This review presents various image segmentation methods using complex networks. Image segmentation is one of the important steps in image analysis as it helps analyze and understand complex images. At first, it has been tried to classify complex networks based on how it being used in image segmentation. In computer vision and image processing applications, image segmentation is essential for analyzing complex images with irregular shapes, textures, or overlapping boundaries. Advanced algorithms make use of machine learning, clustering, edge detection, and region-growing techniques. Graph theory principles combined with community detection-based methods allow for more precise analysis and interpretation of complex images. Hybrid approaches combine multiple techniques for comprehensive, robust segmentation, improving results in computer vision and image processing tasks.
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We present a fully-integrated lattice Boltzmann (LB) method for fluid--structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid--fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. With simulations of complex suspensions mixing, we highlight potentials of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.
Colocalization analyses assess whether two traits are affected by the same or distinct causal genetic variants in a single gene region. A class of Bayesian colocalization tests are now routinely used in practice; for example, for genetic analyses in drug development pipelines. In this work, we consider an alternative frequentist approach to colocalization testing that examines the proportionality of genetic associations with each trait. The proportional colocalization approach uses markedly different assumptions to Bayesian colocalization tests, and therefore can provide valuable complementary evidence in cases where Bayesian colocalization results are inconclusive or sensitive to priors. We propose a novel conditional test of proportional colocalization, prop-coloc-cond, that aims to account for the uncertainty in variant selection, in order to recover accurate type I error control. The test can be implemented straightforwardly, requiring only summary data on genetic associations. Simulation evidence and an empirical investigation into GLP1R gene expression demonstrates how tests of proportional colocalization can offer important insights in conjunction with Bayesian colocalization tests.
Detecting specific structures in a network has been a very active theme of research in distributed computing for at least a decade. In this paper, we start the study of subgraph detection from the perspective of local certification. Remember that a local certification is a distributed mechanism enabling the nodes of a network to check the correctness of the current configuration, thanks to small pieces of information called certificates. Our main question is: For a given graph $H$, what is the minimum certificate size that allows checking that the network does not contain $H$ as a (possibly induced) subgraph? We show a variety of lower and upper bounds, uncovering an interesting interplay between the optimal certificate size, the size of the forbidden subgraph, and the locality of the verification. Along the way we introduce several new technical tools, in particular what we call the \emph{layered map}, which is not specific to forbidden subgraphs and that we expect to be useful for certifying many other properties.
A major challenge in computed tomography is reconstructing objects from incomplete data. An increasingly popular solution for these problems is to incorporate deep learning models into reconstruction algorithms. This study introduces a novel approach by integrating a Fourier neural operator (FNO) into the Filtered Backprojection (FBP) reconstruction method, yielding the FNO back projection (FNO-BP) network. We employ moment conditions for sinogram extrapolation to assist the model in mitigating artefacts from limited data. Notably, our deep learning architecture maintains a runtime comparable to classical filtered back projection (FBP) reconstructions, ensuring swift performance during both inference and training. We assess our reconstruction method in the context of the Helsinki Tomography Challenge 2022 and also compare it against regular FBP methods.
The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.
Motion detection is a primary task required for robotic systems to perceive and navigate in their environment. Proposed in the literature bioinspired neuromorphic Time-Difference Encoder (TDE-2) combines event-based sensors and processors with spiking neural networks to provide real-time and energy-efficient motion detection through extracting temporal correlations between two points in space. However, on the algorithmic level, this design leads to loss of direction-selectivity of individual TDEs in textured environments. Here we propose an augmented 3-point TDE (TDE-3) with additional inhibitory input that makes TDE-3 direction-selectivity robust in textured environments. We developed a procedure to train the new TDE-3 using backpropagation through time and surrogate gradients to linearly map input velocities into an output spike count or an Inter-Spike Interval (ISI). Our work is the first instance of training a spiking neuron to have a specific ISI. Using synthetic data we compared training and inference with spike count and ISI with respect to changes in stimuli dynamic range, spatial frequency, and level of noise. ISI turns out to be more robust towards variation in spatial frequency, whereas the spike count is a more reliable training signal in the presence of noise. We performed the first in-depth quantitative investigation of optical flow coding with TDE and compared TDE-2 vs TDE-3 in terms of energy-efficiency and coding precision. Results show that on the network level both detectors show similar precision (20 degree angular error, 88% correlation with ground truth). Yet, due to the more robust direction-selectivity of individual TDEs, TDE-3 based network spike less and hence is more energy-efficient. Reported precision is on par with model-based methods but the spike-based processing of the TDEs provides allows more energy-efficient inference with neuromorphic hardware.
This paper presents a statistical forward model for a Compton imaging system, called Compton imager. This system, under development at the University of Illinois Urbana Champaign, is a variant of Compton cameras with a single type of sensors which can simultaneously act as scatterers and absorbers. This imager is convenient for imaging situations requiring a wide field of view. The proposed statistical forward model is then used to solve the inverse problem of estimating the location and energy of point-like sources from observed data. This inverse problem is formulated and solved in a Bayesian framework by using a Metropolis within Gibbs algorithm for the estimation of the location, and an expectation-maximization algorithm for the estimation of the energy. This approach leads to more accurate estimation when compared with the deterministic standard back-projection approach, with the additional benefit of uncertainty quantification in the low photon imaging setting.
Normalizing flow is a class of deep generative models for efficient sampling and likelihood estimation, which achieves attractive performance, particularly in high dimensions. The flow is often implemented using a sequence of invertible residual blocks. Existing works adopt special network architectures and regularization of flow trajectories. In this paper, we develop a neural ODE flow network called JKO-iFlow, inspired by the Jordan-Kinderleherer-Otto (JKO) scheme, which unfolds the discrete-time dynamic of the Wasserstein gradient flow. The proposed method stacks residual blocks one after another, allowing efficient block-wise training of the residual blocks, avoiding sampling SDE trajectories and score matching or variational learning, thus reducing the memory load and difficulty in end-to-end training. We also develop adaptive time reparameterization of the flow network with a progressive refinement of the induced trajectory in probability space to improve the model accuracy further. Experiments with synthetic and real data show that the proposed JKO-iFlow network achieves competitive performance compared with existing flow and diffusion models at a significantly reduced computational and memory cost.
Nowadays, the Convolutional Neural Networks (CNNs) have achieved impressive performance on many computer vision related tasks, such as object detection, image recognition, image retrieval, etc. These achievements benefit from the CNNs outstanding capability to learn the input features with deep layers of neuron structures and iterative training process. However, these learned features are hard to identify and interpret from a human vision perspective, causing a lack of understanding of the CNNs internal working mechanism. To improve the CNN interpretability, the CNN visualization is well utilized as a qualitative analysis method, which translates the internal features into visually perceptible patterns. And many CNN visualization works have been proposed in the literature to interpret the CNN in perspectives of network structure, operation, and semantic concept. In this paper, we expect to provide a comprehensive survey of several representative CNN visualization methods, including Activation Maximization, Network Inversion, Deconvolutional Neural Networks (DeconvNet), and Network Dissection based visualization. These methods are presented in terms of motivations, algorithms, and experiment results. Based on these visualization methods, we also discuss their practical applications to demonstrate the significance of the CNN interpretability in areas of network design, optimization, security enhancement, etc.
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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