On Cavity Approximations for Graphical Models

We reformulate the Cavity Approximation (CA), a class of algorithms recently introduced for improving the Bethe approximation estimates of marginals in graphical models. In our new formulation, which allows for the treatment of multivalued variables, a further generalization to factor graphs with arbitrary order of interaction factors is explicitly carried out, and a message passing algorithm that implements the first order correction to the Bethe approximation is described. Furthermore we investigate an implementation of the CA for pairwise interactions. In all cases considered we could confirm that CA[k] with increasing $k$ provides a sequence of approximations of markedly increasing precision. Furthermore in some cases we could also confirm the general expectation that the approximation of order $k$, whose computational complexity is $O(N^{k+1})$ has an error that scales as $1/N^{k+1}$ with the size of the system. We discuss the relation between this approach and some recent developments in the field.Comment: Extension to factor graphs and comments on related work adde

Replica symmetry breaking in the `small world' spin glass

We apply the cavity method to a spin glass model on a `small world' lattice, a random bond graph super-imposed upon a 1-dimensional ferromagnetic ring. We show the correspondence with a replicated transfer matrix approach, up to the level of one step replica symmetry breaking (1RSB). Using the scheme developed by M\'ezard & Parisi for the Bethe lattice, we evaluate observables for a model with fixed connectivity and $\pm J$ long range bonds. Our results agree with numerical simulations significantly better than the replica symmetric (RS) theory.Comment: 21 pages, 3 figure

The Fractional exhaled Nitric Oxide (FeNO)- test as add-on test in the diagnostic work-up of asthma:a study protocol

Background: Asthma is a common disease characterized by chronic inflammation of the lower airways, bronchial hyperactivity, and (reversible) airway obstruction. The Global Initiative of Asthma Guideline recommends a flowchart to diagnose asthma with first-step spirometry with reversibility and a bronchial challenge test (BPT) with histamine or methacholine as a second step [1]. The BPT is considered burdensome, time-consuming for patients and staff, can cause side effects, and is expensive. In addition, this test strongly encumbers lung function capacity. Elevated Nitric Oxide (NO) is associated with airway eosinophilic inflammation in asthma patients and can be measured in exhaled air with the Fractional exhaled (Fe) NO-test. This low-burden FeNO-test could be used as an ‘add-on’ test in asthma diagnostics [2, 3]. Methods and analysis: This multi-center prospective study (Trial number: NCT06230458) compares the ‘standard asthma diagnostic work-up’ (spirometry with reversibility and BPT) to the ‘new asthma diagnostics work-up’ (FeNO-test as an intermediate step between the spirometry with reversibility and the BPT), intending to determine the impact of the FeNO-based strategy, in terms of the number of avoided BPTs, cost-effectiveness and reduced burden to the patient and health care. The cost reduction of incorporating the FeNO-test in the new diagnostic algorithm will be established by the number of theoretically avoided BPT. The decrease in burden will be studied by calculating differences in the Visual Analogue Scale (VAS) -score and Asthma Quality of Life Questionnaire (AQLQ) -score after the BPT and FeNO-test with an independent T-test. The accuracy of the FeNO-test will be calculated by comparing the FeNO-test outcomes to the (gold standard) BPTs outcomes in terms of sensitivity and specificity. The intention is to include 171 patients. Ethics and dissemination: The local medical ethics committee approved the proposed study and is considered a low-burden and risk-low study. The local medical ethics committee registration number: R23.005. Strengths and limitations of this study: Strengths: This is the first study that investigates the value of the FeNO-test (cut off ≥ 50 ppb) as an add-on test, to determine the impact of the FeNO-based strategy, in terms of the number of avoided BPTs, cost-effectiveness, and reduced burden on the patient and health care. Limitations: High FeNO levels may also be observed in other diseases such as eosinophilic chronic bronchitis and allergic rhinitis. The FeNO-test can be used to rule in a diagnosis of asthma with confidence, however, due to the poor sensitivity it is not suitable to rule out asthma.</p

The Fractional exhaled Nitric Oxide (FeNO)- test as add-on test in the diagnostic work-up of asthma:a study protocol

Background: Asthma is a common disease characterized by chronic inflammation of the lower airways, bronchial hyperactivity, and (reversible) airway obstruction. The Global Initiative of Asthma Guideline recommends a flowchart to diagnose asthma with first-step spirometry with reversibility and a bronchial challenge test (BPT) with histamine or methacholine as a second step [1]. The BPT is considered burdensome, time-consuming for patients and staff, can cause side effects, and is expensive. In addition, this test strongly encumbers lung function capacity. Elevated Nitric Oxide (NO) is associated with airway eosinophilic inflammation in asthma patients and can be measured in exhaled air with the Fractional exhaled (Fe) NO-test. This low-burden FeNO-test could be used as an ‘add-on’ test in asthma diagnostics [2, 3]. Methods and analysis: This multi-center prospective study (Trial number: NCT06230458) compares the ‘standard asthma diagnostic work-up’ (spirometry with reversibility and BPT) to the ‘new asthma diagnostics work-up’ (FeNO-test as an intermediate step between the spirometry with reversibility and the BPT), intending to determine the impact of the FeNO-based strategy, in terms of the number of avoided BPTs, cost-effectiveness and reduced burden to the patient and health care. The cost reduction of incorporating the FeNO-test in the new diagnostic algorithm will be established by the number of theoretically avoided BPT. The decrease in burden will be studied by calculating differences in the Visual Analogue Scale (VAS) -score and Asthma Quality of Life Questionnaire (AQLQ) -score after the BPT and FeNO-test with an independent T-test. The accuracy of the FeNO-test will be calculated by comparing the FeNO-test outcomes to the (gold standard) BPTs outcomes in terms of sensitivity and specificity. The intention is to include 171 patients. Ethics and dissemination: The local medical ethics committee approved the proposed study and is considered a low-burden and risk-low study. The local medical ethics committee registration number: R23.005. Strengths and limitations of this study: Strengths: This is the first study that investigates the value of the FeNO-test (cut off ≥ 50 ppb) as an add-on test, to determine the impact of the FeNO-based strategy, in terms of the number of avoided BPTs, cost-effectiveness, and reduced burden on the patient and health care. Limitations: High FeNO levels may also be observed in other diseases such as eosinophilic chronic bronchitis and allergic rhinitis. The FeNO-test can be used to rule in a diagnosis of asthma with confidence, however, due to the poor sensitivity it is not suitable to rule out asthma.</p

Survey propagation at finite temperature: application to a Sourlas code as a toy model

In this paper we investigate a finite temperature generalization of survey propagation, by applying it to the problem of finite temperature decoding of a biased finite connectivity Sourlas code for temperatures lower than the Nishimori temperature. We observe that the result is a shift of the location of the dynamical critical channel noise to larger values than the corresponding dynamical transition for belief propagation, as suggested recently by Migliorini and Saad for LDPC codes. We show how the finite temperature 1-RSB SP gives accurate results in the regime where competing approaches fail to converge or fail to recover the retrieval state

Effect of coupling asymmetry on mean-field solutions of direct and inverse Sherrington-Kirkpatrick model

We study how the degree of symmetry in the couplings influences the performance of three mean field methods used for solving the direct and inverse problems for generalized Sherrington-Kirkpatrick models. In this context, the direct problem is predicting the potentially time-varying magnetizations. The three theories include the first and second order Plefka expansions, referred to as naive mean field (nMF) and TAP, respectively, and a mean field theory which is exact for fully asymmetric couplings. We call the last of these simply MF theory. We show that for the direct problem, nMF performs worse than the other two approximations, TAP outperforms MF when the coupling matrix is nearly symmetric, while MF works better when it is strongly asymmetric. For the inverse problem, MF performs better than both TAP and nMF, although an ad hoc adjustment of TAP can make it comparable to MF. For high temperatures the performance of TAP and MF approach each other

The Making of the Finnish Polar Silk Road : Status in Spring 2019

Peer reviewe

A deep active inference model of the rubber-hand illusion

Understanding how perception and action deal with sensorimotor conflicts, such as the rubber-hand illusion (RHI), is essential to understand how the body adapts to uncertain situations. Recent results in humans have shown that the RHI not only produces a change in the perceived arm location, but also causes involuntary forces. Here, we describe a deep active inference agent in a virtual environment, which we subjected to the RHI, that is able to account for these results. We show that our model, which deals with visual high-dimensional inputs, produces similar perceptual and force patterns to those found in humans.Comment: 8 pages, 3 figures, Accepted in 1st International Workshop on Active Inference, in Conjunction with European Conference of Machine Learning 2020. The final authenticated publication is available online at https://doi.org/10.1007/978-3-030-64919-7_1

Mepolizumab add-on therapy in a real world cohort of patients with severe eosinophilic asthma: response rate, effectiveness, and safety

Introduction: Severe eosinophilic asthma is an incapacitating disease. Mepolizumab, a humanized anti-interleukin-5 monoclonal antibody, proved to be effective as an add-on therapy in patients with severe eosinophilic asthma. However, only data from randomized controlled trials are available and real world data are lacking. Methods: A retrospective observational longitudinal study was conducted in a real world cohort of patients with severe eosinophilic asthma treated with mepolizumab. The primary objective was to determine response rate, based on a global evaluation of treatment effectiveness by the treating pulmonologist. Secondary objectives were to assess exacerbation frequency, systemic maintenance glucocorticoid usage, Asthma Control Questionnaire (ACQ), lung function, and adverse events. Results: Seventy-eight patients were included. Treatment with mepolizumab was considered beneficial and was therefore continued in 75.6% of patients 12 months from the initiation of mepolizumab. The most common reason for drop-out was insufficient response. Secondary objectives: 12 months from the initiation of mepolizumab there was a decrease of 3.2 (CI 2.5–4.1; p < 0.001) severe asthma exacerbations per year, a decrease of ACQ of 0.80 points (CI 0.49–1.12; p < 0.001), and an increase of 3.7 (CI 0.3–7.2; p = 0.034) percent of predicted FEV1 compared to baseline. At baseline 51.3% of patients were treated with systemic glucocorticoid maintenance therapy, compared to 15.4% (p < 0.001) of patients 12 months from the initiation of mepolizumab. No serious adverse events considered to be related to mepolizumab were reported. Conclusion: This study confirms that mepolizumab add-on therapy is effective and safe in a real world cohort of patients with severe eosinophilic asthma

Palaeomagnetic and synchrotron analysis of \u3e1.95 Ma fossil-bearing palaeokarst at Haasgat, South Africa

Palaeomagnetic analysis indicates that Haasgat, a fossil-bearing palaeocave in the Gauteng Province of South Africa, is dominated by reversed magnetic polarity in its oldest, deepest layers and normal polarity in the younger layers. The presence of in-situ Equus specimens suggests an age of less than ~2.3 Ma, while morphological analysis of faunal specimens from the ex-situ assemblage suggests an age greater than 1.8 Ma. Given this faunal age constraint, the older reversed polarity sections most likely date to the beginning of the Matuyama Chron (2.58–1.95 Ma), while the younger normal polarity deposits likely date to the very beginning of the Olduvai Sub-Chron (1.95–1.78 Ma). The occurrence of a magnetic reversal from reversed to normal polarity recorded in the sequence indicates the deposits of the Bridge Section date to ~1.95 Ma. All the in-situ fossil deposits that have been noted are older than the 1.95 Ma reversal, but younger than 2.3 Ma. Haasgat therefore dates to an interesting time period in South African human evolution that saw the last occurrence of two australopith species at ~2.05–2.02 Ma (Sts5 Australopithecus africanus from Sterkfontein Member 4) to ~1.98 Ma ( Australopithecus sediba from Malapa) and the first occurrence of early Homo (Sk847), Paranthropus and the Oldowan within Swartkrans Member 1 between ~2.0 Ma and ~1.8 Ma