Mapping neuroanatomy, in the pursuit of linking hypothesized computational models consistent with observed functions to the actual physical structures, is a long-standing fundamental problem in neuroscience. One primary interest is in mapping the network structure of neural circuits by identifying the morphology of each neuron and the locations of synaptic connections between neurons, a field called connectomics.

The paper is well-written, with lots of details provided. The studied problem is definitely of great impact and would significantly benefit the community of neuroscience. The reviewer noticed the large size of the problem and appreciates the considerable amount of works achieved, as described by the paper. On the other hand, I also want to point out some associated weakness: 1. To my understanding, two aspects which are the keys to the segmentation performance are: (1) The local DNN evaluation of shape descriptors in terms of energy, and (2) The back-end guidance of (super)voxel agglomeration.

In this work, we propose a set of physics-informed geometric operators (GOs) to enrich the geometric data provided for training surrogate/discriminative models, dimension reduction, and generative models, typically employed for performance prediction, dimension reduction, and creating data-driven parameterisations, respectively. However, as both the input and output streams of these models consist of low-level shape representations, they often fail to capture shape characteristics essential for performance analyses. Therefore, the proposed GOs exploit the differential and integral properties of shapes--accessed through Fourier descriptors, curvature integrals, geometric moments, and their invariants--to infuse high-level intrinsic geometric information and physics into the feature vector used for training, even when employing simple model architectures or low-level parametric descriptions. We showed that for surrogate modelling, along with the inclusion of the notion of physics, GOs enact regularisation to reduce over-fitting and enhance generalisation to new, unseen designs. Furthermore, through extensive experimentation, we demonstrate that for dimension reduction and generative models, incorporating the proposed GOs enriches the training data with compact global and local geometric features. This significantly enhances the quality of the resulting latent space, thereby facilitating the generation of valid and diverse designs. Lastly, we also show that GOs can enable learning parametric sensitivities to a great extent. Consequently, these enhancements accelerate the convergence rate of shape optimisers towards optimal solutions.

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

In this paper, a new system based on combinations of a shape descriptor and a contour descriptor has been proposed for classifying inserts in milling processes according to their wear level following a computer vision based approach. To describe the wear region shape we have proposed a new descriptor called ShapeFeat and its contour has been characterized using the method BORCHIZ that, to the best of our knowledge, achieves the best performance for tool wear monitoring following a computer vision-based approach. Results show that the combination of BORCHIZ with ShapeFeat using a late fusion method improves the classification performance significantly, obtaining an accuracy of 91.44% in the binary classification (i.e. the classification of the wear as high or low) and 82.90% using three target classes (i.e. classification of the wear as high, medium or low). These results outperform the ones obtained by both descriptors used on their own, which achieve accuracies of 88.70 and 80.67% for two and three classes, respectively, using ShapeFeat and 87.06 and 80.24% with B-ORCHIZ. This study yielded encouraging results for the manufacturing community in order to classify automatically the inserts in terms of their wear for milling processes.

In recent years, the results of view-based 3D shape recognition methods have saturated, and models with excellent performance cannot be deployed on memory-limited devices due to their huge size of parameters. To address this problem, we introduce a compression method based on knowledge distillation for this field, which largely reduces the number of parameters while preserving model performance as much as possible. Specifically, to enhance the capabilities of smaller models, we design a high-performing large model called Group Multi-view Vision Transformer (GMViT). In GMViT, the view-level ViT first establishes relationships between view-level features. Additionally, to capture deeper features, we employ the grouping module to enhance view-level features into group-level features. Finally, the group-level ViT aggregates group-level features into complete, well-formed 3D shape descriptors. Notably, in both ViTs, we introduce spatial encoding of camera coordinates as innovative position embeddings. Furthermore, we propose two compressed versions based on GMViT, namely GMViT-simple and GMViT-mini. To enhance the training effectiveness of the small models, we introduce a knowledge distillation method throughout the GMViT process, where the key outputs of each GMViT component serve as distillation targets. Extensive experiments demonstrate the efficacy of the proposed method. The large model GMViT achieves excellent 3D classification and retrieval results on the benchmark datasets ModelNet, ShapeNetCore55, and MCB. The smaller models, GMViT-simple and GMViT-mini, reduce the parameter size by 8 and 17.6 times, respectively, and improve shape recognition speed by 1.5 times on average, while preserving at least 90% of the classification and retrieval performance.

Inspired by the recent achievements of machine learning in diverse domains, data-driven metamaterials design has emerged as a compelling paradigm that can unlock the potential of multiscale architectures. The model-centric research trend, however, lacks principled frameworks dedicated to data acquisition, whose quality propagates into the downstream tasks. Often built by naive space-filling design in shape descriptor space, metamaterial datasets suffer from property distributions that are either highly imbalanced or at odds with design tasks of interest. To this end, we present t-METASET: an active-learning-based data acquisition framework aiming to guide both diverse and task-aware data generation. Distinctly, we seek a solution to a commonplace yet frequently overlooked scenario at early stages of data-driven design of metamaterials: when a massive (~O(10^4 )) shape-only library has been prepared with no properties evaluated. The key idea is to harness a data-driven shape descriptor learned from generative models, fit a sparse regressor as a start-up agent, and leverage metrics related to diversity to drive data acquisition to areas that help designers fulfill design goals. We validate the proposed framework in three deployment cases, which encompass general use, task-specific use, and tailorable use. Two large-scale mechanical metamaterial datasets are used to demonstrate the efficacy. Applicable to general image-based design representations, t-METASET could boost future advancements in data-driven design.

The sensitivity of heterogeneous energetic (HE) materials (propellants, explosives, and pyrotechnics) is critically dependent on their microstructure. Initiation of chemical reactions occurs at hot spots due to energy localization at sites of porosities and other defects. Emerging multi-scale predictive models of HE response to loads account for the physics at the meso-scale, i.e. at the scale of statistically representative clusters of particles and other features in the microstructure. Meso-scale physics is infused in machine-learned closure models informed by resolved meso-scale simulations. Since microstructures are stochastic, ensembles of meso-scale simulations are required to quantify hot spot ignition and growth and to develop models for microstructure-dependent energy deposition rates. We propose utilizing generative adversarial networks (GAN) to spawn ensembles of synthetic heterogeneous energetic material microstructures. The method generates qualitatively and quantitatively realistic microstructures by learning from images of HE microstructures. We show that the proposed GAN method also permits the generation of new morphologies, where the porosity distribution can be controlled and spatially manipulated. Such control paves the way for the design of novel microstructures to engineer HE materials for targeted performance in a materials-by-design framework.

How humans can distinguish between general categories of objects? Are the subcategories of living things visually distinctive? In a number of semantic-category deficits, patients are good at making broad categorization but are unable to remember fine and specific details. It has been well accepted that general information about concepts are more robust to damages related to semantic memory. Results from patients with semantic memory disorders demonstrate the loss of ability in subcategory recognition. While bottom-up feature construction has been studied in detail, little attention has been served to top-down approach and the type of features that could account for general categorization. In this paper, we show that broad categories of animal and plant are visually distinguishable without processing textural information. To this aim, we utilize shape descriptors with an additional phase of feature learning. The results are evaluated with both supervised and unsupervised learning mechanisms. The obtained results demonstrate that global encoding of visual appearance of objects accounts for high discrimination between animal and plant object categories.

Left atrium shape has been shown to be an independent predictor of recurrence after atrial fibrillation (AF) ablation. Shape-based representation is imperative to such an estimation process, where correspondence-based representation offers the most flexibility and ease-of-computation for population-level shape statistics. Nonetheless, population-level shape representations in the form of image segmentation and correspondence models derived from cardiac MRI require significant human resources with sufficient anatomy-specific expertise. In this paper, we propose a machine learning approach that uses deep networks to estimate AF recurrence by predicting shape descriptors directly from MRI images, with NO image pre-processing involved. We also propose a novel data augmentation scheme to effectively train a deep network in a limited training data setting. We compare this new method of estimating shape descriptors from images with the state-of-the-art correspondence-based shape modeling that requires image segmentation and correspondence optimization. Results show that the proposed method and the current state-of-the-art produce statistically similar outcomes on AF recurrence, eliminating the need for expensive pre-processing pipelines and associated human labor.