Academia is a competitive environment. Early Career Researchers (ECRs) are limited in experience and resources and especially need achievements to secure and expand their careers. To help with these issues, this book offers a new approach for conducting research using the combination of mindsponge innovative thinking and Bayesian analytics. This is not just another analytics book. 1. A new perspective on psychological processes: Mindsponge is a novel approach for examining the human mind’s information processing mechanism. This conceptual framework is used (...) to construct models in studies. The framework is highly flexible and widely applicable for many different types of information processes. The mindsponge approach can help researchers discover interesting ideas or even formulate their very own theories when investigating psychosocial phenomena. This approach brings a fresh wind to the current landscape of social sciences and humanities (SSH). 2. Easy-to-follow analysis protocol: The Bayesian Mindsponge Framework (BMF analytics) is useful in terms of computing and visualizing power but also easy to learn and apply. Contrary to being intimidating, the Bayesian analytics section of this book is presented in a reader-friendly manner with a detailed yet clear step-by-step procedure. Examples are from published BMF articles, allowing readers to immediately practice the method and quickly create their own applications. With educational purposes in mind, the book is very suitable for ECRs who are looking to innovate their research methods. 3. Advocating for low-cost, high-quality research: Doing science can be very costly. Mindsponge innovative thinking and BMF analytics help produce impactful studies using openly available data on online repositories. This is based on the authors’ previous works and experiences. The book presents examples of employing the open R package bayesvl on secondary data from different sources. With less financial constraints, researchers can have more freedom of thought to pursue their curiosity and creativity. ECRs in low- and middle-income countries may find this aspect crucial in their careers. 4. Support and collaboration: The authors share their insights from experiences in the academic publishing system to help readers get through the processes of manuscript writing and peer-reviewing more easily. The authors are also ready to support other researchers with further inquiries and collaboration opportunities at the following website, mindsponge(dot)info. This book is for: a) ECRs whose only abundant resources are their innovation capacity and strength of will; b) Researchers in SSH who want to explore a novel approach to thinking and study conducting; c) Low- and middle-income countries’ researchers looking for a cost-effective research protocol; and, d) Innovative thinkers who want to turn their interesting thoughts into good publications. (shrink)

The study of cultural evolution has taken on an increasingly interdisciplinary and diverse approach in explicating phenomena of cultural transmission and adoptions. Inspired by this computational movement, this study uses Bayesian networks analysis, combining both the frequentist and the Hamiltonian Markov chain Monte Carlo (MCMC) approach, to investigate the highly representative elements in the cultural evolution of a Vietnamese city’s architecture in the early 20th century. With a focus on the façade design of 68 old houses in Hanoi’s (...) Old Quarter (based on 78 data lines extracted from 248 photos), the study argues that it is plausible to look at the aesthetics, architecture, and designs of the house façade to find traces of cultural evolution in Vietnam, which went through more than six decades of French colonization and centuries of sociocultural influence from China. The in-depth technical analysis, though refuting the presumed model on the probabilistic dependency among the variables, yields several results, the most notable of which is the strong influence of Buddhism over the decorations of the house façade. Particularly, in the top 5 networks with the best Bayesian Information Criterion (BIC) scores and p<0.05, the variable for decorations (DC) always has a direct probabilistic dependency on the variable B for Buddhism. The paper then checks the robustness of these models using Hamiltonian MCMC method and find the posterior distributions of the models’ coefficients all satisfy the technical requirement. Finally, this study suggests integrating Bayesian statistics in the social sciences in general and for the study of cultural evolution and architectural transformation in particular. (shrink)

We argue that Hamiltonian mechanics is more fundamental than Lagrangian mechanics. Our argument provides a non-metaphysical strategy for privileging one formulation of a theory over another: ceteris paribus, a more general formulation is more fundamental. We illustrate this criterion through a novel interpretation of classical mechanics, based on three physical conditions. Two of these conditions suffice for recovering Hamiltonian mechanics. A third condition is necessary for Lagrangian mechanics. Hence, Lagrangian systems are a proper subset of Hamiltonian systems. (...) Finally, we provide a geometric interpretation of the principle of stationary action and rebut arguments for privileging Lagrangian mechanics. (shrink)

La, V. P., & Vuong, Q. H. (2019). bayesvl: Visually learning the graphical structure of Bayesian networks and performing MCMC with ‘Stan’. The Comprehensive R Archive Network (CRAN).

The exponential growth of social data both in volume and complexity has increasingly exposed many of the shortcomings of the conventional frequentist approach to statistics. The scientific community has called for careful usage of the approach and its inference. Meanwhile, the alternative method, Bayesian statistics, still faces considerable barriers toward a more widespread application. The bayesvl R package is an open program, designed for implementing Bayesian modeling and analysis using the Stan language’s no-U-turn (NUTS) sampler. The package combines the ability (...) to construct Bayesian network models using directed acyclic graphs (DAGs), the Markov chain Monte Carlo (MCMC) simulation technique, and the graphic capability of the ggplot2 package. As a result, it can improve the user experience and intuitive understanding when constructing and analyzing Bayesian network models. A case example is offered to illustrate the usefulness of the package for Big Data analytics and cognitive computing. (shrink)

Chương trình bayesvl được thiết kế với định hướng sư phạm, hỗ trợ các nhà nghiên cứu ngành khoa học xã hội và nhân văn sử dụng mô hình lưới Bayesian, mô phỏng MCMC, hình ảnh hóa các thông số kĩ thuật và phân tích dữ liệu xã hội. bayesvl được phát hành chính thức trên hệ thống thư viện chuẩn của R là Comprehensive R Archive Network (CRAN) vào tháng 5 năm 2019.

An untold aspect of the inexpensiveness of bayesvl was that its developers also ate very little, mostly vegetables.

Products made from animal fur and skin have been a major part of human civilization. However, in modern society, the unsustainable consumption of these products – often considered luxury goods – has many negative environmental impacts. This study explores how people’s perceptions of biodiversity affect their attitudes and behaviors toward consumption. To investigate the information process deeper, we add the moderation of beliefs about biodiversity loss. Following the Bayesian Mindsponge Framework (BMF) analytics, we use mindsponge-based reasoning for constructing conceptual models (...) and employ Bayesian analysis aided by Markov Chain Monte Carlo (MCMC) algorithms on a dataset of 535 Vietnamese urban residents. The results show that people’s preference for using products made from animal skin/fur is negatively associated with perceived consequences of biodiversity loss when they believe biodiversity loss is real and a major problem. In contrast, if urban residents believe biodiversity loss is unreal or not a significant issue, the association between perceived consequences of biodiversity loss and personal preference happens in the opposite direction. The same effects of biodiversity loss perception on people’s possession of skin/fur products was not found, indicating a more complex information process on behaviors compared to attitudes. Nevertheless, in the scenario that people believe biodiversity loss is not a significant issue, the higher the perceived consequences of biodiversity loss are, the greater number of animal-based products they likely own. Our results suggest that policymakers should not neglect the factor of personal belief besides knowledge and awareness in environmental campaigns. (shrink)

Products made from animal fur and skin have been a major part of human civilization. However, in modern society, the unsustainable consumption of these products – often considered luxury goods – has many negative environmental impacts. This study explores how people’s perceptions of biodiversity affect their attitudes and behaviors toward consumption. To investigate the information process deeper, we add the moderation of beliefs about biodiversity loss. Following the Bayesian Mindsponge Framework (BMF) analytics, we use mindsponge-based reasoning for constructing conceptual models (...) and employ Bayesian analysis aided by Markov Chain Monte Carlo (MCMC) algorithms on a dataset of 535 Vietnamese urban residents. The results show that people’s preference for using products made from animal skin/fur is negatively associated with perceived consequences of biodiversity loss when they believe biodiversity loss is real and a major problem. In contrast, if urban residents believe biodiversity loss is unreal or not a significant issue, the association between perceived consequences of biodiversity loss and personal preference happens in the opposite direction. The same effects of biodiversity loss perception on people’s possession of skin/fur products was not found, indicating a more complex information process on behaviors compared to attitudes. Nevertheless, in the scenario that people believe biodiversity loss is not a significant issue, the higher the perceived consequences of biodiversity loss are, the greater number of animal-based products they likely own. Our results suggest that policymakers should not neglect the factor of personal belief besides knowledge and awareness in environmental campaigns. (shrink)

Mathematically, gauge theories are extraordinarily rich --- so rich, in fact, that it can become all too easy to lose track of the connections between results, and become lost in a mass of beautiful theorems and properties: indeterminism, constraints, Noether identities, local and global symmetries, and so on. -/- One purpose of this short article is to provide some sort of a guide through the mathematics, to the conceptual core of what is actually going on. Its focus is on the (...) Lagrangian, variational-problem description of classical mechanics, from which the link between gauge symmetry and the apparent violation of determinism is easy to understand; only towards the end will the Hamiltonian description be considered. -/- The other purpose is to warn against adopting too unified a perspective on gauge theories. It will be argued that the meaning of the gauge freedom in a theory like general relativity is (at least from the Lagrangian viewpoint) significantly different from its meaning in theories like electromagnetism. The Hamiltonian framework blurs this distinction, and orthodox methods of quantization obliterate it; this may, in fact, be genuine progress, but it is dangerous to be guided by mathematics into conflating two conceptually distinct notions without appreciating the physical consequences. (shrink)

Working in academia is challenging, even more so for those with limited resources and opportunities. Researchers around the world do not have equal working conditions. The paper presents the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. The community coaching method is envisioned by three science philosophies (cost-effectiveness, transparency spirit, and proactive (...) attitude) and established and operated based on the Serendipity-Mindsponge-3D knowledge (SM3D) management framework (i.e., mindsponge thinking and Bayesian Mindsponge Framework analytics serve as the coaching program's foundational theory and analytical tools). The coaching method also embraces Open Science's values for lowering the cost of doing science and encouraging the trainees to be transparent, which is expected to facilitate the self-correcting mechanism of science through open data, open review, and open dialogue. Throughout the training process, members are central beneficiaries by gaining research knowledge and skills, acquiring publication as the training's product, and shifting their mindsets from “I can't do it” to “I can do it,” and at the same time transforming a mentee to be ready for a future mentor's role. The coaching method is thus one of the members, for the member, by the members. -/- • The paper provides the structure, operation method, and conceptual framework of the SM3D Portal's community coaching method, which is built to help Early Career Researchers (ECRs) and researchers in low-resource settings overcome the obstacle of inequality and start their career progress. • The paper presents three major science philosophies envisioning the establishment and operation of scholarly community coaching. • The paper employs the mindsponge theory and BMF analytics to construct a conceptual framework explaining how an environment is created to help shift members’ mindsets from “I can't do it” to “I can do it.”. (shrink)

I defend the extremist position that the fundamental ontology of the world consists of a vector in Hilbert space evolving according to the Schrödinger equation. The laws of physics are determined solely by the energy eigenspectrum of the Hamiltonian. The structure of our observed world, including space and fields living within it, should arise as a higher-level emergent description. I sketch how this might come about, although much work remains to be done.

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers yield precisely (...) the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind–brain problem is a formidable task because no physical mechanism is able to explain how the brain generates the unobservable, inner psychological world of conscious experiences and how in turn those conscious experiences steer the (...) underlying brain processes toward desired behavior. Yet, this setback does not establish that consciousness is non-physical. Modern quantum physics affirms the interplay between two types of physical entities in Hilbert space: unobservable quantum states, which are vectors describing what exists in the physical world, and quantum observables, which are operators describing what can be observed in quantum measurements. Quantum no-go theorems further provide a framework for studying quantum brain dynamics, which has to be governed by a physically admissible Hamiltonian. Comprising consciousness of unobservable quantum information integrated in quantum brain states explains the origin of the inner privacy of conscious experiences and revisits the dynamic timescale of conscious processes to picosecond conformational transitions of neural biomolecules. The observable brain is then an objective construction created from classical bits of information, which are bound by Holevo’s theorem, and obtained through the measurement of quantum brain observables. Thus, quantum information theory clarifies the distinction between the unobservable mind and the observable brain, and supports a solid physical foundation for consciousness research. (shrink)

We study the question of how to decompose Hilbert space into a preferred tensor-product factorization without any pre-existing structure other than a Hamiltonian operator, in particular the case of a bipartite decomposition into "system" and "environment." Such a decomposition can be defined by looking for subsystems that exhibit quasi-classical behavior. The correct decomposition is one in which pointer states of the system are relatively robust against environmental monitoring (their entanglement with the environment does not continually and dramatically increase) and (...) remain localized around approximately-classical trajectories. We present an in-principle algorithm for finding such a decomposition by minimizing a combination of entanglement growth and internal spreading of the system. Both of these properties are related to locality in different ways. This formalism could be relevant to the emergence of spacetime from quantum entanglement. (shrink)

In the first month of 2024, there was a significant increase in the number of downloads for the Bayesian stats / MCMC computing program, bayesvl, developed by AISDL running on R and Stan. The following RDocumentation (CRAN) graph illustrates the noticeable leap in data for January 2024.

In this paper I argue that we can solve the interpretation problem of quantum mechanics and the question of ontology of Quantum Field Theory on the basis of simple metaphysical position: The connection of the phase space with the ancient Theory of Logi of Beings, which is, by giving ontological meaning to the entities which "live" at the phase space, the Hamiltonian or Lagrangian formalism. There is a physical subject of such functions and it is the logos of a (...) being. Therefore we can refer to the logical space as the total sum of logi of being. The result of this position is that we can attribute to the wave function a physical meaning, a special case of logos of a being and also give an ontological meaning at a quantum field. The developed metaphysical scheme can interpret the quantum paradoxes, by using the commonly accepted mathematical formalism. It can also interpret certain issues of Quantum Field Theory, although further study of this topic is necessary. (shrink)

Five years ago, on May 24, 2019, the computer program ‘bayesvl’ was officially published on R under the name “bayesvl: Visually Learning the Graphical Structure of Bayesian Networks and Performing MCMC with ‘Stan’”. This program (or package) was developed by two founders of the SM3D Portal, Vuong Quan Hoang and La Viet Phuong, to improve the productivity of conducting social research. The package was designed with a pedagogical orientation, supporting users in familiarizing themselves with Bayesian statistical methods, MCMC (...) simulation, and visualization of technical diagnoses and results. (shrink)

Compared with traditional statistics, only a few social scientists employ Bayesian analyses. The existing software programs for implementing Bayesian analyses such as OpenBUGS, WinBUGS, JAGS, and rstanarm can be daunting given that their complex computer codes involve a steep learning curve. In contrast, this paper introduces a new open software for implementing Bayesian network modelling and analysis: the bayesvl R package. The package aims at providing an intuitive gateway for beginners of Bayesian statistics to construct and analyse mathematical models in (...) social sciences... (shrink)

We study the conservation of energy, or lack thereof, when measurements are performed in quantum mechanics. The expectation value of the Hamiltonian of a system changes when wave functions collapse in accordance with the standard textbook treatment of quantum measurement, but one might imagine that the change in energy is compensated by the measuring apparatus or environment. We show that this is not true; the change in the energy of a state after measurement can be arbitrarily large, independent of (...) the physical measurement process. In Everettian quantum theory, while the expectation value of the Hamiltonian is conserved for the wave function of the universe, it is not constant within individual worlds. It should therefore be possible to experimentally measure violations of conservation of energy, and we suggest an experimental protocol for doing so. (shrink)

In the paper we will employ set theory to study the formal aspects of quantum mechanics without explicitly making use of space-time. It is demonstrated that von Neuman and Zermelo numeral sets, previously efectively used in the explanation of Hardy’s paradox, follow a Heisenberg quantum form. Here monadic union plays the role of time derivative. The logical counterpart of monadic union plays the part of the Hamiltonian in the commutator. The use of numerals and monadic union in the classical (...) probability resolution of Hardy’s paradox [1] is supported with the present derivation of a commutator for sets. (shrink)

A new non-Archimedean approach to interacted quantum fields is presented. In proposed approach, a field operator φ(x,t) no longer a standard tempered operator-valued distribution, but a non-classical operator-valued function. We prove using this novel approach that the quantum field theory with Hamiltonian P(φ)_4 exists and that the corresponding C^*­ algebra of bounded observables satisfies all the Haag-Kastler axioms except Lorentz covariance. We prove that the λ(φ^2n )_4,n≥2 quantum field theory models are Lorentz covariant.

Schrödinger’s equation says that the Hamiltonian is the generator of time translations. This seems to imply that any reasonable definition of time operator must be conjugate to the Hamiltonian. Then both time and energy must have the same spectrum since conjugate operators are unitarily equivalent. Clearly this is not always true: normal Hamiltonians have lower bounded spectrum and often only have discrete eigenvalues, whereas we typically desire that time can take any real value. Pauli concluded that constructing a (...) general a time operator is impossible. Here we show how the Pauli argument fails when one uses an external system to track time, so that time arises as correlations between the system and the clock. In this case, the time operator is conjugate to the clock Hamiltonian and not to the system Hamiltonian, but its eigenvalues still satisfy the Schrödinger equation for arbitrary system Hamiltonians. (shrink)

The methodology title on BMF analytics is now in its third year of service to our research community, enabling many researchers to implement their research pursuits.

A new non-Archimedean approach to interacted quantum fields is presented. In proposed approach, a field operator φ(x,t) no longer a standard tempered operator-valued distribution, but a non-classical operator-valued function. We prove using this novel approach that the quantum field theory with Hamiltonian P(φ)_4 exists and that the corresponding C^*­ algebra of bounded observables satisfies all the Haag-Kastler axioms except Lorentz covariance. We prove that the λ(φ^4 )_4 quantum field theory model is Lorentz covariant.

An analysis of the classical-quantum correspondence shows that it needs to identify a preferred class of coordinate systems, which defines a torsionless connection. One such class is that of the locally-geodesic systems, corresponding to the Levi-Civita connection. Another class, thus another connection, emerges if a preferred reference frame is available. From the classical Hamiltonian that rules geodesic motion, the correspondence yields two distinct Klein-Gordon equations and two distinct Dirac-type equations in a general metric, depending on the connection used. Each (...) of these two equations is generally-covariant, transforms the wave function as a four-vector, and differs from the Fock-Weyl gravitational Dirac equation (DFW equation). One obeys the equivalence principle in an often-accepted sense, whereas the DFW equation obeys that principle only in an extended sense. (shrink)