arXiv subjects

Tomas Veloz

Publications and source records attributed to Tomas Veloz.

At least 19 recordsLinked to original sources

arXiv2026

Synergy and Complementarity: The Generative Basis of Chemical Organizations

Identifying structural features ensuring the persistence of a reaction network is fundamental for understanding the evolution and complexification of biological entities. By defining organizations as subsets of species that are closed and self-maintaining, Chemical Organization Theory (COT) shows that organizations enable filtering out the regions of the phase space where attractors can exist. Despite various theoretical explorations current methods to compute the organizations face unclear combinatorial challenges. In this article, we first perform a systematic study of such combinatorial challenges and identify a criteria of productive novelty and irreducibility that separate relevant from redundant combinations. Second, we identify the minimal building blocks that shall be combined to build organizations, called elementary reaction closures (ERC), and characterize them as a hierarchy. Third, we show that all persistent modules can be generated as combination of ERCs only, and operationalize two properties among ERCs, synergy and complementarity, that define a sufficient criteria to build such generators in a minimal way. Fourth we show that every relevant persistent module can be built from such minimal sequences of ERCs. We next show that the synergies and complementarities we use to generate persistent modules not only scale radically slower than usual combinatorial methods. We quantify these structures across $438$ biological reaction networks from the BioModels and BiGG databases. The proportion of fundamental synergies and complementarities among all ERC pairs shrinks as networks grow even as raw counts increase, confirming that larger biological networks achieve persistence through a progressively smaller and more selective sets. We do not prescribe algorithms to compute organizations, discuss how algorithms based on our results could permit applying COT.

q-bio.MN↗

arXiv2024

Analyizing the Conjunction Fallacy as a Fact

Since the seminal paper by Tversky and Kahneman, the conjunction fallacy has been the subject of multiple debates and become a fundamental challenge for cognitive theories in decision-making. In this article, we take a rather uncommon perspective on this phenomenon. Instead of trying to explain the nature or causes of the conjunction fallacy (intensional definition), we analyze its range of factual possibilities (extensional definition). We show that the majority of research on the conjunction fallacy, according to our sample of experiments reviewed which covers literature between 1983 and 2016, has focused on a narrow part of the a priori factual possibilities, implying that explanations of the conjunction fallacy are fundamentally biased by the short scope of possibilities explored. The latter is a rather curious aspect of the research evolution in the conjunction fallacy considering that the very nature of it is motivated by extensional considerations.

cs.AI↗

arXiv2020

On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model

Measures to reduce the impact of the COVID-19 pandemic require a mix of logistic, political and social capacity. Depending on the country, different approaches to increase hospitalization capacity or to properly apply lock-downs are observed. In order to better understand the impact of these measures we have developed a compartmental model which, on the one hand allows to calibrate the reduction of movement of people within and among different areas, and on the other hand it incorporates a hospitalization dynamics that differentiates the available kinds of treatment that infected people can receive. By bounding the hospitalization capacity, we are able to study in detail the interplay between mobility and hospitalization capacity.

q-bio.PE↗

arXiv2019

The Complexity-Stability Debate, Chemical Organization Theory, and the Identi cation of Non-Classical Structures in Ecology

We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT provides a novel conceptual landscape plenty of analytic tools to explore the interplay between structure and stability of ecological systems. Given a large set of species and their interactions, COT identifies, in a computationally feasible way, each and every sub-collection of species that is closed and self-maintaining. These sub-collections, called organizations, correspond to the groups of species that can survive together (co-exist) in the long-term. Thus, the set of organizations contains all the stable regimes that can possibly happen in the dynamics of the ecological system. From here, we propose to conceive the notion of stability from the properties of the organizations, and thus apply the vast knowledge on the stability of reaction networks to the Complexity-Stability debate. As an example of the potential of COT to introduce new mathematical tools, we show that the set of organizations can be equipped with suitable joint and meet operators, and that for certain ecological systems the organizational structure is a non-boolean lattice, providing in this way an unexpected connection between logico-algebraic structures, popular in the foundations of quantum theory, and ecology.

q-bio.PE↗

arXiv2019

Measuring Conceptual Entanglement in Collections of Documents

Conceptual entanglement is a crucial phenomenon in quantum cognition because it implies that classical probabilities cannot model non--compositional conceptual phenomena. While several psychological experiments have been developed to test conceptual entanglement, this has not been explored in the context of Natural Language Processing. In this paper, we apply the hypothesis that words of a document are traces of the concepts that a person has in mind when writing the document. Therefore, if these concepts are entangled, we should be able to observe traces of their entanglement in the documents. In particular, we test conceptual entanglement by contrasting language simulations with results obtained from a text corpus. Our analysis indicates that conceptual entanglement is strongly linked to the way in which language is structured. We discuss the implications of this finding in the context of conceptual modeling and of Natural Language Processing.

cs.CL↗

arXiv2019

A Non-Phylogenetic Conceptual Network Architecture for Organizing Classes of Material Artifacts into Cultural Lineages

The application of phylogenetic techniques to the documentation of cultural history can present a distorted picture due to horizontal transmission and blending. Moreover, the units of cultural transmission must be communicable concepts, rather than conveniently measurable attributes, and relatedness between elements of culture often resides at the conceptual level, something not captured by phylogenetic methods, which focus on measurable attributes. (For example, mortars and pestles are as related as two artifacts could be, despite little similarity at the attribute level.) This paper introduces a new, cognitively inspired framework for chronicling material cultural history, building on Lipo's (2005) network-based computational approach. We show that by incorporating not just superficial attributes of artifact samples (e.g. fluting) but also conceptual knowledge (e.g. information about function), a different pattern of cultural ancestry emerges.

q-bio.PE↗

arXiv2019

Modeling the Role of Context Dependency in the Recognition and Manifestation of Entrepreneurial Opportunity

The paper uses the SCOP theory of concepts to model the role of environmental context on three levels of entrepreneurial opportunity: idea generation, idea development, and entrepreneurial decision. The role of contextual-fit in the generation and development of ideas is modeled as the collapse of their superposition state into one of the potential states that composes this superposition. The projection of this collapsed state on the socio-economic basis results in interference of the developed idea with the perceptions of the supporting community, undergoing an eventual collapse for an entrepreneurial decision that reflects the shared vision of its stakeholders. The developed idea may continue to evolve due to continuous or discontinuous changes in the environment. The model offers unique insights into the effects of external influences on entrepreneurial decisions.

q-bio.NC↗

arXiv2019

A Conceptual Network-Based Approach to Inferring the Cultural Evolutionary History of the Baltic Psaltery

The application of conventional phylogenetic techniques for inferring cultural history is problematic due to differences in the nature of information transmission in biological and cultural realms. In culture, units of transmission are not just measurable attributes, but communicable concepts. Therefore, relatedness amongst cultural elements often resides at the conceptual level not captured by traditional phylogenetic methods. This paper takes a cognitively inspired approach to analyzing material cultural history. We show that combining data for physical attributes of cultural artifacts with conceptual information can uncover cultural influences among different ethnolinguistic groups, and reveal new patterns of cultural ancestry. Using the Baltic psaltery, a musical instrument with a well-documented ethnographic and archaeological record, we recovered a previously unacknowledged pattern of historical relationship that is more congruent with geographical distribution and temporal data than is obtained with other approaches.

cs.DL↗

arXiv2019

Quantum entanglement in physical and cognitive systems: a conceptual analysis and a general representation

We provide a general description of the phenomenon of entanglement in bipartite systems, as it manifests in micro and macro physical systems, as well as in human cognitive processes. We do so by observing that when genuine coincidence measurements are considered, the violation of the 'marginal laws', in addition to the Bell-CHSH inequality, is also to be expected. The situation can be described in the quantum formalism by considering the presence of entanglement not only at the level of the states, but also at the level of the measurements. However, at the "local'" level of a specific joint measurement, a description where entanglement is only incorporated in the state remains always possible, by adopting a fine-tuned tensor product representation. But contextual tensor product representations should only be considered when there are good reasons to describe the outcome-states as (non-entangled) product states. This will not in general be true, hence, the entangement resource will have to generally be allocated both in the states and in the measurements. In view of the numerous violations of the marginal laws observed in physics' laboratories, it remains unclear to date if entanglement in micro-physical systems is to be understood only as an 'entanglement of the states', or also as an 'entanglement of the measurements'. But even if measurements would also be entangled, the corresponding violation of the marginal laws (no-signaling conditions) would not for this imply that a superluminal communication would be possible.

q-bio.NC↗

arXiv2018

Quantum Theory Methods as a Possible Alternative for the Double-Blind Gold Standard of Evidence-Based Medicine: Outlining a New Research Program

We motivate the possibility of using notions and methods derived from quantum physics, and more specifically from the research field known as 'quantum cognition', to optimally model different situations in the field of medicine, its decision-making processes and ensuing practices, particularly in relation to chronic and rare diseases. This also as a way to devise alternative approaches to the generally adopted double-blind gold standard.

q-bio.NC↗

arXiv2018

Modeling Meaning Associated with Documental Entities: Introducing the Brussels Quantum Approach

We show that the Brussels operational-realistic approach to quantum physics and quantum cognition offers a fundamental strategy for modeling the meaning associated with collections of documental entities. To do so, we take the World Wide Web as a paradigmatic example and emphasize the importance of distinguishing the Web, made of printed documents, from a more abstract meaning entity, which we call the Quantum Web, or QWeb, where the former is considered to be the collection of traces that can be left by the latter, in specific measurements, similarly to how a non-spatial quantum entity, like an electron, can leave localized traces of impact on a detection screen. The double-slit experiment is extensively used to illustrate the rationale of the modeling, which is guided by how physicists constructed quantum theory to describe the behavior of the microscopic entities. We also emphasize that the superposition principle and the associated interference effects are not sufficient to model all experimental probabilistic data, like those obtained by counting the relative number of documents containing certain words and co-occurrences of words. For this, additional effects, like context effects, must also be taken into consideration.

cs.IR↗

arXiv2018

Modeling Human Decision-making: An Overview of the Brussels Quantum Approach

We present the fundamentals of the quantum theoretical approach we have developed in the last decade to model cognitive phenomena that resisted modeling by means of classical logical and probabilistic structures, like Boolean, Kolmogorovian and, more generally, set theoretical structures. We firstly sketch the operational-realistic foundations of conceptual entities, i.e. concepts, conceptual combinations, propositions, decision-making entities, etc. Then, we briefly illustrate the application of the quantum formalism in Hilbert space to represent combinations of natural concepts, discussing its success in modeling a wide range of empirical data on concepts and their conjunction, disjunction and negation. Next, we naturally extend the quantum theoretical approach to model some long-standing `fallacies of human reasoning', namely, the `conjunction fallacy' and the `disjunction effect'. Finally, we put forward an explanatory hypothesis according to which human reasoning is a defined superposition of `emergent reasoning' and `logical reasoning', where the former generally prevails over the latter. The quantum theoretical approach explains human fallacies as the consequence of genuine quantum structures in human reasoning, i.e. `contextuality', `emergence', `entanglement', `interference' and `superposition'. As such, it is alternative to the Kahneman-Tversky research programme, which instead aims to explain human fallacies in terms of `individual heuristics and biases'.

q-bio.NC↗

arXiv2018

From Quantum Axiomatics to Quantum Conceptuality

Since its inception, many physicists have seen in quantum mechanics the possibility, if not the necessity, of bringing cognitive aspects into the play, which were instead absent, or unnoticed, in the previous classical theories. In this article, we outline the path that led us to support the hypothesis that our physical reality is fundamentally conceptual-like and cognitivistic-like. However, contrary to the 'abstract ego hypothesis' introduced by John von Neumann and further explored, in more recent times, by Henry Stapp, our approach does not rely on the measurement problem as expressing a possible 'gap in physical causation', which would point to a reality lying beyond the mind-matter distinction. On the contrary, in our approach the measurement problem is considered to be essentially solved, at least for what concerns the origin of quantum probabilities, which we have reasons to believe they would be epistemic. Our conclusion that conceptuality and cognition would be an integral part of all physical processes comes instead from the observation of the striking similarities between the non-spatial behavior of the quantum micro-physical entities and that of the human concepts. This gave birth to a new interpretation of quantum mechanics, called the 'conceptualistic interpretation', currently under investigation within our group in Brussels.

quant-ph↗

arXiv2018

Quantum cognition goes beyond-quantum: modeling the collective participant in psychological measurements

In psychological measurements, two levels should be distinguished: the 'individual level', relative to the different participants in a given cognitive situation, and the 'collective level', relative to the overall statistics of their outcomes, which we propose to associate with a notion of 'collective participant'. When the distinction between these two levels is properly formalized, it reveals why the modeling of the collective participant generally requires beyond-quantum - non-Bornian - probabilistic models, when sequential measurements at the individual level are considered, and this though a pure quantum description remains valid for single measurement situations.

q-bio.NC↗

arXiv2018

Towards a Quantum World Wide Web

We elaborate a quantum model for the meaning associated with corpora of written documents, like the pages forming the World Wide Web. To that end, we are guided by how physicists constructed quantum theory for microscopic entities, which unlike classical objects cannot be fully represented in our spatial theater. We suggest that a similar construction needs to be carried out by linguists and computational scientists, to capture the full meaning carried by collections of documental entities. More precisely, we show how to associate a quantum-like 'entity of meaning' to a 'language entity formed by printed documents', considering the latter as the collection of traces that are left by the former, in specific results of search actions that we describe as measurements. In other words, we offer a perspective where a collection of documents, like the Web, is described as the space of manifestation of a more complex entity - the QWeb - which is the object of our modeling, drawing its inspiration from previous studies on operational-realistic approaches to quantum physics and quantum modeling of human cognition and decision-making. We emphasize that a consistent QWeb model needs to account for the observed correlations between words appearing in printed documents, e.g., co-occurrences, as the latter would depend on the 'meaning connections' existing between the concepts that are associated with these words. In that respect, we show that both 'context and interference (quantum) effects' are required to explain the probabilities calculated by counting the relative number of documents containing certain words and co-ocurrrences of words.

cs.AI↗

arXiv2017

On the Conceptuality Interpretation of Quantum and Relativity Theories

How can we explain the strange behavior of quantum and relativistic entities? Why do they behave in ways that defy our intuition about how physical entities should behave, considering our ordinary experience of the world around us? In this article, we address these questions by showing that the comportment of quantum and relativistic entities is not that strange after all, if we only consider what their nature might possibly be: not an objectual one, but a conceptual one. This not in the sense that quantum and relativistic entities would be human concepts, but in the sense that they would share with the latter a same conceptual nature, similarly to how electromagnetic and sound waves, although very different entities, can share a same undulatory nature. When this hypothesis is adopted, i.e., when a 'conceptuality interpretation' about the deep nature of physical entities is taken seriously, many of the interpretational difficulties disappear and our physical world is back making sense, though our view of it becomes radically different from what our classical prejudice made us believe in the first place.

physics.hist-ph↗

arXiv2017

Spin and Wind Directions I: Identifying Entanglement in Nature and Cognition

We present a cognitive psychology experiment where participants were asked to select pairs of spatial directions that they considered to be the best example of 'Two Different Wind Directions'. Data are shown to violate the CHSH version of Bell's inequality with the same magnitude as in typical Bell-test experiments with entangled spins. Wind directions thus appear to be conceptual entities connected through meaning, in human cognition, in a similar way as spins appear to be entangled in experiments conducted in physics laboratories. This is the first part of a two-part article. In the second part we present a symmetrized version of the same experiment for which we provide a quantum modeling of the collected data in Hilbert space.

q-bio.NC↗

arXiv2017

Spin and Wind Directions II: A Bell State Quantum Model

In the first half of this two-part article, we analyzed a cognitive psychology experiment where participants were asked to select pairs of directions that they considered to be the best example of 'Two Different Wind Directions', and showed that the data violate the CHSH version of Bell's inequality, with same magnitude as in typical Bell-test experiments in physics. In this second part, we complete our analysis by presenting a symmetrized version of the experiment, still violating the CHSH inequality but now also obeying the marginal law, for which we provide a full quantum modeling in Hilbert space, using a singlet state and suitably chosen product measurements. We also address some of the criticisms that have been recently directed at experiments of this kind, according to which they would not highlight the presence of genuine forms of entanglement. We explain that these criticisms are based on a view of entanglement that is too restrictive, thus unable to capture all possible ways physical and conceptual entities can connect and form systems behaving as a whole. We also provide an example of a mechanical model showing that the violations of the marginal law and Bell inequalities are generally to be associated with different mechanisms.

q-bio.NC↗