Probabilistic Relational Models (PRMs) are a framework for compactly representing uncertainties (actually probabilities). They result from the combination of Bayesian Networks (BNs), Object-Oriented languages, and relational models. They are specifically designed for their efficient construction, maintenance and exploitation for very large scale problems, where BNs are known to perform poorly. Actually, in large-scale problems, it is often the case that BNs result from the combination of patterns (small BN fragments) repeated many times. PRMs exploit this feature by defining these patterns (...) only once (the so-called PRM’s classes) and using them through multiple instances, as prescribed by the Object-Oriented paradigm. This design induces low construction and maintenance costs. In addition, by exploiting the classes’ structures, PRM’s state-of-the-art inference algorithm “Structured Variable Elimination” (SVE) significantly outperforms BN’s classical inference algorithms (e.g., Variable Elimination, VE; Local Conditioning, LC). SVE is actually an extension of VE that simply exploits classes to avoid redundant computations. In this article, we show that SVE can be enhanced using LC. Although LC is often thought as being outperformed by VE-like algorithms in BNs, we do think that it should play an important role for PRMs because its features are very well suited for best exploiting PRM classes. In this article, relying on Faÿ and Jaffray’s works, we show how LC can be used in conjunction with VE and deduce an extension of SVE that outperforms it for large-scale problems. Numerical experiments highlight the practical efficiency of our algorithm. (shrink)

In this study, I show how Plato in the Parmenides reprises the encounter with the Phaedo’s Antisthenes, whom I elsewhere assumed to be one of the various tis that get examined in the dialogue. Now, with the Parme­nides’ tis, a similar situation arises: this Antisthenes embodies such characteristics as being “an expert in many areas”, “not without natural gifts” and “capable of following with critical intelligence” the logoi taken from “distant premises.” In the four logoi of the gumnasia, I highlight (...) how Plato, in developing his exercise, proceeds on his own way without openly arguing with any tis and how, despite his detached attitude, his hodos, while interweaving with that of his colleague Antisthenes, enters into a conflict. I then demonstrate how the two paths, despite having a common aporetic beginning (the objections of Gorgias to Parmenides and the testimony of Proclus against Antisthenes), at times overlap and at times are mutually exclusive. From this, I also argue that whoever wrote the dialogue must have been aware that the path, although appar­ently linear and rectilinear, was in fact bumpy and tortuous. (shrink)

This paper examines the fifth deduction (160b4-163b5) of the second part of the Parmenides and its connection with the Sophist. I argue that, far from providing us with clear formulations of arguments and theses developed in the Sophist, D5 aims to stimulate us to reflect on two main problems, which are relevant for the ontology and the theory of predication of the Sophist. First, the ontological requirements of the extra-linguistic correlates of contentful thought and meaningful speech. Second, the function of (...) being in the mechanism of the relation of participation. (shrink)

While mass spectrometry (MS)‐based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the (...) proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. (shrink)

This chapter presents the perceptual reality monitoring theory of consciousness (PRM). PRM is a higher-order theory of consciousness. It holds that consciousness involves monitoring the reliability of one’s own sensory signals. I explain how a perceptual reality monitoring mechanism computes the higher order representations that are crucial for consciousness. While PRM accounts for the difference between conscious and unconscious states, it does not explain, on its own, why experiences feel the way they do—the phenomenal character of experience. PRM is compatible (...) with multiple theories of phenomenal character. Here, I show how to combine it with ‘Mental Quality Space’ theory. I finish by presenting empirical evidence for PRM, as well as some of its predictions. (shrink)

Homology is a fundamental concept in biology. However, the metaphysical status of homology, especially whether a homolog is a part of an individual or a member of a natural kind, is still a matter of intense debate. The proponents of the individuality view of homology criticize the natural kind view of homology by pointing out that homologs are subject to evolutionary transformation, and natural kinds do not change in the evolutionary process. Conversely, some proponents of the natural kind view of (...) homology argue that a homolog can be construed both as a part of an individual and a member of a natural kind. They adopt the Homeostatic Property Cluster theory of natural kinds, and the theory seems to strongly support their construal. Note that this construal implies the acceptance of essentialism. However, looking back on the history of the concept of homology, we should not overlook the fact that the individuality view was proposed to reject the essentialist interpretation of homology. Moreover, the essentialist notions of natural kinds can, in our view, mislead biologists about the phenomena of homology. Consequently, we need a non-essentialist view of homology, which we name the “persistently reproducible module” view. This view highlights both the individual-like and kind-like aspects of homologs while stripping down both essentialist and anti-essentialist interpretations of homology. In this article, we articulate the PRM view of homology and explain why it is recommended over the other two views. (shrink)

Evidence suggests that one reason doctors provide certain interventions in assisted reproductive technologies (ART) is because of patient demand. This is particularly the case when it comes to unproven interventions such as ‘add‐ons’ to in vitro fertilisation (IVF) cycles, or providing IVF cycles that are highly unlikely to succeed. Doctors tend to accede to demands for such interventions because patients are willing to do and pay ‘whatever it takes’ to have a baby. However, there is uncertainty as to what moral (...) weight should be placed on patient‐led demands in ART, including whether it is acceptable for such demands to be invoked as a justification for intervention. We address this issue in this paper. We start by elucidating what we mean by ‘patient‐led demand’ and synthesise some of the evidence for this phenomenon. We then argue that a doctor's professional role morality (PRM) yields special responsibilities, particularly in commercialised healthcare settings such as ART, because of the nature of professions as social institutions that are distinct from markets. We argue on this basis that, while there may be reasons (consistent with PRM) for doctors to accede to patient demand, this is not always the case. There is often a gap in justification between acceding to patient‐led demands and providing contested interventions, particularly in commercial settings. As a result, acceding to demand in such settings needs a strong justification to be consistent with PRM. (shrink)

In book VI of his Parmenides commentary, Proclus surveys the previous Neoplatonic interpretations of the “hypotheses” of Plato’s Parmenides, starting with Amelius, a disciple of Plotinus. This paper analyses Amelius’ exegesis of the hypotheses. After presenting the extant evidence about his Parmenides commentary, I explore three puzzling aspects of his interpretation: 1) unlike most Neoplatonists, Amelius distinguished eight hypotheses instead of nine. I argue that he considered the last section (Prm. 165e2-166c2) to be devoid of any positive content and merged (...) it with the previous one – contrary to the modern advocates of an eight-fold divisio textus. 2) Amelius assumed that each hypothesis deals with one layer of reality, but the precise meaning of some identifications is elusive: what are the three kinds of matter matched to hypotheses 5-7? I show that these three material layers probably correspond to three entities whose existence is posited on the basis of the Timaeus: the chōra/prime matter, the level of the element-traces, and the ordered universe. 3) In at least one point, Amelius’ exegesis disrupts the descending hierarchical ordering of the subject-matters of the hypotheses (i.e. from the highest to the lowest-ranked entity), which was an undisputed governing principle of the Neoplatonic interpretations. This irregularity depends, as I argue, on a further interpretative rule: the negative quality of a hypothesis (except for the first one) is taken to indicate some sort of debasement of the corresponding entity. Since, in the second part of the Parmenides, the negative hypotheses alternate with the positive ones, this further principle clashed with the linear downward arrangement implied by the hierarchical principle. In the conclusion of the paper, I sketch how the insights gained by this analysis can shed some light on the subsequent development of the ancient Parmenides exegesis. (shrink)

Plato’s Parmenides is one of the main sources to reconstruct Zeno’s ideas. It has usually been held that Plato presents him there as a follower of Parmenides, whose book intends to defend his master’s argument against those who try to ridicule it. The aim of this paper is to demonstrate that Plato never presents Zeno as an advocate of monism, but rather as an expert on the antilogikètékhne, which is used by him to examine and refute pluralism as well as (...) monism. In order to prove this hypothesis, I will consider first the testimony of the Phaedrus, and specially Phdr. 261d6–8 (dk 29 a 13), where Plato explains some characteristics of the antilogiké that are essential to understand the goals of Zeno’s method. Then I will analyze some passages of the Parmenides (Prm. 127a7-d5, 128a1-e4, dk 29 a 11–12; 127d6-128a1; 135d3-6; 136a4-b6; 136e1-4) to show how this method is presented as an intellectual gymnastic, which could be considered as a propaedeutic for the acquisition of truth and knowledge. (shrink)

This chapter contains sections titled: Theory and Critique of Forms in the Parmenides Scope of Forms (Prm. 130b1–e4) Whole–Part Dilemma (Prm. 130e4–131e7) Largeness Regress (Prm. 132a1–b2) Likeness Regress (Prm. 132c12–133a7) Conclusion.

While refutation is usually related to Plato's early, Socratic, dialogues, this paper is aimed at exploring the link between refutation and dialectic in some of his middle and late dialogues. First, it argues that refutation assumes a constructive role in the Phaedo, where the best logos is the least refutable, and also in the Republic, where the philosopher is invited to fight his way through all elenchoi. Then, it tries to show that the gymnasia of Prm. 130a ff. is aimed (...) at training young Socrates to come to the aid of the theory he embraces preventing it from being refuted. He should travel and explore all the paths, by assuming a hypothesis as well as the opposite one. This methodology paves the way on which Plato advances in the Sophist, where the antinomic structure of the gymnasia gives way to a “constructive” dialectic in which the aporia is solved and a thesis is established by refutation. The last section of this paper is devoted to analysing Sph. 251c-252e, where the positive and constructive function of the elenchus is especially clear. Plato argues for the symploke eidon by exploring all the hypotheses that are open to the search and refuting those that ultimately represent obstacles to his position. The symploke is the truth which remains when all the hypotheses that contradict it have been refuted. The conclusion is that the elenchus does not disappear but is put at the service of the truth, as an essential part of the method for attaining a positive doctrine. (shrink)