We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

This chapter discusses several kinds of reduction that are often found in the biomedical sciences, in contrast to reduction in fields such as physics. This includes reduction as a methodological assumption for how to investigate phenomena like complex diseases, and reduction as a conceptual tool for relating distinct models of the same phenomenon. The case of Parkinson’s disease illustrates a wide variety of ways in which reductionism is an important tool in medicine.

One might be inclined to assume, given the mouse donning its cover, that the behavior of interest in Nicole Nelson's book Model Behavior (2018) is that of organisms like mice that are widely used as “stand-ins” for investigating the causes of human behavior. Instead, Nelson's ethnographic study focuses on the strategies adopted by a community of rodent behavioral researchers to identify and respond to epistemic challenges they face in using mice as models to understand the causes of disordered human (...) behaviors associated with mental illness. Although Nelson never explicitly describes the knowledge production activities in which her behavioral geneticist research subjects engage as “exemplary”, the question of whether or not these activities constitute “model behavior(s)”—generalizable norms for engaging in scientific research—is one of the many thought-provoking questions raised by her book. As a philosopher of science interested in this question, I take it up here. (shrink)

Over the past 25 years, several new “medicines” have come screeching onto health care’s various platforms, including narrative medicine, personalized medicine, precision medicine and person-centred medicine. Philosopher Miriam Solomon calls the first three of these movements different “ways of knowing” or “methods,” and argues that they are each a response to shortcomings of methods that came before them. They should also be understood as reactions to the current dominant model of medicine. In this article, I will describe our dominant (...) model, which I call “the new medical model.” I will argue that several towering problems in modern medicine can be traced to its philosophical foundations, which calls for philosophical analysis. (shrink)

Animal models have long been used to investigate human mental disorders, including depression, anxiety, and schizophrenia. This practice is usually justified in terms of the benefits (to humans) outweighing the costs (to the animals). I argue on utility maximization grounds that we should phase out animal models in neuropsychiatric research. Our leading theories of how human minds and behavior evolved invoke sociocultural factors whose relation to nonhuman minds, societies, and behavior has not been homologized. Thus it is not at all (...) clear that we are gaining the epistemic or clinical benefits we want from this animal-based research. (shrink)

Business models for biomedical research prescribe decentralization due to market selection pressures. I argue that decentralized biomedical research does not match four normative philosophical models of the role of values in science. Non-epistemic values affect the internal stages of for-profit biomedical science. Publication planning, effected by Contract Research Organizations, inhibits mechanisms for transformative criticism. The structure of contracted research precludes attribution of responsibility for foreseeable harm resulting from methodological choices. The effectiveness of business strategies leads to overrepresentation (...) of profit values versus the values of the general public. These disconnects in respect to the proper role of values in science results from structural issues ultimately linked to the distinct goals of business versus applied science, and so it seems likely that disconnects will also be found in other dimensions of attempts to combine business and science. The volume and integration in the publishing community of decentralized biomedical research imply that the entire community of biomedical research science cannot match the normative criteria of community-focused models of values in science. Several proposals for changing research funding structure might successfully relieve market pressures that drive decentralization. (shrink)

Biomedical science has been remarkably successful in explaining illness by categorizing diseases and then by identifying localizable lesions such as a virus and neoplasm in the body that cause those diseases. Not surprisingly, researchers have aspired to apply this powerful paradigm to addiction. So, for example, in a review of the neuroscience of addiction literature, Hyman and Malenka (2001, p. 695) acknowledge a general consensus among addiction researchers that “[a]ddiction can appropriately be considered as a chronic medical illness.” Like (...) other diseases, “Once addiction has taken hold, it tends to follow a chronic course.” (Koob and La Moal 2006, p. ?). Working from this perspective, much effort has gone into characterizing the symptomology of addiction and the brain changes that underlie them. Evidence for involvement of dopamine transmission changes in the ventral tegmental area (VTA) and nucleus accumbens (NAc) have received the greatest attention. Kauer and Malenka (2007, p. 844) put it well: “drugs of abuse can co-opt synaptic plasticity mechanisms in brain circuits involved in reinforcement and reward processing”. Our goal in this chapter to provide an explicit description of the assumptions of medical models, the different forms they may take, and the challenges they face in providing explanations with solid evidence of addiction. <br>. (shrink)

There has recently been an explosion of formal models of signalling, which have been developed to learn about different aspects of meaning. This paper discusses whether that success can also be used to provide an original naturalistic theory of meaning in terms of information or some related notion. In particular, it argues that, although these models can teach us a lot about different aspects of content, at the moment they fail to support the idea that meaning just is some kind (...) of information. As an alternative, I suggest a more modest approach to the relationship between informational notions used in models and semantic properties in the natural world. (shrink)

We discuss potential biorisks from large language models (LLMs). AI assistants based on LLMs such as ChatGPT have been shown to significantly reduce barriers to entry for actors wishing to synthesize dangerous, potentially novel pathogens and chemical weapons. The harms from deploying such bioagents could be further magnified by AI-assisted misinformation. We endorse several policy responses to these dangers, including prerelease evaluations of biomedical AIs by subject-matter experts, enhanced surveillance and lab screening procedures, restrictions on AI training data, and (...) access controls on biomedical AI. We conclude with a suggestion about future research directions in bioethics. (shrink)

In this paper, we discuss the processes of racialisation on the example of biomedical research. We argue that applying the concept of racialisation in biomedical research can be much more precise, informative and suitable than currently used categories, such as race and ethnicity. For this purpose, we construct a model of the different processes affecting and co-shaping the racialisation of an individual, and consider these in relation to biomedical research, particularly to studies on hypertension. We finish (...) with a discussion on the potential application of our proposition to institutional guidelines on the use of racial categories in biomedical research. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of (...) these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

I argue that verbal models should be included in a philosophical account of the scientific practice of modelling. Weisberg (2013) has directly opposed this thesis on the grounds that verbal structures, if they are used in science, only merely describe models. I look at examples from Darwin's On the Origin of Species (1859) of verbally constructed narratives that I claim model the general phenomenon of evolution by natural selection. In each of the cases I look at, a particular scenario (...) is described that involves at least some fictitious elements but represents the salient causal components of natural selection. I pronounce the importance of prioritising observation of scientific practice for the philosophy of modelling and I suggest that there are other likely model types that are excluded from philosophical accounts. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises (...) ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in (...) order to provide a more rational basis for using ontologies and related artifacts to advance integration of data and enhance interoperability of associated reasoning systems. We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies as long as the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models. (shrink)

Our philosophical understanding of mental illness is being shaped by neuroscience. However, it has the paradoxical effect of igniting two radically opposed groups of philosophical views. On one side, skepticism and denialism assume that, lacking clear biological mechanisms and etiologies for most mental illnesses, we should infer they are constructions best explained by means of social factors. This is strongly associated with medical nihilism: it considers psychiatry more harmful than benign. On the other side of the divide, naturalism and reductionism (...) are on the look for failures in the biological functioning of the organism whenever a genuine mental illness occurs. Psychiatry as currently practiced, accordingly, exhibits the gaps of an ongoing research programme; a yet to be completed neuroscience would link mental illnesses with identifiable biological mechanisms. Both sides of this divide claim to be fostered by scientific discoveries and advances in neuroscience, when taken at face value. Against this background, we argue instead for a modest view. To that end, we draw attention to some nuances in the scientific realism debate. While contending that neuroscientific theories and models aim to provide true representations of their target systems, and can justifiably claim to have attained some, we argue that our confidence should not be placed beforehand in specific features of these scientific representations. Hence, it would be unwarranted to extract morals for psychiatry from posits (or their absence) in neuroscientific explanations of mental illnesses. To illustrate our position, we examine some recent discoveries in neuroscience concerning bipolar disorder. We conclude by linking our topic to a broader issue in the philosophy of medicine: insofar as psychiatry is a biomedical specialty, its classifications of health and disease are guided by pragmatic concerns, as well as by scientific discoveries. (shrink)

Weighing competing obligations and achieving the “greatest balance” of right over wrong guides an individual, an agency or a country in determining what ought to be done in an ethically challenging situation. Conducting controlled human infection model (CHIM) studies in India is one such situation. The ethical challenge in conducting a CHIM study lies in completing the difficult task of introducing standardised, attenuated strains of micro-organisms into normal healthy volunteers, at the same time ensuring the safety of these healthy (...) individuals from potential and completely informed risks in a fashion that is transparent and accountable. The bar is further raised against the background of already fragile public confidence in biomedical research in India; especially when “deliberate” introduction of microbial agents into healthy individuals is involved, with the larger altruistic objective of gain to society as a whole. -/- This paper discusses the uses of CHIM studies with respect to the larger scientific Indian research enterprise of the 21st century. It further explores etic and emic perspectives in conducting such trials in India and seeks to generate an ethical coherence to the justification for conducting CHIM studies in India. The paper deliberates on ethical issues arising out of conducting CHIM studies and reflects on how developing the capacity for CHIM studies in India is likely to strengthen the health research and development sector in the country. -/- . (shrink)

Patient-centered care (PCC) is an approach to healthcare that values patients’ preference, need, and autonomy. The estimation of healthcare partly depends on how well PCC is implemented. In addition, the result of clinical research can inform the assessment of the implementation of PCC. In clinical research, health-related quality of life (HRQL) theoretical models offer a conceptual toolbox that informs clinical research and guides the hypotheses generation. Wilson and Cleary (1995) developed the most widely used HRQL theoretical model (Bakas et (...) al., 2012). Ontological assumptions about causation in Wilson and Cleary’s model will influence which kind of hypotheses will be generated. I will argue that Wilson and Cleary’s model instilled a kind of causal bias into hypothesis generation in clinical research on HRQL. Causation from biomedical factors to non-biomedical factors is frequently hypothesized while causation from non-biomedical factors to biomedical factors is rarely hypothesized. It leads to that the interdependence and interaction between constituent parts of patients are ignored, which is an obstacle to the implementation of PCC. In addition, I will propose a revised HRQL theoretical model which avoids the causal bias brought by Wilson and Cleary’s model. By doing so, I leave room for the improvement of the practice of healthcare by analyzing the ontological assumptions about causation. (shrink)

Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understanding have arguably not been achieved in normal and disease biology, including neurodegenerative disease and cancer pathobiology. I argue for a "mechanism-plus-X" paradigm, where mainstay elements of mechanistic models such (...) as hierarchy and correlation are combined with nomological principles such as general operative rules and generative principles. Depending on the question at hand and the nature of the inquiry, X could range from proven physical laws to speculative biological generalizations, such as the notional principle of cellular synchrony. I argue that the "mechanism-plus-X" approach should ultimately aim to move biological inquiries out of the deadlock of oft-encountered mechanistic pitfalls and reposition biology to its former capacity of illuminating fundamental truths about the world. (shrink)

Elimination controversies are ubiquitous in philosophy and the human sciences. For example, it has been suggested that human races, hysteria, intelligence, mental disorder, propositional attitudes such as beliefs and desires, the self, and the super-ego should be eliminated from the list of respectable entities in the human sciences. I argue that eliminativist proposals are often presented in the framework of an oversimplified “phlogiston model” and suggest an alternative account that describes ontological elimination on a gradual scale between criticism of (...) empirical assumptions and conceptual choices. (shrink)

Introduction: the objective of this investigation is to analyses the advances of understanding in the epigenetic processes and to extract conclusions concerning the information-based evolution from the perspective of the Informational Model of Consciousness (IMC). Analysis of epigenetic mechanisms: it is shown that the study of the epigenetic mechanisms are of increasing interest not only to discover the responsible mechanisms of some diseases, but also to observe the acquisition and transmission mechanisms of some traits to the next generation/ transgenerations, (...) without affecting the DNA sequences. These advances were especially supported by the spectacular progresses in the high technological tools like digital microfluidic techniques and semiconductor-based detection systems, allowing to apply sequencing methods of DNA and to observe its structural modifications. The specific typical steps of the epigenetic mechanisms are analysed, showing that these mechanisms could be fully described in terms of information, as signal transmission agents embodying or disembodying information in three different stages and under specific conditions, including especially the signal persistence as a main conditional epigenetic factor. Results concerning the information-assisted evolution from the perspective of IMC: the epigenetic mechanisms are discussed as a function of each component of the informational system of the organism, consisting in memory, decisional operability, emotional reactivity, metabolic driving processes, genetic transmission, genetic info-generator and the info-connection explaining the special extra-power properties of the mind. It is shown that the epigenetic mechanisms could be related to the specific functions of each informational component, mainly exhibiting five levels of integration of information as matter-related information, culminating with the stable integration in the procreation cells and transmission to the next generation. The results were extended to explain the transgenerational adaptive processes of isolated population groups. Conclusion: the epigenetic mechanisms discussed within IMC allow to understand the transgenerational adaptation as an information-assisted proces. (shrink)

Critics of Institutional Review Board (IRB) practices often base their charges on the claim that IRB review began with and is premised upon a "medical model" of research, and hence a "medical model" of risk. Based on this claim, they charge that IRB review, especially in the institutional Reviw boardsocial and behavioral sciences, has experienced "mission creep". This paper argues that this line of critique is fundamentally misguided. While it remains unclear what critics mean by "medical model", (...) the point of contemporary human research subjects regulation remains the same across all domains of research. That point is to protect the autonomy of human subjects, primarily through the use of informed consent. In fields as different as biomedical self-experimentation and ethnography there is the danger of losing sight of subjects' autonomy. Critiques of the so-called medical model are sometimes libertarian and sometimes utilitarian in spirit. Either way, such critiques have not yet demonstrated that these philosophical schools of thought have the resources to guard against the potential risk of harm that lexically prioritizing the autonomy of human subjects does. Precisely because IRB review recognizes that human subjects research occurs in different fields using different research methods, IRB review requires researchers to explain their particular methods, the particular risks of harm created by these methods, and the implementation of procedures by which subjects may autonomously consent to precisely those risks. (shrink)

Coherence and correspondence are classical contenders as theories of truth. In this paper we examine them instead as interacting factors in the dynamics of belief across epistemic networks. We construct an agent-based model of network contact in which agents are characterized not in terms of single beliefs but in terms of internal belief suites. Individuals update elements of their belief suites on input from other agents in order both to maximize internal belief coherence and to incorporate ‘trickled in’ elements (...) of truth as correspondence. Results, though often intuitive, prove more complex than in simpler models (Hegselmann & Krause 2002, 2006; Grim, Singer, Reade & Fisher 2015). The optimistic finding is that pressures toward internal coherence can exploit and expand on small elements of truth as correspondence is introduced into epistemic networks. Less optimistic results show that pressures for coherence can also work directly against the incorporation of truth, particularly when coherence is established first and new data is introduced later. (shrink)

According to the biomedical model of medicine, the subject of the illness event is the pathology rather than the person diagnosed with the disease. In this view, a body-self becomes a ‘patient’ body-object that can be enrolled in a therapeutic protocol, investigated, assessed, and transformed. How can it be possible for cancer patients to make sense of the opposite dimensions of their body-self and their body-diseased-object? Could a creative embodied approach enable the coping with trauma tied to the (...) experience of illness? By applying a phenomenological approach and auto-ethnographic analysis to the experience of cancer, this visual exploration provides support for rethinking the cancer event through a performative perspective. This work previews images and video material collected over ten years of haematological treatments, video dance performances and physical explorations. This work displays how processes of healing can be set in motion by creative embodied practices, physical explorations and unexpected journeys. By resisting the biomedical model and allowing the emergence of new meanings, it illustrates how dance and performative practices offer ground for transformation. (shrink)

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects (...) of scientific explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment (...) problems, economic forecasting, social science, humanistic and practical achievements. There are about 7,000 neutrosophic researchers, within 89 countries around the globe, that have produced about 4,000 publications and tenths of PhD and MSc theses, within more than two decades. This is the sixth volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation, with an introduction contains a short history of neutrosophics, together with links to the main papers and books. -/- ES: Este es el Sexto volumen de la Enciclopedia de Investigadores Neutróficos, editados a partir de materiales ofrecidos por los autores que respondieron a la invitación del editor. Los autores se enumeran alfabéticamente. La introducción contiene una breve historia de la neutrosófica, y en especial se sus impacto en latinoamérica junto con enlaces a los principales artículos y libros. Conjunto neutrosófico, lógica neutrosófica, probabilidad neutrosófica, estadística neutrosófica, medida neutrosófica, precálculo neutrosófico, cálculo neutrosófico, psicología neutrosófica, sociología neutrosófica etc., están ganando una atención significativa en resolver muchos problemas de la vida real que implican incertidumbre, imprecisión, vaguedad, incompletitud, inconsistencia e indeterminación. En los últimos años, los campos de la neutrosófica se han ampliado y aplicado en diversos campos, tales como: inteligencia artificial, minería de datos, software informática, toma de decisiones en forma incompleta / indeterminada / inconsistente sistemas de información, procesamiento de imágenes, modelado computacional, robótica, diagnóstico médico, ingeniería biomédica, problemas de inversión, previsión económica, ciencias sociales, humanística y la validación y consolidación del conocimiento científico. (shrink)

Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment (...) problems, economic forecasting, social science, humanistic and practical achievements. There are about 7,000 neutrosophic researchers, within 89 countries around the globe, that have produced about 4,000 publications and tenths of PhD and MSc theses, within more than two decades. This is the fifth volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation, with an introduction contains a short history of neutrosophics, together with links to the main papers and books. (shrink)

Automatic detection of diseases and anatomical landmarks in medical images by the use of computers is important and considered a challenging process that could help medical diagnosis and reduce the cost and time of investigational procedures and refine health care systems all over the world. Recently, gastrointestinal (GI) tract disease diagnosis through endoscopic image classification is an active research area in the biomedical field. Several GI tract disease classification methods based on image processing and machine learning techniques have been (...) proposed by diverse research groups in the recent past. However, yet effective and comprehensive deep ensemble neural network-based classification model with high accuracy classification results is not available in the literature. In this thesis, we review ways and mechanisms to use deep learning techniques to research on multi-disease computer-aided detection about gastrointestinal and identify these images. We re-trained five state-of-the-art neural network architectures, VGG16, ResNet, MobileNet, Inception-v3, and Xception on the Kvasir dataset to classify eight categories that include an anatomical landmark (pylorus, z-line, cecum), a diseased state (esophagitis, ulcerative colitis, polyps), or a medical procedure (dyed lifted polyps, dyed resection margins) in the Gastrointestinal Tract. Our models have showed results with a promising accuracy which is a remarkable performance with respect to the state-of-the-art approaches. The resulting accuracies achieved using VGG, ResNet, MobileNet, Inception-v3, and Xception were 98.3%, 92.3%, 97.6%, 90% and 98.2%, respectively. As it appears, the most accurate result has been achieved when retraining VGG16 and Xception neural networks with accuracy reache to 98% due to its high performance on training on ImageNet dataset and internal structure that support classification problems. (shrink)

The goals and tasks of neuroethics formulated by Farahany and Ramos (2020) link epistemological and methodological issues with ethical and social values. The authors refer simultaneously to the social significance and scientific reliability of the BRAIN Initiative. They openly argue that neuroethics should not only examine neuroscientific research in terms of “a rigorous, reproducible, and representative neuroscience research process” as well as “explore the unique nature of the study of the human brain through accurate and representative models of its function (...) and dysfunction”, but also its responsibilities or social consequences. In our commentary, we would like to concentrate on problem selection, which is shortly noticed by Farahany and Ramos, and by BRAIN Initiative’s Neuroethics Report itself. The document raises an important issue related to problem selection, which is strengthening or perpetuating existing prejudices and biases by choosing a research subject: “scientists are prompted to consider how the questions they choose to study in the laboratory might amplify existing biases.” This leads to several further problems: what constitutes bias?; how biases may be embedded in the selection of research programs?; is it possible to conduct completely unbiased research?; who should be a gatekeeper in the case of research that may amplify biases? We try to notice possible answers to these questions in the context of the research on differences (e.g., cognitive, medical, behavioral) between human populations. (shrink)

In addiction, apparently causally significant phenomena occur at a huge number of levels; addiction is affected by biomedical, neurological, pharmacological, clinical, social, and politico-legal factors, among many others. In such a complex, multifaceted field of inquiry, it seems very unlikely that all the many layers of explanation will prove amenable to any simple or straightforward, reductive analysis; if we are to unify the many different sciences of addiction while respecting their causal autonomy, then, what we are likely to need (...) is an integrative framework. In this paper, we propose the theory of “Externalist” or “4E” – for extended, embodied, embedded, and enactive – cognition, which focuses on the empirical and conceptual centrality of the wider extra-neural environment to cognitive and mental processes, as a candidate for such a framework. We begin in Section 2 by outlining how such a perspective might apply to psychiatry more generally, before turning to some of the ways it can illuminate addiction in particular: Section 3 points to a way of dissolving the classic dichotomy between the “choice model” and “disease model” in the addiction literature; Section 4 shows how 4E concepts can clarify the interplay between the addict’s brain and her environment; and Section 5 considers how these insights help to explain the success of some recovery strategies, and may help to inform the development of new ones. (shrink)

This article aims to develop a Lacanian approach to bioethics. Point of departure is the fact that both psychoanalysis and bioethics are practices of language, combining diagnostics with therapy. Subsequently, I will point out how Lacanian linguistics may help us to elucidate the dynamics of both psychoanalytical and bioethical discourse, using the movie One flew over the Cuckoo’s Nest and Sophocles’ tragedy Antigone as key examples. Next, I will explain the ‘topology’ of the bioethical landscape with the help of Lacan’s (...) three dimensions: the imaginary, the symbolical and the real. This will culminate in an assessment of the dynamics of bioethical discourse with the help of Lacan’s theorem of the four discourses. Bioethics, I will argue, is not a homogeneous discourse. Rather, four modalities of bioethical discourse can be distinguished, all of them displaying specific weaknesses and strengths, opportunities and threats. This will be elucidated with the help of two case studies, namely the debates on human reproductive technologies and on the use of animals as biomedical research models. (shrink)

The distinction between clinical research and clinical practice directs how we partition medicine and biomedical science. Reasons for a sharp distinction date historically to the work of the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, especially to its analysis of the “boundaries” between research and practice in the Belmont Report (1978). Belmont presents a segregation model of the research-practice distinction, according to which research and practice form conceptually exclusive sets of activities (...) and interventions. This model is still the standard in federal regulations today. However, the Commission’s deliberations and conclusions about the boundaries are more complicated, nuanced, and instructive than has generally been appreciated. The National Commission did not conclude that practice needs no oversight comparable to the regulation of research. It debated the matter and inclined to the view that the oversight of practice needed to be upgraded, though the Commission stopped short of proposing new regulations for its oversight, largely for prudential political reasons. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

I propose an approach that expands philosophical views of scientific change, on the basis of an analysis of contemporary biomedical research and recent developments in the philosophy of scientific change. Focusing on the establishment of the exposome in epidemiology as a case study and the role of data as a context for contrasting views on change, I discuss change at conceptual, methodological, material, and social levels of biomedical epistemology. Available models of change provide key resources to discuss this (...) type of change, but I present the need for an approach that models transfer, alignment, and influence as key processes of change. I develop this as a pragmatic approach to scientific change, where processes might change substantially depending on specific circumstances, thus contributing to and complementing the debate on a crucial epistemological issue. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in (...) the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

This paper explores how the diagnosis of mental disorder may affect the diagnosed subject’s self-concept by supplying an account that emphasizes the influence of autobiographical and social narratives on self-understanding. It focuses primarily on the diagnoses made according to the criteria provided by the Diagnostic Statistical Manual of Mental Disorders (DSM), and suggests that the DSM diagnosis may function as a source of narrative that affects the subject’s self-concept. Engaging in this analysis by appealing to autobiographies and memoirs written by (...) people diagnosed with mental disorder, the paper concludes that a DSM diagnosis is a double-edged sword for self- concept. On the one hand, it sets the subject’s experience in an established classificatory system which can facilitate self-understanding by providing insight into subject’s condition and guiding her personal growth, as well as treatment and recovery. In this sense, the DSM diagnosis may have positive repercussions on self-development. On the other hand, however, given the DSM’s symptom-based approach and its adoption of the Biomedical Disease model, a diagnosis may force the subject to make sense of her condition divorced from other elements in her life that may be affecting her mental- health. It may lead her frame her experience only as an irreversible imbalance. This form of self-understanding may set limits on the subject’s hopes of recovery and may create impediments to her flourishing. (shrink)

Some types of solar radiation management (SRM) research are ethically problematic because they expose persons, animals, and ecosystems to significant risks. In our earlier work, we argued for ethical norms for SRM research based on norms for biomedical research. Biomedical researchers may not conduct research on persons without their consent, but universal consent is impractical for SRM research. We argue that instead of requiring universal consent, ethical norms for SRM research require only political legitimacy in decision-making about global (...) SRM trials. Using Allen Buchanan & Robert Keohane's model of global political legitimacy, we examine several existing global institutions as possible analogues for a politically legitimate SRM decision-making body. (shrink)

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the (...) notion of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Este artículo considera el problema de justicia en la investigación biomédica en países en desarrollo. En particular se hace foco en la discusión de si el requisito de poner a disposición toda intervención probada efectiva puede ser considerado como una obligación post investigación de los patrocinadores hacia la comunidad anfitriona. Primero, se discuten las concepciones de la Comisión Nacional de Asesoramiento sobre Bioética (NBAC) de los Estados Unidos y de las guías éticas internacionales sobre la obligación post investigación hacia la (...) comunidad. Luego, se examinan las interpretaciones del modelo de disponibilidad razonable y el modelo de beneficios justos sobre la condición de acceso a los beneficios post investigación. Por último, presento y critico el argumento del carácter contraproducente de la obligación post investigación que afirma que la obligación post investigación limita el desarrollo de la investigación y empeora la situación de las poblaciones de los países en desarrollo. [ABSTRACT] This article refers to the problem of justice in biomedical research in developing countries and in particular it focus in the discussion of whether the requirement of making available any effective intervention could be consider a post-trial obligation of the sponsor towards the host community. First, the National Advisory Bioethics Commission’s (NBAC) conception and the international guidelines’ conception of post-trial obligations towards the community are discussed. Second, the interpretation of reasonable availability model and the fair benefits model of the condition of access to post trial benefits are examined. Finally, I present and criticize the moral counterproductive argument which affirms that post trial obligations towards the community prevent new drug research and make population in developing countries worse off. (shrink)

Some recent considerations of religion and psychiatry have drawn a distinction between pathological and spiritual/mystical experiences of mental phenomena typically regarded as within the realm of psychiatry (e.g. depression, hearing voices, seeing visions/hallucinations). Such a distinction has clinical implications, particularly in relation to whether some religious people who suffer from depression, hear voices, or see visions should be biomedically treated. Approaching this question from a theological and philosophical perspective, I draw a distinction between (what I call) ‘spiritual health’ (SH) and (...) ‘potentially transformative’ (PT) theologies, arguing that a PT model is therapeutically and philosophically more sound than a SH one. I then apply this to the clinical debate in critical dialogue with Dein and Durà-Vilà’s 2009 article, ‘The Dark Night of the Soul: spiritual distress and psychiatric implications’. My primary focus is on depression, though the discussion is also relevant to debates about psychosis and schizophrenia. (shrink)

In this paper, we analyze the origin of the links between global bioethics (which we differentiate from biomedical bioethics) and human rights. We understand that we are in a global civilizational crisis, whose roots extend to 1492 today, in which the modern-capitalist model used the discourse of human rights to justify its predatory technocracy. There are three theoretical assumptions that support our analysis: 1) The current conditions in which the technique shows its destructive power over nature (Anthropocene) indicate (...) that none of the ethical antecedents are applicable to such circumstances. In this new context, the kantian categorical imperative has been reconverted into a moral and political duty to not instrumentalize either human beings or nature. We call this new ethical consideration bioethics. 2) The current geopolitical composition of the world must be thought in terms of the global North and the global South, as two regions that are forged in the midst of important processes of globalization of the world-system, and whose main consequence lies in the absence of equity in the distribution of wealth and well-being between the two. 3) The current environmental crisis or climate change, the product of an economic model based on extractive technology, has become one of the most serious threats against human rights. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, (...) let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Addressing concerns about the treatment of psychopaths, Grant Gillett and Flora Huang (2013) argue that we ought to accept a relational or holistic view of psychopathy and APSD rather than the default biomedical-deficit model since the latter “obscures moral truths about the psychopath”. This change in approach to the psychopath will both mitigate at least some of their moral responsibility for the harms they cause, and force communities to incur special obligations, so they claim, because the harms endured (...) by psychopaths will be understood as part of the cause for the harms they are guilty of committing. However, as I will argue, even if we accept that a relational or holistic approach is better suited to understand psychopathy (which is itself contentious), it does not follow that their responsibility is mitigated in a way that causes communities to have special obligations to them as Gillett and Huang suggest. A diagnosis of APSD or psychopathy does not, prima facie, exculpate an agent or suggest a different way of treating them. My discussion will focus on the widely accepted excusing conditions one must meet for responsibility to me mitigated and conclude, contra Gillett and Huang, that psychopaths are no different from you or I with regards to having a causal history that leads to action. Outside forces play a role in all of our behavior. If the psychopath is owed anything because of the way they have come to understand the world then we all are owed that same debt. (shrink)

This paper critically assesses the model of evaluation of scientific research for democratic societies defended by Philip Kitcher. The “significant truth” approach proposes a viable alternative to two classic images of science: that of the “critics”, who believe that science always serves the interests of the powerful and that of the “faithful”, who argue that the pursuit of scientific knowledge is always valuable and necessary. However, the democratic justification of Kitcher’s proposal is not compatible with the ethical problems generated (...) by the international biomedical research in developing countries. To overcome this problem, I revise the national democratic framing of the significant truth approach in light of the theory of justice of John Rawls. (shrink)

This is the first volume of the Encyclopedia of Neutrosophic Researchers, edited from materials offered by the authors who responded to the editor’s invitation. The authors are listed alphabetically. The introduction contains a short history of neutrosophics, together with links to the main papers and books. Neutrosophic set, neutrosophic logic, neutrosophic probability, neutrosophic statistics, neutrosophic measure, neutrosophic precalculus, neutrosophic calculus and so on are gaining significant attention in solving many real life problems that involve uncertainty, impreciseness, vagueness, incompleteness, inconsistent, and (...) indeterminacy. In the past years the fields of neutrosophics have been extended and applied in various fields, such as: artificial intelligence, data mining, soft computing, decision making in incomplete / indeterminate / inconsistent information systems, image processing, computational modelling, robotics, medical diagnosis, biomedical engineering, investment problems, economic forecasting, social science, humanistic and practical achievements. (shrink)