Accurate segmentation of clustered microcalcifications in mammography is crucial for the diagnosis and treatment of breast cancer. Despite exhibiting expert-level accuracy, recent deep learning advancements in medical image segmentation provide insufficient contribution to practical applications, due to the domain shift resulting from differences in patient postures, individual gland density, and imaging modalities of mammography etc. In this paper, a novel framework named MLN-net, which can accurately segment multi-source images using only single source images, is proposed for clustered microcalcification segmentation. We first propose a source domain image augmentation method to generate multi-source images, leading to improved generalization. And a structure of multiple layer normalization (LN) layers is used to construct the segmentation network, which can be found efficient for clustered microcalcification segmentation in different domains. Additionally, a branch selection strategy is designed for measuring the similarity of the source domain data and the target domain data. To validate the proposed MLN-net, extensive analyses including ablation experiments are performed, comparison of 12 baseline methods. Extensive experiments validate the effectiveness of MLN-net in segmenting clustered microcalcifications from different domains and the its segmentation accuracy surpasses state-of-the-art methods. Code will be available at //github.com/yezanting/MLN-NET-VERSON1.
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Software design debt aims to elucidate the rectification attempts of the present design flaws and studies the influence of those to the cost and time of the software. Design smells are a key cause of incurring design debt. Although the impact of design smells on design debt have been predominantly considered in current literature, how design smells are caused due to not following software engineering best practices require more exploration. This research provides a tool which is used for design smell detection in Java software by analyzing large volume of source codes. More specifically, 409,539 Lines of Code (LoC) and 17,760 class files of open source Java software are analyzed here. Obtained results show desirable precision values ranging from 81.01\% to 93.43\%. Based on the output of the tool, a study is conducted to relate the cause of the detected design smells to two software engineering challenges namely "irregular team meetings" and "scope creep". As a result, the gained information will provide insight to the software engineers to take necessary steps of design remediation actions.
Spatiotemporal dynamic medical imaging is critical in clinical applications, such as tomographic imaging of the heart or lung. To address such kind of spatiotemporal imaging problems, essentially, a time-dependent dynamic inverse problem, the variational model with intensity, edge feature and topology preservations was proposed for joint image reconstruction and motion estimation in the previous paper [C. Chen, B. Gris, and O. \"Oktem, SIAM J. Imaging Sci., 12 (2019), pp. 1686--1719], which is suitable to invert the time-dependent sparse sampling data for the motion target with large diffeomorphic deformations. However, the existence of solution to the model has not been given yet. In order to preserve its topological structure and edge feature of the motion target, the unknown velocity field in the model is restricted into the admissible Hilbert space, and the unknown template image is modeled in the space of bounded variation functions. Under this framework, this paper analyzes and proves the solution existence of its time-discretized version from the point view of optimal control. Specifically, there exists a constraint of transport equation in the equivalent optimal control model. We rigorously demonstrate the closure of the equation, including the solution existence and uniqueness, the stability of the associated nonlinear solution operator, and the convergence. Finally, the solution existence of that model can be concluded.
Neural oscillations are considered to be brain-specific signatures of information processing and communication in the brain. They also reflect pathological brain activity in neurological disorders, thus offering a basis for diagnoses and forecasting. Epilepsy is one of the most common neurological disorders, characterized by abnormal synchronization and desynchronization of the oscillations in the brain. About one third of epilepsy cases are pharmacoresistant, and as such emphasize the need for novel therapy approaches, where brain stimulation appears to be a promising therapeutic option. The development of brain stimulation paradigms, however, is often based on generalized assumptions about brain dynamics, although it is known that significant differences occur between patients and brain states. We developed a framework to extract individualized predictive models of epileptic network dynamics directly from EEG data. The models are based on the dominant coherent oscillations and their dynamical coupling, thus combining an established interpretation of dynamics through neural oscillations, with accurate patient-specific features. We show that it is possible to build a direct correspondence between the models of brain-network dynamics under periodic driving, and the mechanism of neural entrainment via periodic stimulation. When our framework is applied to EEG recordings of patients in status epilepticus (a brain state of perpetual seizure activity), it yields a model-driven predictive analysis of the therapeutic performance of periodic brain stimulation. This suggests that periodic brain stimulation can drive pathological states of epileptic network dynamics towards a healthy functional brain state.
We observe a large variety of robots in terms of their bodies, sensors, and actuators. Given the commonalities in the skill sets, teaching each skill to each different robot independently is inefficient and not scalable when the large variety in the robotic landscape is considered. If we can learn the correspondences between the sensorimotor spaces of different robots, we can expect a skill that is learned in one robot can be more directly and easily transferred to the other robots. In this paper, we propose a method to learn correspondences between robots that have significant differences in their morphologies: a fixed-based manipulator robot with joint control and a differential drive mobile robot. For this, both robots are first given demonstrations that achieve the same tasks. A common latent representation is formed while learning the corresponding policies. After this initial learning stage, the observation of a new task execution by one robot becomes sufficient to generate a latent space representation pertaining to the other robot to achieve the same task. We verified our system in a set of experiments where the correspondence between two simulated robots is learned (1) when the robots need to follow the same paths to achieve the same task, (2) when the robots need to follow different trajectories to achieve the same task, and (3) when complexities of the required sensorimotor trajectories are different for the robots considered. We also provide a proof-of-the-concept realization of correspondence learning between a real manipulator robot and a simulated mobile robot.
Twitter bots are a controversial element of the platform, and their negative impact is well known. In the field of scientific communication, they have been perceived in a more positive light, and the accounts that serve as feeds alerting about scientific publications are quite common. However, despite being aware of the presence of bots in the dissemination of science, no large-scale estimations have been made nor has it been evaluated if they can truly interfere with altmetrics. Analyzing a dataset of 3,744,231 papers published between 2017 and 2021 and their associated 51,230,936 Twitter mentions, our goal was to determine the volume of publications mentioned by bots and whether they skew altmetrics indicators. Using the BotometerLite API, we categorized Twitter accounts based on their likelihood of being bots. The results showed that 11,073 accounts (0.23% of total users) exhibited automated behavior, contributing to 4.72% of all mentions. A significant bias was observed in the activity of bots. Their presence was particularly pronounced in disciplines such as Mathematics, Physics, and Space Sciences, with some specialties even exceeding 70% of the tweets. However, these are extreme cases, and the impact of this activity on altmetrics varies by speciality, with minimal influence in Arts & Humanities and Social Sciences. This research emphasizes the importance of distinguishing between specialties and disciplines when using Twitter as an altmetric.
Computer-assisted diagnostic and prognostic systems of the future should be capable of simultaneously processing multimodal data. Multimodal deep learning (MDL), which involves the integration of multiple sources of data, such as images and text, has the potential to revolutionize the analysis and interpretation of biomedical data. However, it only caught researchers' attention recently. To this end, there is a critical need to conduct a systematic review on this topic, identify the limitations of current work, and explore future directions. In this scoping review, we aim to provide a comprehensive overview of the current state of the field and identify key concepts, types of studies, and research gaps with a focus on biomedical images and texts joint learning, mainly because these two were the most commonly available data types in MDL research. This study reviewed the current uses of multimodal deep learning on five tasks: (1) Report generation, (2) Visual question answering, (3) Cross-modal retrieval, (4) Computer-aided diagnosis, and (5) Semantic segmentation. Our results highlight the diverse applications and potential of MDL and suggest directions for future research in the field. We hope our review will facilitate the collaboration of natural language processing (NLP) and medical imaging communities and support the next generation of decision-making and computer-assisted diagnostic system development.
Artificial neural networks thrive in solving the classification problem for a particular rigid task, acquiring knowledge through generalized learning behaviour from a distinct training phase. The resulting network resembles a static entity of knowledge, with endeavours to extend this knowledge without targeting the original task resulting in a catastrophic forgetting. Continual learning shifts this paradigm towards networks that can continually accumulate knowledge over different tasks without the need to retrain from scratch. We focus on task incremental classification, where tasks arrive sequentially and are delineated by clear boundaries. Our main contributions concern 1) a taxonomy and extensive overview of the state-of-the-art, 2) a novel framework to continually determine the stability-plasticity trade-off of the continual learner, 3) a comprehensive experimental comparison of 11 state-of-the-art continual learning methods and 4 baselines. We empirically scrutinize method strengths and weaknesses on three benchmarks, considering Tiny Imagenet and large-scale unbalanced iNaturalist and a sequence of recognition datasets. We study the influence of model capacity, weight decay and dropout regularization, and the order in which the tasks are presented, and qualitatively compare methods in terms of required memory, computation time, and storage.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.
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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