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The early detection of cancer is a challenging problem in medicine. The blood sera of cancer patients are enriched with heterogeneous secretory lipid bound extracellular vesicles (EVs), which present a complex repertoire of information and biomarkers, representing their cell of origin, that are being currently studied in the field of liquid biopsy and cancer screening. Vibrational spectroscopies provide non-invasive approaches for the assessment of structural and biophysical properties in complex biological samples. In this pilot study, multiple Raman spectroscopy measurements were performed on the EVs extracted from the blood sera of 9 patients consisting of four different cancer subtypes (colorectal cancer, hepatocellular carcinoma, breast cancer and pancreatic cancer) and five healthy patients (controls). FTIR (Fourier Transform Infrared) spectroscopy measurements were performed as a complementary approach to Raman analysis, on two of the four cancer subtypes. The AdaBoost Random Forest Classifier, Decision Trees, and Support Vector Machines (SVM) distinguished the baseline corrected Raman spectra of cancer EVs from those of healthy controls (18 spectra) with a classification accuracy of above 90 percent when reduced to a spectral frequency range of 1800 to 1940 inverse cm and subjected to a 50:50 training: testing split. FTIR classification accuracy on 14 spectra showed an 80 percent classification accuracy. Our findings demonstrate that basic machine learning algorithms are powerful applied intelligence tools to distinguish the complex vibrational spectra of cancer patient EVs from those of healthy patients. These experimental methods hold promise as valid and efficient liquid biopsy for artificial intelligence-assisted early cancer screening.

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機器學習系(xi)統(tong)設計系(xi)統(tong)評估標準

Conjoint analysis is a popular experimental design used to measure multidimensional preferences. Researchers examine how varying a factor of interest, while controlling for other relevant factors, influences decision-making. Currently, there exist two methodological approaches to analyzing data from a conjoint experiment. The first focuses on estimating the average marginal effects of each factor while averaging over the other factors. Although this allows for straightforward design-based estimation, the results critically depend on the distribution of other factors and how interaction effects are aggregated. An alternative model-based approach can compute various quantities of interest, but requires researchers to correctly specify the model, a challenging task for conjoint analysis with many factors and possible interactions. In addition, a commonly used logistic regression has poor statistical properties even with a moderate number of factors when incorporating interactions. We propose a new hypothesis testing approach based on the conditional randomization test to answer the most fundamental question of conjoint analysis: Does a factor of interest matter {\it in any way} given the other factors? Our methodology is solely based on the randomization of factors, and hence is free from assumptions. Yet, it allows researchers to use any test statistic, including those based on complex machine learning algorithms. As a result, we are able to combine the strengths of the existing design-based and model-based approaches. We illustrate the proposed methodology through conjoint analysis of immigration preferences and political candidate evaluation. We also extend the proposed approach to test for regularity assumptions commonly used in conjoint analysis.

The widespread adoption of electronic health records (EHRs) and subsequent increased availability of longitudinal healthcare data has led to significant advances in our understanding of health and disease with direct and immediate impact on the development of new diagnostics and therapeutic treatment options. However, access to EHRs is often restricted due to their perceived sensitive nature and associated legal concerns, and the cohorts therein typically are those seen at a specific hospital or network of hospitals and therefore not representative of the wider population of patients. Here, we present HealthGen, a new approach for the conditional generation of synthetic EHRs that maintains an accurate representation of real patient characteristics, temporal information and missingness patterns. We demonstrate experimentally that HealthGen generates synthetic cohorts that are significantly more faithful to real patient EHRs than the current state-of-the-art, and that augmenting real data sets with conditionally generated cohorts of underrepresented subpopulations of patients can significantly enhance the generalisability of models derived from these data sets to different patient populations. Synthetic conditionally generated EHRs could help increase the accessibility of longitudinal healthcare data sets and improve the generalisability of inferences made from these data sets to underrepresented populations.

The emergence and dynamics of filamentary structures associated with edge-localized modes (ELMs) inside tokamak plasmas during high-confinement mode is regularly studied using Electron Cyclotron Emission Imaging (ECEI) diagnostic systems. Such diagnostics allow us to infer electron temperature variations, often across a poloidal cross-section. Previously, detailed analysis of these filamentary dynamics and classification of the precursors to edge-localized crashes has been done manually. We present a machine-learning-based model, capable of automatically identifying the position, spatial extend, and amplitude of ELM filaments. The model is a deep convolutional neural network that has been trained and optimized on an extensive set of manually labeled ECEI data from the KSTAR tokamak. Once trained, the model achieves a $93.7\%$ precision and allows us to robustly identify plasma filaments in unseen ECEI data. The trained model is used to characterize ELM filament dynamics in a single H-mode plasma discharge. We identify quasi-periodic oscillations of the filaments size, total heat content, and radial velocity. The detailed dynamics of these quantities appear strongly correlated with each other and appear qualitatively different during the pre-crash and ELM crash phases.

The Wiener-Hopf equations are a Toeplitz system of linear equations that naturally arise in several applications in time series. These include the update and prediction step of the stationary Kalman filter equations and the prediction of bivariate time series. The celebrated Wiener-Hopf technique is usually used for solving these equations and is based on a comparison of coefficients in a Fourier series expansion. However, a statistical interpretation of both the method and solution is opaque. The purpose of this note is to revisit the (discrete) Wiener-Hopf equations and obtain an alternative solution that is more aligned with classical techniques in time series analysis. Specifically, we propose a solution to the Wiener-Hopf equations that combines linear prediction with deconvolution. The Wiener-Hopf solution requires the spectral factorization of the underlying spectral density function. For ease of evaluation it is often assumed that the spectral density is rational. This allows one to obtain a computationally tractable solution. However, this leads to an approximation error when the underlying spectral density is not a rational function. We use the proposed solution with Baxter's inequality to derive an error bound for the rational spectral density approximation.

Without a specific functional context, non-functional requirements can only be approached as cross-cutting concerns and treated uniformly across all features of an application. This neglects, however, the heterogeneity of non-functional requirements that arises from stakeholder interests and the distinct functional scopes of software systems, which mutually influence how these non-functional requirements have to be satisfied. Earlier studies showed that the different types and objectives of non-functional requirements result in either vague or unbalanced specification of non-functional requirements. We propose a task analytic approach for eliciting and modeling user tasks to approach the stakeholders' pursued interests towards the software product. Stakeholder interests are structurally related to user tasks and each interest can be specified individually as a constraint of a specific user task. These constraints support DevOps teams with important guidance on how the interest of the stakeholder can be satisfied in the software lifecycle sufficiently. We propose a structured approach, intertwining task-oriented functional requirements with non-functional stakeholder interests to specify constraints on the level of user tasks. We also present results of a case study with domain experts, which reveals that our task modeling and interest-tailoring method increases the comprehensibility of non-functional requirements as well as their impact on the functional requirements, i.e., the users' tasks.

There is growing interest in the detection and characterization of gravitational waves from postmerger oscillations of binary neutron stars. These signals contain information about the nature of the remnant and the high-density and out-of-equilibrium physics of the postmerger processes, which would complement any electromagnetic signal. However, the construction of binary neutron star postmerger waveforms is much more complicated than for binary black holes: (i) there are theoretical uncertainties in the neutron-star equation of state and other aspects of the high-density physics, (ii) numerical simulations are expensive and available ones only cover a small fraction of the parameter space with limited numerical accuracy, and (iii) it is unclear how to parametrize the theoretical uncertainties and interpolate across parameter space. In this work, we describe the use of a machine-learning method called a conditional variational autoencoder (CVAE) to construct postmerger models for hyper/massive neutron star remnant signals based on numerical-relativity simulations. The CVAE provides a probabilistic model, which encodes uncertainties in the training data within a set of latent parameters. We estimate that training such a model will ultimately require $\sim 10^4$ waveforms. However, using synthetic training waveforms as a proof-of-principle, we show that the CVAE can be used as an accurate generative model and that it encodes the equation of state in a useful latent representation.

A finite element solution of an ion channel dielectric continuum model such as Poisson-Boltzmann equation (PBE) and a system of Poisson-Nernst-Planck equations (PNP) requires tetrahedral meshes for an ion channel protein region, a membrane region, and an ionic solvent region as well as an interface fitted irregular tetrahedral mesh of a simulation box domain. However, generating these meshes is very difficult and highly technical due to the related three regions having very complex geometrical shapes. Currently, an ion channel mesh generation software package developed in Lu's research group is one available in the public domain. To significantly improve its mesh quality and computer performance, in this paper, new numerical schemes for generating membrane and solvent meshes are presented and implemented in Python, resulting in a new ion channel mesh generation software package. Numerical results are then reported to demonstrate the efficiency of the new numerical schemes and the quality of meshes generated by the new package for ion channel proteins with ion channel pores having different geometric complexities.

The area of Data Analytics on graphs promises a paradigm shift as we approach information processing of classes of data, which are typically acquired on irregular but structured domains (social networks, various ad-hoc sensor networks). Yet, despite its long history, current approaches mostly focus on the optimization of graphs themselves, rather than on directly inferring learning strategies, such as detection, estimation, statistical and probabilistic inference, clustering and separation from signals and data acquired on graphs. To fill this void, we first revisit graph topologies from a Data Analytics point of view, and establish a taxonomy of graph networks through a linear algebraic formalism of graph topology (vertices, connections, directivity). This serves as a basis for spectral analysis of graphs, whereby the eigenvalues and eigenvectors of graph Laplacian and adjacency matrices are shown to convey physical meaning related to both graph topology and higher-order graph properties, such as cuts, walks, paths, and neighborhoods. Next, to illustrate estimation strategies performed on graph signals, spectral analysis of graphs is introduced through eigenanalysis of mathematical descriptors of graphs and in a generic way. Finally, a framework for vertex clustering and graph segmentation is established based on graph spectral representation (eigenanalysis) which illustrates the power of graphs in various data association tasks. The supporting examples demonstrate the promise of Graph Data Analytics in modeling structural and functional/semantic inferences. At the same time, Part I serves as a basis for Part II and Part III which deal with theory, methods and applications of processing Data on Graphs and Graph Topology Learning from data.

Machine learning methods are powerful in distinguishing different phases of matter in an automated way and provide a new perspective on the study of physical phenomena. We train a Restricted Boltzmann Machine (RBM) on data constructed with spin configurations sampled from the Ising Hamiltonian at different values of temperature and external magnetic field using Monte Carlo methods. From the trained machine we obtain the flow of iterative reconstruction of spin state configurations to faithfully reproduce the observables of the physical system. We find that the flow of the trained RBM approaches the spin configurations of the maximal possible specific heat which resemble the near criticality region of the Ising model. In the special case of the vanishing magnetic field the trained RBM converges to the critical point of the Renormalization Group (RG) flow of the lattice model. Our results suggest an alternative explanation of how the machine identifies the physical phase transitions, by recognizing certain properties of the configuration like the maximization of the specific heat, instead of associating directly the recognition procedure with the RG flow and its fixed points. Then from the reconstructed data we deduce the critical exponent associated to the magnetization to find satisfactory agreement with the actual physical value. We assume no prior knowledge about the criticality of the system and its Hamiltonian.

This paper reports on modern approaches in Information Extraction (IE) and its two main sub-tasks of Named Entity Recognition (NER) and Relation Extraction (RE). Basic concepts and the most recent approaches in this area are reviewed, which mainly include Machine Learning (ML) based approaches and the more recent trend to Deep Learning (DL) based methods.

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