The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated $(Y, Dy)Ba_2Cu_3O_{7-\delta}$ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.
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Hate detection has long been a challenging task for the NLP community. The task becomes complex in a code-mixed environment because the models must understand the context and the hate expressed through language alteration. Compared to the monolingual setup, we see very less work on code-mixed hate as large-scale annotated hate corpora are unavailable to make the study. To overcome this bottleneck, we propose using native language hate samples. We hypothesise that in the era of multilingual language models (MLMs), hate in code-mixed settings can be detected by majorly relying on the native language samples. Even though the NLP literature reports the effectiveness of MLMs on hate detection in many cross-lingual settings, their extensive evaluation in a code-mixed scenario is yet to be done. This paper attempts to fill this gap through rigorous empirical experiments. We considered the Hindi-English code-mixed setup as a case study as we have the linguistic expertise for the same. Some of the interesting observations we got are: (i) adding native hate samples in the code-mixed training set, even in small quantity, improved the performance of MLMs for code-mixed hate detection, (ii) MLMs trained with native samples alone observed to be detecting code-mixed hate to a large extent, (iii) The visualisation of attention scores revealed that, when native samples were included in training, MLMs could better focus on the hate emitting words in the code-mixed context, and (iv) finally, when hate is subjective or sarcastic, naively mixing native samples doesn't help much to detect code-mixed hate. We will release the data and code repository to reproduce the reported results.
Successive image generation using cyclic transformations is demonstrated by extending the CycleGAN model to transform images among three different categories. Repeated application of the trained generators produces sequences of images that transition among the different categories. The generated image sequences occupy a more limited region of the image space compared with the original training dataset. Quantitative evaluation using precision and recall metrics indicates that the generated images have high quality but reduced diversity relative to the training dataset. Such successive generation processes are characterized as chaotic dynamics in terms of dynamical system theory. Positive Lyapunov exponents estimated from the generated trajectories confirm the presence of chaotic dynamics, with the Lyapunov dimension of the attractor found to be comparable to the intrinsic dimension of the training data manifold. The results suggest that chaotic dynamics in the image space defined by the deep generative model contribute to the diversity of the generated images, constituting a novel approach for multi-class image generation. This model can be interpreted as an extension of classical associative memory to perform hetero-association among image categories.
Differential abundance analysis is a key component of microbiome studies. While dozens of methods for it exist, currently, there is no consensus on the preferred methods. Correctness of results in differential abundance analysis is an ambiguous concept that cannot be evaluated without employing simulated data, but we argue that consistency of results across datasets should be considered as an essential quality of a well-performing method. We compared the performance of 14 differential abundance analysis methods employing datasets from 54 taxonomic profiling studies based on 16S rRNA gene or shotgun sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from independent studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, the highest consistency without unnecessary reduction in sensitivity was attained by analyzing relative abundances with a non-parametric method (Wilcoxon test or ordinal regression model) or linear regression (MaAsLin2). Comparable performance was also attained by analyzing presence/absence of taxa with logistic regression.
We present LinApart, a routine designed for efficiently performing the univariate partial fraction decomposition of large symbolic expressions. Our method is based on an explicit closed formula for the decomposition of rational functions with fully factorized denominators. We provide implementations in both the Wolfram Mathematica and C languages, made available at //github.com/fekeshazy/LinApart . The routine can provide very significant performance gains over available tools such as the Apart command in Mathematica.
The problems of optimal recovering univariate functions and their derivatives are studied. To solve these problems, two variants of the truncation method are constructed, which are order-optimal both in the sense of accuracy and in terms of the amount of involved Galerkin information. For numerical summation, it has been established how the parameters characterizing the problem being solved affect its stability.
Given a finite set of matrices with integer entries, the matrix mortality problem asks if there exists a product of these matrices equal to the zero matrix. We consider a special case of this problem where all entries of the matrices are nonnegative. This case is equivalent to the NFA mortality problem, which, given an NFA, asks for a word $w$ such that the image of every state under $w$ is the empty set. The size of the alphabet of the NFA is then equal to the number of matrices in the set. We study the length of shortest such words depending on the size of the alphabet. We show that this length for an NFA with $n$ states can be at least $2^n - 1$, $2^{(n - 4)/2}$ and $2^{(n - 2)/3}$ if the size of the alphabet is, respectively, equal to $n$, three and two.
We explore a class of splitting schemes employing implicit-explicit (IMEX) time-stepping to achieve accurate and energy-stable solutions for thin-film equations and Cahn-Hilliard models with variable mobility. This splitting method incorporates a linear, constant coefficient implicit step, facilitating efficient computational implementation. We investigate the influence of stabilizing splitting parameters on the numerical solution computationally, considering various initial conditions. Furthermore, we generate energy-stability plots for the proposed methods, examining different choices of splitting parameter values and timestep sizes. These methods enhance the accuracy of the original bi-harmonic-modified (BHM) approach, while preserving its energy-decreasing property and achieving second-order accuracy. We present numerical experiments to illustrate the performance of the proposed methods.
In many statistical modeling problems, such as classification and regression, it is common to encounter sparse and blocky coefficients. Sparse fused Lasso is specifically designed to recover these sparse and blocky structured features, especially in cases where the design matrix has ultrahigh dimensions, meaning that the number of features significantly surpasses the number of samples. Quantile loss is a well-known robust loss function that is widely used in statistical modeling. In this paper, we propose a new sparse fused lasso classification model, and develop a unified multi-block linearized alternating direction method of multipliers algorithm that effectively selects sparse and blocky features for regression and classification. Our algorithm has been proven to converge with a derived linear convergence rate. Additionally, our algorithm has a significant advantage over existing methods for solving ultrahigh dimensional sparse fused Lasso regression and classification models due to its lower time complexity. Note that the algorithm can be easily extended to solve various existing fused Lasso models. Finally, we present numerical results for several synthetic and real-world examples, which demonstrate the robustness, scalability, and accuracy of the proposed classification model and algorithm
Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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