Overcoming the Domain Gap in Contrastive Learning of Neural Action Representations

A fundamental goal in neuroscience is to understand the relationship between neural activity and behavior. For example, the ability to extract behavioral intentions from neural data, or neural decoding, is critical for developing effective brain machine interfaces. Although simple linear models have been applied to this challenge, they cannot identify important non-linear relationships. Thus, a self-supervised means of identifying non-linear relationships between neural dynamics and behavior, in order to compute neural representations, remains an important open problem. To address this challenge, we generated a new multimodal dataset consisting of the spontaneous behaviors generated by fruit flies, Drosophila melanogaster -- a popular model organism in neuroscience research. The dataset includes 3D markerless motion capture data from six camera views of the animal generating spontaneous actions, as well as synchronously acquired two-photon microscope images capturing the activity of descending neuron populations that are thought to drive actions. Standard contrastive learning and unsupervised domain adaptation techniques struggle to learn neural action representations (embeddings computed from the neural data describing action labels) due to large inter-animal differences in both neural and behavioral modalities. To overcome this deficiency, we developed simple yet effective augmentations that close the inter-animal domain gap, allowing us to extract behaviorally relevant, yet domain agnostic, information from neural data. This multimodal dataset and our new set of augmentations promise to accelerate the application of self-supervised learning methods in neuroscience.

MeshUDF: Fast and Differentiable Meshing of Unsigned Distance Field Networks

Recent work modelling 3D open surfaces train deep neural networks to approximate Unsigned Distance Fields (UDFs) and implicitly represent shapes. To convert this representation to an explicit mesh, they either use computationally expensive methods to mesh a dense point cloud sampling of the surface, or distort the surface by inflating it into a Signed Distance Field (SDF). By contrast, we propose to directly mesh deep UDFs as open surfaces with an extension of marching cubes, by locally detecting surface crossings. Our method is order of magnitude faster than meshing a dense point cloud, and more accurate than inflating open surfaces. Moreover, we make our surface extraction differentiable, and show it can help fit sparse supervision signals.

Learning to Align Sequential Actions in the Wild

State-of-the-art methods for self-supervised sequential action alignment rely on deep networks that find correspondences across videos in time. They either learn frame-to-frame mapping across sequences, which does not leverage temporal information, or assume monotonic alignment between each video pair, which ignores variations in the order of actions. As such, these methods are not able to deal with common real-world scenarios that involve background frames or videos that contain non-monotonic sequence of actions. In this paper, we propose an approach to align sequential actions in the wild that involve diverse temporal variations. To this end, we propose an approach to enforce temporal priors on the optimal transport matrix, which leverages temporal consistency, while allowing for variations in the order of actions. Our model accounts for both monotonic and non-monotonic sequences and handles background frames that should not be aligned. We demonstrate that our approach consistently outperforms the state-of-the-art in self-supervised sequential action representation learning on four different benchmark datasets.

Temporally-Consistent Surface Reconstruction using Metrically-Consistent Atlases

We propose a method for unsupervised reconstruction of a temporally-consistent sequence of surfaces from a sequence of time-evolving point clouds. It yields dense and semantically meaningful correspondences between frames. We represent the reconstructed surfaces as atlases computed by a neural network, which enables us to establish correspondences between frames. The key to making these correspondences semantically meaningful is to guarantee that the metric tensors computed at corresponding points are as similar as possible. We have devised an optimization strategy that makes our method robust to noise and global motions, without a priori correspondences or pre-alignment steps. As a result, our approach outperforms state-of-the-art ones on several challenging datasets. The code is available at https://github.com/bednarikjan/temporally_coherent_surface_reconstruction.

3D Reconstruction of Curvilinear Structures with Stereo Matching DeepConvolutional Neural Networks

Curvilinear structures frequently appear in microscopy imaging as the object of interest. Crystallographic defects, i.e., dislocations, are one of the curvilinear structures that have been repeatedly investigated under transmission electron microscopy (TEM) and their 3D structural information is of great importance for understanding the properties of materials. 3D information of dislocations is often obtained by tomography which is a cumbersome process since it is required to acquire many images with different tilt angles and similar imaging conditions. Although, alternative stereoscopy methods lower the number of required images to two, they still require human intervention and shape priors for accurate 3D estimation. We propose a fully automated pipeline for both detection and matching of curvilinear structures in stereo pairs by utilizing deep convolutional neural networks (CNNs) without making any prior assumption on 3D shapes. In this work, we mainly focus on 3D reconstruction of dislocations from stereo pairs of TEM images.

Localized Persistent Homologies for more Effective Deep Learning

Persistent Homologies have been successfully used to increase the performance of deep networks trained to detect curvilinear structures and to improve the topological quality of the results. However, existing methods are very global and ignore the location of topological features. In this paper, we introduce an approach that relies on a new filtration function to account for location during network training. We demonstrate experimentally on 2D images of roads and 3D image stacks of neuronal processes that networks trained in this manner are better at recovering the topology of the curvilinear structures they extract.

DEBOSH: Deep Bayesian Shape Optimization

Shape optimization is at the heart of many industrial applications, such as aerodynamics, heat transfer, and structural analysis. It has recently been shown that Graph Neural Networks (GNNs) can predict the performance of a shape quickly and accurately and be used to optimize more effectively than traditional techniques that rely on response-surfaces obtained by Kriging. However, GNNs suffer from the fact that they do not evaluate their own accuracy, which is something Bayesian Optimization methods require. Therefore, estimating confidence in generated predictions is necessary to go beyond straight deterministic optimization, which is less effective. In this paper, we demonstrate that we can use Ensembles-based technique to overcome this limitation and outperform the state-of-the-art. Our experiments on diverse aerodynamics and structural analysis tasks prove that adding uncertainty to shape optimization significantly improves the quality of resulting shapes and reduces the time required for the optimization.

HybridSDF: Combining Free Form Shapes and Geometric Primitives for effective Shape Manipulation

CAD modeling typically involves the use of simple geometric primitives whereas recent advances in deep-learning based 3D surface modeling have opened new shape design avenues. Unfortunately, these advances have not yet been accepted by the CAD community because they cannot be integrated into engineering workflows. To remedy this, we propose a novel approach to effectively combining geometric primitives and free-form surfaces represented by implicit surfaces for accurate modeling that preserves interpretability, enforces consistency, and enables easy manipulation.

DeepMesh: Differentiable Iso-Surface Extraction

Geometric Deep Learning has recently made striking progress with the advent of continuous Deep Implicit Fields. They allow for detailed modeling of watertight surfaces of arbitrary topology while not relying on a 3D Euclidean grid, resulting in a learnable parameterization that is unlimited in resolution. Unfortunately, these methods are often unsuitable for applications that require an explicit mesh-based surface representation because converting an implicit field to such a representation relies on the Marching Cubes algorithm, which cannot be differentiated with respect to the underlying implicit field. In this work, we remove this limitation and introduce a differentiable way to produce explicit surface mesh representations from Deep Implicit Fields. Our key insight is that by reasoning on how implicit field perturbations impact local surface geometry, one can ultimately differentiate the 3D location of surface samples with respect to the underlying deep implicit field. We exploit this to define DeepMesh -- end-to-end differentiable mesh representation that can vary its topology. We use two different applications to validate our theoretical insight: Single view 3D Reconstruction via Differentiable Rendering and Physically-Driven Shape Optimization. In both cases our end-to-end differentiable parameterization gives us an edge over state-of-the-art algorithms.

Weakly Supervised Volumetric Image Segmentation with Deformed Templates

There are many approaches that use weak-supervision to train networks to segment 2D images. By contrast, existing 3D approaches rely on full-supervision of a subset of 2D slices of the 3D image volume. In this paper, we propose an approach that is truly weakly-supervised in the sense that we only need to provide a sparse set of 3D point on the surface of target objects, an easy task that can be quickly done. We use the 3D points to deform a 3D template so that it roughly matches the target object outlines and we introduce an architecture that exploits the supervision provided by coarse template to train a network to find accurate boundaries. We evaluate the performance of our approach on Computed Tomography (CT), Magnetic Resonance Imagery (MRI) and Electron Microscopy (EM) image datasets. We will show that it outperforms a more traditional approach to weak-supervision in 3D at a reduced supervision cost.