The reconstruction kernel in computed tomography (CT) generation determines the texture of the image. Consistency in reconstruction kernels is important as the underlying CT texture can impact measurements during quantitative image analysis. Harmonization (i.e., kernel conversion) minimizes differences in measurements due to inconsistent reconstruction kernels. Existing methods investigate harmonization of CT scans in single or multiple manufacturers. However, these methods require paired scans of hard and soft reconstruction kernels that are spatially and anatomically aligned. Additionally, a large number of models need to be trained across different kernel pairs within manufacturers. In this study, we adopt an unpaired image translation approach to investigate harmonization between and across reconstruction kernels from different manufacturers by constructing a multipath cycle generative adversarial network (GAN). We use hard and soft reconstruction kernels from the Siemens and GE vendors from the National Lung Screening Trial dataset. We use 50 scans from each reconstruction kernel and train a multipath cycle GAN. To evaluate the effect of harmonization on the reconstruction kernels, we harmonize 50 scans each from Siemens hard kernel, GE soft kernel and GE hard kernel to a reference Siemens soft kernel (B30f) and evaluate percent emphysema. We fit a linear model by considering the age, smoking status, sex and vendor and perform an analysis of variance (ANOVA) on the emphysema scores. Our approach minimizes differences in emphysema measurement and highlights the impact of age, sex, smoking status and vendor on emphysema quantification.
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Generation of simulated detector response to collision products is crucial to data analysis in particle physics, but computationally very expensive. One subdetector, the calorimeter, dominates the computational time due to the high granularity of its cells and complexity of the interactions. Generative models can provide more rapid sample production, but currently require significant effort to optimize performance for specific detector geometries, often requiring many models to describe the varying cell sizes and arrangements, without the ability to generalize to other geometries. We develop a $\textit{geometry-aware}$ autoregressive model, which learns how the calorimeter response varies with geometry, and is capable of generating simulated responses to unseen geometries without additional training. The geometry-aware model outperforms a baseline unaware model by over $50\%$ in several metrics such as the Wasserstein distance between the generated and the true distributions of key quantities which summarize the simulated response. A single geometry-aware model could replace the hundreds of generative models currently designed for calorimeter simulation by physicists analyzing data collected at the Large Hadron Collider. This proof-of-concept study motivates the design of a foundational model that will be a crucial tool for the study of future detectors, dramatically reducing the large upfront investment usually needed to develop generative calorimeter models.
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.
We study single-image super-resolution algorithms for photons at collider experiments based on generative adversarial networks. We treat the energy depositions of simulated electromagnetic showers of photons and neutral-pion decays in a toy electromagnetic calorimeter as 2D images and we train super-resolution networks to generate images with an artificially increased resolution by a factor of four in each dimension. The generated images are able to reproduce features of the electromagnetic showers that are not obvious from the images at nominal resolution. Using the artificially-enhanced images for the reconstruction of shower-shape variables and of the position of the shower center results in significant improvements. We additionally investigate the utilization of the generated images as a pre-processing step for deep-learning photon-identification algorithms and observe improvements in the case of training samples of small size.
SCONE-GAN presents an end-to-end image translation, which is shown to be effective for learning to generate realistic and diverse scenery images. Most current image-to-image translation approaches are devised as two mappings: a translation from the source to target domain and another to represent its inverse. While successful in many applications, these approaches may suffer from generating trivial solutions with limited diversity. That is because these methods learn more frequent associations rather than the scene structures. To mitigate the problem, we propose SCONE-GAN that utilises graph convolutional networks to learn the objects dependencies, maintain the image structure and preserve its semantics while transferring images into the target domain. For more realistic and diverse image generation we introduce style reference image. We enforce the model to maximize the mutual information between the style image and output. The proposed method explicitly maximizes the mutual information between the related patches, thus encouraging the generator to produce more diverse images. We validate the proposed algorithm for image-to-image translation and stylizing outdoor images. Both qualitative and quantitative results demonstrate the effectiveness of our approach on four dataset.
Most sequence sketching methods work by selecting specific $k$-mers from sequences so that the similarity between two sequences can be estimated using only the sketches. Estimating sequence similarity is much faster using sketches than using sequence alignment, hence sketching methods are used to reduce the computational requirements of computational biology software packages. Applications using sketches often rely on properties of the $k$-mer selection procedure to ensure that using a sketch does not degrade the quality of the results compared with using sequence alignment. In particular the window guarantee ensures that no long region of the sequence goes unrepresented in the sketch. A sketching method with a window guarantee corresponds to a Decycling Set, aka an unavoidable sets of $k$-mers. Any long enough sequence must contain a $k$-mer from any decycling set (hence, it is unavoidable). Conversely, a decycling set defines a sketching method by selecting the $k$-mers from the set. Although current methods use one of a small number of sketching method families, the space of decycling sets is much larger, and largely unexplored. Finding decycling sets with desirable characteristics is a promising approach to discovering new sketching methods with improved performance (e.g., with small window guarantee). The Minimum Decycling Sets (MDSs) are of particular interest because of their small size. Only two algorithms, by Mykkeltveit and Champarnaud, are known to generate two particular MDSs, although there is a vast number of alternative MDSs. We provide a simple method that allows one to explore the space of MDSs and to find sets optimized for desirable properties. We give evidence that the Mykkeltveit sets are close to optimal regarding one particular property, the remaining path length.
We propose a straightforward solution for detecting scarce topics in unbalanced short-text datasets. Our approach, named CWUTM (Topic model based on co-occurrence word networks for unbalanced short text datasets), Our approach addresses the challenge of sparse and unbalanced short text topics by mitigating the effects of incidental word co-occurrence. This allows our model to prioritize the identification of scarce topics (Low-frequency topics). Unlike previous methods, CWUTM leverages co-occurrence word networks to capture the topic distribution of each word, and we enhanced the sensitivity in identifying scarce topics by redefining the calculation of node activity and normalizing the representation of both scarce and abundant topics to some extent. Moreover, CWUTM adopts Gibbs sampling, similar to LDA, making it easily adaptable to various application scenarios. Our extensive experimental validation on unbalanced short-text datasets demonstrates the superiority of CWUTM compared to baseline approaches in discovering scarce topics. According to the experimental results the proposed model is effective in early and accurate detection of emerging topics or unexpected events on social platforms.
Quadratic NURBS-based discretizations of the Galerkin method suffer from volumetric locking when applied to nearly-incompressible linear elasticity. Volumetric locking causes not only smaller displacements than expected, but also large-amplitude spurious oscillations of normal stresses. Continuous-assumed-strain (CAS) elements have been recently introduced to remove membrane locking in quadratic NURBS-based discretizations of linear plane curved Kirchhoff rods (Casquero et al., CMAME, 2022). In this work, we propose two generalizations of CAS elements (named CAS1 and CAS2 elements) to overcome volumetric locking in quadratic NURBS-based discretizations of nearly-incompressible linear elasticity. CAS1 elements linearly interpolate the strains at the knots in each direction for the term in the variational form involving the first Lam\'e parameter while CAS2 elements linearly interpolate the dilatational strains at the knots in each direction. For both element types, a displacement vector with C1 continuity across element boundaries results in assumed strains with C0 continuity across element boundaries. In addition, the implementation of the two locking treatments proposed in this work does not require any additional global or element matrix operations such as matrix inversions or matrix multiplications. The locking treatments are applied at the element level and the nonzero pattern of the global stiffness matrix is preserved. The numerical examples solved in this work show that CAS1 and CAS2 elements, using either two or three Gauss-Legrendre quadrature points per direction, are effective locking treatments since they not only result in more accurate displacements for coarse meshes, but also remove the spurious oscillations of normal stresses.
We consider the community recovery problem on a multilayer variant of the hypergraph stochastic block model (HSBM). Each layer is associated with an independent realization of a d-uniform HSBM on N vertices. Given the similarity matrix containing the aggregated number of hyperedges incident to each pair of vertices, the goal is to obtain a partition of the N vertices into disjoint communities. In this work, we investigate a semidefinite programming (SDP) approach and obtain information-theoretic conditions on the model parameters that guarantee exact recovery both in the assortative and the disassortative cases.
Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.
Scene graph generation (SGG) and human-object interaction (HOI) detection are two important visual tasks aiming at localising and recognising relationships between objects, and interactions between humans and objects, respectively. Prevailing works treat these tasks as distinct tasks, leading to the development of task-specific models tailored to individual datasets. However, we posit that the presence of visual relationships can furnish crucial contextual and intricate relational cues that significantly augment the inference of human-object interactions. This motivates us to think if there is a natural intrinsic relationship between the two tasks, where scene graphs can serve as a source for inferring human-object interactions. In light of this, we introduce SG2HOI+, a unified one-step model based on the Transformer architecture. Our approach employs two interactive hierarchical Transformers to seamlessly unify the tasks of SGG and HOI detection. Concretely, we initiate a relation Transformer tasked with generating relation triples from a suite of visual features. Subsequently, we employ another transformer-based decoder to predict human-object interactions based on the generated relation triples. A comprehensive series of experiments conducted across established benchmark datasets including Visual Genome, V-COCO, and HICO-DET demonstrates the compelling performance of our SG2HOI+ model in comparison to prevalent one-stage SGG models. Remarkably, our approach achieves competitive performance when compared to state-of-the-art HOI methods. Additionally, we observe that our SG2HOI+ jointly trained on both SGG and HOI tasks in an end-to-end manner yields substantial improvements for both tasks compared to individualized training paradigms.
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