Uncertainty quantification in graph-based classification of high dimensional data

Classification of high dimensional data finds wide-ranging applications. In many of these applications equipping the resulting classification with a measure of uncertainty may be as important as the classification itself. In this paper we introduce, develop algorithms for, and investigate the properties of, a variety of Bayesian models for the task of binary classification; via the posterior distribution on the classification labels, these methods automatically give measures of uncertainty. The methods are all based around the graph formulation of semi-supervised learning. We provide a unified framework which brings together a variety of methods which have been introduced in different communities within the mathematical sciences. We study probit classification in the graph-based setting, generalize the level-set method for Bayesian inverse problems to the classification setting, and generalize the Ginzburg-Landau optimization-based classifier to a Bayesian setting; we also show that the probit and level set approaches are natural relaxations of the harmonic function approach introduced in [Zhu et al 2003]. We introduce efficient numerical methods, suited to large data-sets, for both MCMC-based sampling as well as gradient-based MAP estimation. Through numerical experiments we study classification accuracy and uncertainty quantification for our models; these experiments showcase a suite of datasets commonly used to evaluate graph-based semi-supervised learning algorithms.Comment: 33 pages, 14 figure

Stable mode-locked pulses from mid-infrared semiconductor lasers

We report the unequivocal demonstration of mid-infrared mode-locked pulses from a semiconductor laser. The train of short pulses was generated by actively modulating the current and hence the optical gain in a small section of an edge-emitting quantum cascade laser (QCL). Pulses with pulse duration at full-width-at-half-maximum of about 3 ps and energy of 0.5 pJ were characterized using a second-order interferometric autocorrelation technique based on a nonlinear quantum well infrared photodetector. The mode-locking dynamics in the QCLs was modelled and simulated based on Maxwell-Bloch equations in an open two-level system. We anticipate our results to be a significant step toward a compact, electrically-pumped source generating ultrashort light pulses in the mid-infrared and terahertz spectral ranges.Comment: 26 pages, 4 figure

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

Investigation of the microstructure of the fine-grained YPO4_4:Gd ceramics with xenotime structure after Xe irradiation

The paper reports on the preparation of xenotime-structured ceramics by the Spark Plasma Sintering (SPS) method. Phosphates Y$_{0.95}$Gd$_{0.05}$PO$_4$ (YPO$_4$:Gd) were obtained by the sol-gel method. The synthesized nanopowders are collected in large agglomerates 10-50 mkm in size. Ceramics has a fine-grained microstructure and a high relative density (98.67%). The total time of the SPS process was approximately 18 min. High-density sintered ceramics YPO$_4$:Gd with a xenotime structure were irradiated with Xe$^{+26}$ ions (E = 167 MeV) to fluences of $1\times10^{12}$-$3\times 10^{13}$ cm$^{-2}$. Complete amorphization at maximum fluence was not achieved. As the fluence increases, an insignificant increase in the depth of the amorphous layer is observed. According to the results of grazing incidence XRD (GIXRD), with an increase in fluence from $1\times10^{12}$-$3\times 10^{13}$ cm$^{-2}$, an increase in the volume fraction of the amorphous structure from 20 to 70% is observed. The intensity of XRD peak 200 YPO$_4$:Gd after recovery annealing (700$^\circ$C, 18 h) reached a value of ~80% of the initial intensity I0.Comment: 16 pages, 10 figure

Science Models as Value-Added Services for Scholarly Information Systems

The paper introduces scholarly Information Retrieval (IR) as a further dimension that should be considered in the science modeling debate. The IR use case is seen as a validation model of the adequacy of science models in representing and predicting structure and dynamics in science. Particular conceptualizations of scholarly activity and structures in science are used as value-added search services to improve retrieval quality: a co-word model depicting the cognitive structure of a field (used for query expansion), the Bradford law of information concentration, and a model of co-authorship networks (both used for re-ranking search results). An evaluation of the retrieval quality when science model driven services are used turned out that the models proposed actually provide beneficial effects to retrieval quality. From an IR perspective, the models studied are therefore verified as expressive conceptualizations of central phenomena in science. Thus, it could be shown that the IR perspective can significantly contribute to a better understanding of scholarly structures and activities.Comment: 26 pages, to appear in Scientometric

A graph-based integration of multimodal brain imaging data for the detection of early mild cognitive impairment (E-MCI)

Alzheimer's disease (AD) is the most common cause of dementia in older adults. By the time an individual has been diagnosed with AD, it may be too late for potential disease modifying therapy to strongly influence outcome. Therefore, it is critical to develop better diagnostic tools that can recognize AD at early symptomatic and especially pre-symptomatic stages. Mild cognitive impairment (MCI), introduced to describe a prodromal stage of AD, is presently classified into early and late stages (E-MCI, L-MCI) based on severity. Using a graph-based semi-supervised learning (SSL) method to integrate multimodal brain imaging data and select valid imaging-based predictors for optimizing prediction accuracy, we developed a model to differentiate E-MCI from healthy controls (HC) for early detection of AD. Multimodal brain imaging scans (MRI and PET) of 174 E-MCI and 98 HC participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort were used in this analysis. Mean targeted region-of-interest (ROI) values extracted from structural MRI (voxel-based morphometry (VBM) and FreeSurfer V5) and PET (FDG and Florbetapir) scans were used as features. Our results show that the graph-based SSL classifiers outperformed support vector machines for this task and the best performance was obtained with 66.8% cross-validated AUC (area under the ROC curve) when FDG and FreeSurfer datasets were integrated. Valid imaging-based phenotypes selected from our approach included ROI values extracted from temporal lobe, hippocampus, and amygdala. Employing a graph-based SSL approach with multimodal brain imaging data appears to have substantial potential for detecting E-MCI for early detection of prodromal AD warranting further investigation

Rhythmic dynamics and synchronization via dimensionality reduction : application to human gait

Reliable characterization of locomotor dynamics of human walking is vital to understanding the neuromuscular control of human locomotion and disease diagnosis. However, the inherent oscillation and ubiquity of noise in such non-strictly periodic signals pose great challenges to current methodologies. To this end, we exploit the state-of-the-art technology in pattern recognition and, specifically, dimensionality reduction techniques, and propose to reconstruct and characterize the dynamics accurately on the cycle scale of the signal. This is achieved by deriving a low-dimensional representation of the cycles through global optimization, which effectively preserves the topology of the cycles that are embedded in a high-dimensional Euclidian space. Our approach demonstrates a clear advantage in capturing the intrinsic dynamics and probing the subtle synchronization patterns from uni/bivariate oscillatory signals over traditional methods. Application to human gait data for healthy subjects and diabetics reveals a significant difference in the dynamics of ankle movements and ankle-knee coordination, but not in knee movements. These results indicate that the impaired sensory feedback from the feet due to diabetes does not influence the knee movement in general, and that normal human walking is not critically dependent on the feedback from the peripheral nervous system

Закупка научного оборудования из средств грантов для центров коллективного пользования и уникальных научных установок

This study is devoted to identifying typical problems in the field of scientific equipment procurement in the interests of core shared research facilities and large-scale research facilities and developing approaches to their solution. The paper provides an analysis on the practice of purchasing scientific equipment, conducted on the basis of statistical data obtained from representatives of core shared research facilities and large-scale research facilities that received governmental support in 2019–2021, as well as on the data of a sociological survey. As a result, the hypotheses put forward by the authors about the predominance of foreign-made scientific equipment in the procurement structure, about the decrease in the average cost of purchased equipment in 2019–2021, about the presence of significant unevenness of scientific equipment by subclasses in the procurement structure of scientific equipment, about the presence of similar organizational problems in the field of procurement of scientific equipment. The article suggests a number of approaches to solving the identified problems arising from the formulations of 4 proven hypotheses.Настоящее исследование посвящено выявлению типовых проблем в области организации закупок научного оборудования в интересах центров коллективного пользования и уникальных научных установок, и разработке подходов к их решению. В работе дается анализ практики закупки научного оборудования, проведенный на основе статистических данных, полученных от представителей центров коллективного пользования и уникальных научных установок, получивших государственную поддержку в 2019–2021 гг., а также на данных социологического опроса. В результате нашли свое подтверждение выдвинутые авторами гипотезы о преобладании в структуре закупок научного оборудования иностранного производства, снижении средней стоимости закупленного оборудования в 2019–2021 гг., наличии значимой неравномерности по подклассам научного оборудования в структуре закупок научного оборудования, наличии однотипных проблем организационного характера в области организации закупок научного оборудования. В статье предложен ряд подходов к решению выявленных проблем, вытекающих из формулировок 4 доказанных гипотез