of cognitive systems. All the actors in cognitive science: philosophers, engineers, neurobiologists, cognitive psychologists, computer scientists etc. are akin to discover along its pages new unforeseen connections through the development of concepts and formal theories described in the book. Practitioners of both pure and applied mathematics e.g., network theorists, will be delighted with the mapping of abstract mathematical concepts in the terra incognita of cognition.
Integral Biomathics, 2012
Leslie S. Smith, Neuroscience and Natural Computing, UK l.s.smith@cs.stir.ac.uk 2 _______________... more Leslie S. Smith, Neuroscience and Natural Computing, UK l.s.smith@cs.stir.ac.uk 2 ______________________________________________________________________________ Note: This White Paper is not a concise report on the research program we seek to elaborate in INBIOSA. It has been conceived as a 'living' document, progressively developed along the months by discussions among scientists with differing formations and states of mind. We have chosen to respect their personalities, at the risk of some lack of homogeneity and repetitions between different passages. Also, incompleteness, inconsistences and antagonisms could not be completely avoided.
By 2050 it is estimated that the number of worldwide Alzheimer’s disease (AD) patients will quadr... more By 2050 it is estimated that the number of worldwide Alzheimer’s disease (AD) patients
will quadruple from the current number of 36 million people. To date, no single test, prior
to postmortem examination, can confirm that a person suffers from AD.Therefore, there is
a strong need for accurate and sensitive tools for the early diagnoses of AD. The complex
etiology and multiple pathogenesis of AD call for a system-level understanding of the currently
available biomarkers and the study of new biomarkers via network-based modeling
of heterogeneous data types. In this review,we summarize recent research on the study of
AD as a connectivity syndrome.We argue that a network-based approach in biomarker discovery
will provide key insights to fully understand the network degeneration hypothesis
(disease starts in specific network areas and progressively spreads to connected areas of
the initial loci-networks) with a potential impact for early diagnosis and disease-modifying
treatments.We introduce a new framework for the quantitative study of biomarkers that
can help shorten the transition between academic research and clinical diagnosis in AD.
The paper discusses how neural and mental processes correlate for developing cognitive abilities ... more The paper discusses how neural and mental processes correlate for developing cognitive abilities like
memory or spatial representation and allowing the emergence of higher cognitive processes up to
embodied cognition, consciousness and creativity. It is done via the presentation of MENS (for Memory
Evolutive Neural System), a mathematical methodology, based on category theory, which encompasses
the neural and mental systems and analyzes their dynamics in the process of ‘becoming’. Using the
categorical notion of a colimit, it describes the generation of mental objects through the iterative
binding of distributed synchronous assemblies of neurons, and presents a new rationale of spatial
representation in the hippocampus (Gomez-Ramirez and Sanz, 2011). An important result is that the
degeneracy of the neural code (Edelman, 1989) is the property allowing for the formation of mental
objects and cognitive processes of increasing complexity order, with multiple neuronal realizabilities;
it is essential “to explain certain empirical phenomena like productivity and systematicity of thought
and thinking (Aydede 2010)”. Rather than restricting the discourse to linguistics or philosophy of
mind, the formal methods used in MENS lead to precise notions of Compositionality, Productivity and
Systematicity, which overcome the dichotomic debate of classicism vs. connectionism and their
multiple facets. It also allows developing the naturalized phenomenology approach asked for by
Varela (1996) which “seeks articulations by mutual constraints between phenomena present in
experience and the correlative field of phenomena established by the cognitive sciences”, while
avoiding their pitfalls.
The seriousness of the current crisis urgently demands new economic thinking that breaks the aust... more The seriousness of the current crisis urgently demands new economic thinking that breaks the austerity vs. deficit spending circle in economic policy. The core tenet of the paper is that the most important problems that natural and social science are facing today are inverse problems, and that a new approach that goes beyond optimization is necessary. The approach presented here is radical in the sense that it identifies the roots in key assumptions in economic theory such as optimal behavior and stability to provide an inverse thinking perspective to economic modeling, of use in economic and financial stability policy. The inverse problem provides a truly multidisciplinary platform where related problems from different disciplines can be studied under a common approach with comparable results.
From Brains to Systems, Jan 1, 2011
… ophthalmology & visual …, Jan 1, 1999
PURPOSE. TO investigate in vivo the survival of abducens motoneurons (AMNs) at different periods ... more PURPOSE. TO investigate in vivo the survival of abducens motoneurons (AMNs) at different periods of time after a single intramuscular injection of the neurotoxin botulinum toxin A (BTxA) or doxorubicin (DXR).
In this paper is presented the theoretical framework for the construction on a foundational ontol... more In this paper is presented the theoretical framework for the construction on a foundational ontology with cognitive bias and solid philosophical specifications, that relates how sensory robot information, is grounded and linked to internal a conceptual system symbols. We expect that from this starting point, semantic technologies will permit to access, share and enhance robot knowledge in a more performant and distributed way.
Complex Medical Engineering (CME) …, Jan 1, 2012
While it is widely recognised that, on the one hand, reductionistic approaches are inadequate to ... more While it is widely recognised that, on the one hand, reductionistic approaches are inadequate to deal with the multifactorial and complex nature of health and disease, and on the other hand, a system level understanding of the normal and pathological functioning of biological systems is sorely needed; no clear procedure have been put forth about the actual implementation of such a program. In this paper we review the tools and the mode of thinking that systems biology has set forward in the last twenty years, pinpointing its key methodological and epistemic aspects, together with the technical obstacles and conceptual limitations that it is faced with. A new approach conducive to a system level understanding of biomedical systems is thus proposed.
From Brains to Systems, Jan 1, 2011
It goes without saying that in science, experiments are essential; hypothesis need to be contrast... more It goes without saying that in science, experiments are essential; hypothesis need to be contrasted against empirical results in order to build scientific theories. In a system of overwhelming complexity like the brain, it is very likely that hidden variables, unknown by the experimentalist, are interacting with those few elements of which the values are expected and can be validated or rejected in the laboratory. Thus, at the end of the day, the experimentalist is refuting or validating tentative models that are somehow prisoners of the lack of knowledge about the structure of the system. The global picture being missing, a key is to look for the fundamental structure which must be found not in the objects, but in the relationships between the objects-their morphisms. How components at the same level interact (the objects here being neurons) and how superior levels constrain those levels below and emerge from those above is tackled here with a mathematical tooling. The mathematical theory of categories is proposed as a valid foundational framework for theoretical modeling in brain sciences.
Towards a Service- …, Jan 1, 2011
This paper discusses the rebirth of the old quest for the principles of biology along the discour... more This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization.
tierra.aslab.upm.es
Page 1. Universidad Politécnica de Madrid A New Foundation for Representation in Cognitive and Br... more Page 1. Universidad Politécnica de Madrid A New Foundation for Representation in Cognitive and Brain Science: Category Theory and the Hippocampus Jaime David Gómez Ram´ırez jd.gomez@upm.es 2010 Page 2. Page 3. To my wife and my son, with love. Page 4. Page 5. ...
… : Tracing the Road to Reality, P. …, Jan 1, 2012
The Escherichia coli is a bacterium that comfortingly lives in the human gut and one of the best ... more The Escherichia coli is a bacterium that comfortingly lives in the human gut and one of the best known living organisms. The sensitivity of this cell to environmental changes is reflected in two kind of movements that can be observed in a swimming bacterium: "run" towards an attractant, for example food, and "tumbling", in which a new direction is chosen randomly for the next "run".
Advances in experimental …, Jan 1, 2011
1. Adv Exp Med Biol. 2011;718:1-6. Introduction: from brains to the machines of the future. Sanz ... more 1. Adv Exp Med Biol. 2011;718:1-6. Introduction: from brains to the machines of the future. Sanz R, Hernández C, Gómez-Ramirez J. PMID: 21744205 [PubMed - indexed for MEDLINE]. Publication Types: Editorial; Introductory Journal Article. MeSH Terms. ...
Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineer... more Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineers who use analytic and synthetic methods both to understand the astonishing processing properties of biological systems and specifically of the brain, and to exploit such knowledge to advance engineering methods to build artificial systems with higher levels of cognitive competence. BICS is a meeting point of brain scientists and cognitive systems engineers where cross-domain ideas are fostered in the hope of getting emerging insights ...
Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineer... more Brain Inspired Cognitive Systems-BICS 2010 aims to bring together leading scientists and engineers who use analytic and synthetic methods both to understand the astonishing processing properties of biological systems and specifically of the brain, and to exploit such knowledge to advance engineering methods to build artificial systems with higher levels of cognitive competence. BICS is a meeting point of brain scientists and cognitive systems engineers where cross-domain ideas are fostered in the hope of getting emerging insights ...
Cognitive Computation, Jan 1, 2012
Abstract The stupendous technical development of brain measuring techniques, notably neuroimaging... more Abstract The stupendous technical development of brain measuring techniques, notably neuroimaging, have produced a massive amount of data about the brain at all levels. Nevertheless, the global picture of brain functioning is still missing. While an unified theory of cognition seems today unrealistic, the project of building an unified theory of the brain has already started. For example, Karl Friston[1], [2], is putting forward the free energy principle as a quantifiable framework, where several global brain theories can be merged. This integrative ...
arXiv preprint arXiv:1208.3460, Jan 1, 2012
The purpose of the book is to advance in the understanding of brain function by defining a genera... more The purpose of the book is to advance in the understanding of brain function by defining a general framework for representation based on category theory. The idea is to bring this mathematical formalism into the domain of neural representation of physical spaces, setting the basis for a theory of mental representation, able to relate empirical findings, uniting them into a sound theoretical corpus.
The innovative approach presented in the book provides a horizon of interdisciplinary collaboration that aims to set up a common agenda that synthesizes mathematical formalization and empirical procedures in a systemic way. Category theory has been successfully applied to qualitative analysis, mainly in theoretical computer science to deal with programming language semantics. Nevertheless, the potential of category theoretic tools for quantitative analysis of networks has not been tackled so far. Statistical methods to investigate graph structure typically rely on network parameters. Category theory can be seen as an abstraction of graph theory. Thus, new categorical properties can be added into network analysis and graph theoretic constructs can be accordingly extended in more fundamental basis. By generalizing networks using category theory we can address questions and elaborate answers in a more fundamental way without waiving graph theoretic tools. The vital issue is to establish a new framework for quantitative analysis of networks using the theory of categories, in which computational neuroscientists and network theorists may tackle in more efficient ways the dynamics of brain cognitive networks.
The intended audience of the book is researchers who wish to explore thevalidity of mathematical principles in the understanding of cognitive systems. All the actors in cognitive science: philosophers, engineers, neurobiologists, cognitive psychologists, computer scientists etc. are akin to discover along its pages new unforeseen connections through the development of concepts and formal theories described in the book. Practitioners of both pure and applied mathematics e.g., network theorists, will be delighted with the mapping of abstract mathematical concepts in the terra incognita of cognition.