We introduce CartiMorph, a framework for automated knee articular cartilage morphometrics. It takes an image as input and generates quantitative metrics for cartilage subregions, including the percentage of full-thickness cartilage loss (FCL), mean thickness, surface area, and volume. CartiMorph leverages the power of deep learning models for hierarchical image feature representation. Deep learning models were trained and validated for tissue segmentation, template construction, and template-to-image registration. We established methods for surface-normal-based cartilage thickness mapping, FCL estimation, and rule-based cartilage parcellation. Our cartilage thickness map showed less error in thin and peripheral regions. We evaluated the effectiveness of the adopted segmentation model by comparing the quantitative metrics obtained from model segmentation and those from manual segmentation. The root-mean-squared deviation of the FCL measurements was less than 8%, and strong correlations were observed for the mean thickness (Pearson's correlation coefficient $\rho \in [0.82,0.97]$), surface area ($\rho \in [0.82,0.98]$) and volume ($\rho \in [0.89,0.98]$) measurements. We compared our FCL measurements with those from a previous study and found that our measurements deviated less from the ground truths. We observed superior performance of the proposed rule-based cartilage parcellation method compared with the atlas-based approach. CartiMorph has the potential to promote imaging biomarkers discovery for knee osteoarthritis.
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A problem related to the development of algorithms designed to find the structure of artificial neural network used for behavioural (black-box) modelling of selected dynamic processes has been addressed in this paper. The research has included four original proposals of algorithms dedicated to neural network architecture search. Algorithms have been based on well-known optimisation techniques such as evolutionary algorithms and gradient descent methods. In the presented research an artificial neural network of recurrent type has been used, whose architecture has been selected in an optimised way based on the above-mentioned algorithms. The optimality has been understood as achieving a trade-off between the size of the neural network and its accuracy in capturing the response of the mathematical model under which it has been learnt. During the optimisation, original specialised evolutionary operators have been proposed. The research involved an extended validation study based on data generated from a mathematical model of the fast processes occurring in a pressurised water nuclear reactor.
We describe a software package, TomOpt, developed to optimise the geometrical layout and specifications of detectors designed for tomography by scattering of cosmic-ray muons. The software exploits differentiable programming for the modeling of muon interactions with detectors and scanned volumes, the inference of volume properties, and the optimisation cycle performing the loss minimisation. In doing so, we provide the first demonstration of end-to-end-differentiable and inference-aware optimisation of particle physics instruments. We study the performance of the software on a relevant benchmark scenarios and discuss its potential applications.
StreamBed is a capacity planning system for stream processing. It predicts, ahead of any production deployment, the resources that a query will require to process an incoming data rate sustainably, and the appropriate configuration of these resources. StreamBed builds a capacity planning model by piloting a series of runs of the target query in a small-scale, controlled testbed. We implement StreamBed for the popular Flink DSP engine. Our evaluation with large-scale queries of the Nexmark benchmark demonstrates that StreamBed can effectively and accurately predict capacity requirements for jobs spanning more than 1,000 cores using a testbed of only 48 cores.
The increasing capacities of large language models (LLMs) present an unprecedented opportunity to scale up data analytics in the humanities and social sciences, augmenting and automating qualitative analytic tasks previously typically allocated to human labor. This contribution proposes a systematic mixed methods framework to harness qualitative analytic expertise, machine scalability, and rigorous quantification, with attention to transparency and replicability. 16 machine-assisted case studies are showcased as proof of concept. Tasks include linguistic and discourse analysis, lexical semantic change detection, interview analysis, historical event cause inference and text mining, detection of political stance, text and idea reuse, genre composition in literature and film; social network inference, automated lexicography, missing metadata augmentation, and multimodal visual cultural analytics. In contrast to the focus on English in the emerging LLM applicability literature, many examples here deal with scenarios involving smaller languages and historical texts prone to digitization distortions. In all but the most difficult tasks requiring expert knowledge, generative LLMs can demonstrably serve as viable research instruments. LLM (and human) annotations may contain errors and variation, but the agreement rate can and should be accounted for in subsequent statistical modeling; a bootstrapping approach is discussed. The replications among the case studies illustrate how tasks previously requiring potentially months of team effort and complex computational pipelines, can now be accomplished by an LLM-assisted scholar in a fraction of the time. Importantly, this approach is not intended to replace, but to augment researcher knowledge and skills. With these opportunities in sight, qualitative expertise and the ability to pose insightful questions have arguably never been more critical.
The problem of multi-object tracking (MOT) consists in detecting and tracking all the objects in a video sequence while keeping a unique identifier for each object. It is a challenging and fundamental problem for robotics. In precision agriculture the challenge of achieving a satisfactory solution is amplified by extreme camera motion, sudden illumination changes, and strong occlusions. Most modern trackers rely on the appearance of objects rather than motion for association, which can be ineffective when most targets are static objects with the same appearance, as in the agricultural case. To this end, on the trail of SORT [5], we propose AgriSORT, a simple, online, real-time tracking-by-detection pipeline for precision agriculture based only on motion information that allows for accurate and fast propagation of tracks between frames. The main focuses of AgriSORT are efficiency, flexibility, minimal dependencies, and ease of deployment on robotic platforms. We test the proposed pipeline on a novel MOT benchmark specifically tailored for the agricultural context, based on video sequences taken in a table grape vineyard, particularly challenging due to strong self-similarity and density of the instances. Both the code and the dataset are available for future comparisons.
Prediction is a classic challenge in spatial statistics and the inclusion of spatial covariates can greatly improve predictive performance when incorporated into a model with latent spatial effects. It is desirable to develop flexible regression models that allow for nonlinearities and interactions in the covariate structure. Machine learning models have been suggested in the spatial context, allowing for spatial dependence in the residuals, but fail to provide reliable uncertainty estimates. In this paper, we investigate a novel combination of a Gaussian process spatial model and a Bayesian Additive Regression Tree (BART) model. The computational burden of the approach is reduced by combining Markov chain Monte Carlo (MCMC) with the Integrated Nested Laplace Approximation (INLA) technique. We study the performance of the method via simulations and use the model to predict anthropometric responses, collected via household cluster samples in Kenya.
Earth system models suffer from various structural and parametric errors in their representation of nonlinear, multi-scale processes, leading to uncertainties in their long-term projections. The effects of many of these errors (particularly those due to fast physics) can be quantified in short-term simulations, e.g., as differences between the predicted and observed states (analysis increments). With the increase in the availability of high-quality observations and simulations, learning nudging from these increments to correct model errors has become an active research area. However, most studies focus on using neural networks, which while powerful, are hard to interpret, are data-hungry, and poorly generalize out-of-distribution. Here, we show the capabilities of Model Error Discovery with Interpretability and Data Assimilation (MEDIDA), a general, data-efficient framework that uses sparsity-promoting equation-discovery techniques to learn model errors from analysis increments. Using two-layer quasi-geostrophic turbulence as the test case, MEDIDA is shown to successfully discover various linear and nonlinear structural/parametric errors when full observations are available. Discovery from spatially sparse observations is found to require highly accurate interpolation schemes. While NNs have shown success as interpolators in recent studies, here, they are found inadequate due to their inability to accurately represent small scales, a phenomenon known as spectral bias. We show that a general remedy, adding a random Fourier feature layer to the NN, resolves this issue enabling MEDIDA to successfully discover model errors from sparse observations. These promising results suggest that with further development, MEDIDA could be scaled up to models of the Earth system and real observations.
Surface defect inspection is of great importance for industrial manufacture and production. Though defect inspection methods based on deep learning have made significant progress, there are still some challenges for these methods, such as indistinguishable weak defects and defect-like interference in the background. To address these issues, we propose a transformer network with multi-stage CNN (Convolutional Neural Network) feature injection for surface defect segmentation, which is a UNet-like structure named CINFormer. CINFormer presents a simple yet effective feature integration mechanism that injects the multi-level CNN features of the input image into different stages of the transformer network in the encoder. This can maintain the merit of CNN capturing detailed features and that of transformer depressing noises in the background, which facilitates accurate defect detection. In addition, CINFormer presents a Top-K self-attention module to focus on tokens with more important information about the defects, so as to further reduce the impact of the redundant background. Extensive experiments conducted on the surface defect datasets DAGM 2007, Magnetic tile, and NEU show that the proposed CINFormer achieves state-of-the-art performance in defect detection.
We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.
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.
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