Colonoscopy screening is the gold standard procedure for assessing abnormalities in the colon and rectum, such as ulcers and cancerous polyps. Measuring the abnormal mucosal area and its 3D reconstruction can help quantify the surveyed area and objectively evaluate disease burden. However, due to the complex topology of these organs and variable physical conditions, for example, lighting, large homogeneous texture, and image modality estimating distance from the camera aka depth) is highly challenging. Moreover, most colonoscopic video acquisition is monocular, making the depth estimation a non-trivial problem. While methods in computer vision for depth estimation have been proposed and advanced on natural scene datasets, the efficacy of these techniques has not been widely quantified on colonoscopy datasets. As the colonic mucosa has several low-texture regions that are not well pronounced, learning representations from an auxiliary task can improve salient feature extraction, allowing estimation of accurate camera depths. In this work, we propose to develop a novel multi-task learning (MTL) approach with a shared encoder and two decoders, namely a surface normal decoder and a depth estimator decoder. Our depth estimator incorporates attention mechanisms to enhance global context awareness. We leverage the surface normal prediction to improve geometric feature extraction. Also, we apply a cross-task consistency loss among the two geometrically related tasks, surface normal and camera depth. We demonstrate an improvement of 14.17% on relative error and 10.4% improvement on $\delta_{1}$ accuracy over the most accurate baseline state-of-the-art BTS approach. All experiments are conducted on a recently released C3VD dataset; thus, we provide a first benchmark of state-of-the-art methods.
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Background: Pain assessment in individuals with neurological conditions, especially those with limited self-report ability and altered facial expressions, presents challenges. Existing measures, relying on direct observation by caregivers, lack sensitivity and specificity. In cerebral palsy, pain is a common comorbidity and a reliable evaluation protocol is crucial. Thus, having an automatic system that recognizes facial expressions could be of enormous help when diagnosing pain in this type of patient. Objectives: 1) to build a dataset of facial pain expressions in individuals with cerebral palsy, and 2) to develop an automated facial recognition system based on deep learning for pain assessment addressed to this population. Methods: Ten neural networks were trained on three pain image databases, including the UNBC-McMaster Shoulder Pain Expression Archive Database, the Multimodal Intensity Pain Dataset, and the Delaware Pain Database. Additionally, a curated dataset (CPPAIN) was created, consisting of 109 preprocessed facial pain expression images from individuals with cerebral palsy, categorized by two physiotherapists using the Facial Action Coding System observational scale. Results: InceptionV3 exhibited promising performance on the CP-PAIN dataset, achieving an accuracy of 62.67% and an F1 score of 61.12%. Explainable artificial intelligence techniques revealed consistent essential features for pain identification across models. Conclusion: This study demonstrates the potential of deep learning models for robust pain detection in populations with neurological conditions and communication disabilities. The creation of a larger dataset specific to cerebral palsy would further enhance model accuracy, offering a valuable tool for discerning subtle and idiosyncratic pain expressions. The insights gained could extend to other complex neurological conditions.
The goal of radiation therapy for cancer is to deliver prescribed radiation dose to the tumor while minimizing dose to the surrounding healthy tissues. To evaluate treatment plans, the dose distribution to healthy organs is commonly summarized as dose-volume histograms (DVHs). Normal tissue complication probability (NTCP) modelling has centered around making patient-level risk predictions with features extracted from the DVHs, but few have considered adapting a causal framework to evaluate the safety of alternative treatment plans. We propose causal estimands for NTCP based on deterministic and stochastic interventions, as well as propose estimators based on marginal structural models that impose bivariable monotonicity between dose, volume, and toxicity risk. The properties of these estimators are studied through simulations, and their use is illustrated in the context of radiotherapy treatment of anal canal cancer patients.
We consider Maxwell eigenvalue problems on uncertain shapes with perfectly conducting TESLA cavities being the driving example. Due to the shape uncertainty, the resulting eigenvalues and eigenmodes are also uncertain and it is well known that the eigenvalues may exhibit crossings or bifurcations under perturbation. We discuss how the shape uncertainties can be modelled using the domain mapping approach and how the deformation mapping can be expressed as coefficients in Maxwell's equations. Using derivatives of these coefficients and derivatives of the eigenpairs, we follow a perturbation approach to compute approximations of mean and covariance of the eigenpairs. For small perturbations, these approximations are faster and more accurate than Monte Carlo or similar sampling-based strategies. Numerical experiments for a three-dimensional 9-cell TESLA cavity are presented.
Non-significant randomized control trials can hide subgroups of good responders to experimental drugs, thus hindering subsequent development. Identifying such heterogeneous treatment effects is key for precision medicine and many post-hoc analysis methods have been developed for that purpose. While several benchmarks have been carried out to identify the strengths and weaknesses of these methods, notably for binary and continuous endpoints, similar systematic empirical evaluation of subgroup analysis for time-to-event endpoints are lacking. This work aims to fill this gap by evaluating several subgroup analysis algorithms in the context of time-to-event outcomes, by means of three different research questions: Is there heterogeneity? What are the biomarkers responsible for such heterogeneity? Who are the good responders to treatment? In this context, we propose a new synthetic and semi-synthetic data generation process that allows one to explore a wide range of heterogeneity scenarios with precise control on the level of heterogeneity. We provide an open source Python package, available on Github, containing our generation process and our comprehensive benchmark framework. We hope this package will be useful to the research community for future investigations of heterogeneity of treatment effects and subgroup analysis methods benchmarking.
Nosocomial infections have important consequences for patients and hospital staff: they worsen patient outcomes and their management stresses already overburdened health systems. Accurate judgements of whether an infection is nosocomial helps staff make appropriate choices to protect other patients within the hospital. Nosocomiality cannot be properly assessed without considering whether the infected patient came into contact with high risk potential infectors within the hospital. We developed a Bayesian model that integrates epidemiological, contact and pathogen genetic data to determine how likely an infection is to be nosocomial and the probability of given infection candidates being the source of the infection.
Recently, a family of unconventional integrators for ODEs with polynomial vector fields was proposed, based on the polarization of vector fields. The simplest instance is the by now famous Kahan discretization for quadratic vector fields. All these integrators seem to possess remarkable conservation properties. In particular, it has been proved that, when the underlying ODE is Hamiltonian, its polarization discretization possesses an integral of motion and an invariant volume form. In this note, we propose a new algebraic approach to derivation of the integrals of motion for polarization discretizations.
During multiple testing, researchers often adjust their alpha level to control the familywise error rate for a statistical inference about a joint union alternative hypothesis (e.g., "H1 or H2"). However, in some cases, they do not make this inference and instead make separate inferences about each of the individual hypotheses that comprise the joint hypothesis (e.g., H1 and H2). For example, a researcher might use a Bonferroni correction to adjust their alpha level from the conventional level of 0.050 to 0.025 when testing H1 and H2, find a significant result for H1 (p < 0.025) and not for H2 (p > .0.025), and so claim support for H1 and not for H2. However, these separate individual inferences do not require an alpha adjustment. Only a statistical inference about the union alternative hypothesis "H1 or H2" requires an alpha adjustment because it is based on "at least one" significant result among the two tests, and so it depends on the familywise error rate. When a researcher corrects their alpha level during multiple testing but does not make an inference about the union alternative hypothesis, their correction is redundant. In the present article, I discuss this redundant correction problem, including its associated loss of statistical power and its potential causes vis-\`a-vis error rate confusions and the alpha adjustment ritual. I also provide three illustrations of redundant corrections from recent psychology studies. I conclude that redundant corrections represent a symptom of statisticism, and I call for a more nuanced and context-specific approach to multiple testing corrections.
Randomized controlled clinical trials provide the gold standard for evidence generation in relation to the effectiveness of a new treatment in medical research. Relevant information from previous studies may be desirable to incorporate in the design of a new trial, with the Bayesian paradigm providing a coherent framework to formally incorporate prior knowledge. Many established methods involve the use of a discounting factor, sometimes related to a measure of `similarity' between historical sources and the new trial. However, it is often the case that the sample size is highly nonlinear in those discounting factors. This hinders communication with subject-matter experts to elicit sensible values for borrowing strength at the trial design stage. Focusing on a sample size formula that can incorporate historical data from multiple sources, we propose a linearization technique such that the sample size changes evenly over values of the discounting factors (hereafter referred to as `weights'). Our approach leads to interpretable weights that directly represent the dissimilarity between historical and new trial data on the probability scale, and could therefore facilitate easier elicitation of expert opinion on their values. Inclusion of historical data in the design of clinical trials is not common practice. Part of the reason might be difficulty in interpretability of discrepancy parameters. We hope our work will help to bridge this gap and encourage uptake of these innovative methods. Keywords: Bayesian sample size determination; Commensurate priors; Historical borrowing; Prior aggregation; Uniform shrinkage.
Optical coherence tomography (OCT) suffers from speckle noise, causing the deterioration of image quality, especially in high-resolution modalities like visible light OCT (vis-OCT). The potential of conventional supervised deep learning denoising methods is limited by the difficulty of obtaining clean data. Here, we proposed an innovative self-supervised strategy called Sub2Full (S2F) for OCT despeckling without clean data. This approach works by acquiring two repeated B-scans, splitting the spectrum of the first repeat as a low-resolution input, and utilizing the full spectrum of the second repeat as the high-resolution target. The proposed method was validated on vis-OCT retinal images visualizing sublaminar structures in outer retina and demonstrated superior performance over conventional Noise2Noise and Noise2Void schemes. The code is available at //github.com/PittOCT/Sub2Full-OCT-Denoising.
In recent years, the Adaptive Antoulas-Anderson AAA algorithm has established itself as the method of choice for solving rational approximation problems. Data-driven Model Order Reduction (MOR) of large-scale Linear Time-Invariant (LTI) systems represents one of the many applications in which this algorithm has proven to be successful since it typically generates reduced-order models (ROMs) efficiently and in an automated way. Despite its effectiveness and numerical reliability, the classical AAA algorithm is not guaranteed to return a ROM that retains the same structural features of the underlying dynamical system, such as the stability of the dynamics. In this paper, we propose a novel algebraic characterization for the stability of ROMs with transfer function obeying the AAA barycentric structure. We use this characterization to formulate a set of convex constraints on the free coefficients of the AAA model that, whenever verified, guarantee by construction the asymptotic stability of the resulting ROM. We suggest how to embed such constraints within the AAA optimization routine, and we validate experimentally the effectiveness of the resulting algorithm, named stabAAA, over a set of relevant MOR applications.
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