Protein Conformation Generation via Force-Guided SE(3) Diffusion Models

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event sampling and long equilibration time problems, hindering their applications in general protein systems. Recently, deep generative modeling techniques, especially diffusion models, have been employed to generate novel protein conformations. However, existing score-based diffusion methods cannot properly incorporate important physical prior knowledge to guide the generation process, causing large deviations in the sampled protein conformations from the equilibrium distribution. In this paper, to overcome these limitations, we propose a force-guided SE(3) diffusion model, ConfDiff, for protein conformation generation. By incorporating a force-guided network with a mixture of data-based score models, ConfDiff can can generate protein conformations with rich diversity while preserving high fidelity. Experiments on a variety of protein conformation prediction tasks, including 12 fast-folding proteins and the Bovine Pancreatic Trypsin Inhibitor (BPTI), demonstrate that our method surpasses the state-of-the-art method.

NocPlace: Nocturnal Visual Place Recognition Using Generative and Inherited Knowledge Transfer

Visual Place Recognition (VPR) is crucial in computer vision, aiming to retrieve database images similar to a query image from an extensive collection of known images. However, like many vision-related tasks, learning-based VPR often experiences a decline in performance during nighttime due to the scarcity of nighttime images. Specifically, VPR needs to address the cross-domain problem of night-to-day rather than just the issue of a single nighttime domain. In response to these issues, we present NocPlace, which leverages a generated large-scale, multi-view, nighttime VPR dataset to embed resilience against dazzling lights and extreme darkness in the learned global descriptor. Firstly, we establish a day-night urban scene dataset called NightCities, capturing diverse nighttime scenarios and lighting variations across 60 cities globally. Following this, an unpaired image-to-image translation network is trained on this dataset. Using this trained translation network, we process an existing VPR dataset, thereby obtaining its nighttime version. The NocPlace is then fine-tuned using night-style images, the original labels, and descriptors inherited from the Daytime VPR model. Comprehensive experiments on various nighttime VPR test sets reveal that NocPlace considerably surpasses previous state-of-the-art methods.

Cross Domain Early Crop Mapping using CropGAN and CNN Classifier

Driven by abundant satellite imagery, machine learning-based approaches have recently been promoted to generate high-resolution crop cultivation maps to support many agricultural applications. One of the major challenges faced by these approaches is the limited availability of ground truth labels. In the absence of ground truth, existing work usually adopts the "direct transfer strategy" that trains a classifier using historical labels collected from other regions and then applies the trained model to the target region. Unfortunately, the spectral features of crops exhibit inter-region and inter-annual variability due to changes in soil composition, climate conditions, and crop progress, the resultant models perform poorly on new and unseen regions or years. This paper presents the Crop Generative Adversarial Network (CropGAN) to address the above cross-domain issue. Our approach does not need labels from the target domain. Instead, it learns a mapping function to transform the spectral features of the target domain to the source domain (with labels) while preserving their local structure. The classifier trained by the source domain data can be directly applied to the transformed data to produce high-accuracy early crop maps of the target domain. Comprehensive experiments across various regions and years demonstrate the benefits and effectiveness of the proposed approach. Compared with the widely adopted direct transfer strategy, the F1 score after applying the proposed CropGAN is improved by 13.13% - 50.98%

NeuSD: Surface Completion with Multi-View Text-to-Image Diffusion

We present a novel method for 3D surface reconstruction from multiple images where only a part of the object of interest is captured. Our approach builds on two recent developments: surface reconstruction using neural radiance fields for the reconstruction of the visible parts of the surface, and guidance of pre-trained 2D diffusion models in the form of Score Distillation Sampling (SDS) to complete the shape in unobserved regions in a plausible manner. We introduce three components. First, we suggest employing normal maps as a pure geometric representation for SDS instead of color renderings which are entangled with the appearance information. Second, we introduce the freezing of the SDS noise during training which results in more coherent gradients and better convergence. Third, we propose Multi-View SDS as a way to condition the generation of the non-observable part of the surface without fine-tuning or making changes to the underlying 2D Stable Diffusion model. We evaluate our approach on the BlendedMVS dataset demonstrating significant qualitative and quantitative improvements over competing methods.

Factored-NeuS: Reconstructing Surfaces, Illumination, and Materials of Possibly Glossy Objects

We develop a method that recovers the surface, materials, and illumination of a scene from its posed multi-view images. In contrast to prior work, it does not require any additional data and can handle glossy objects or bright lighting. It is a progressive inverse rendering approach, which consists of three stages. First, we reconstruct the scene radiance and signed distance function (SDF) with our novel regularization strategy for specular reflections. Our approach considers both the diffuse and specular colors, which allows for handling complex view-dependent lighting effects for surface reconstruction. Second, we distill light visibility and indirect illumination from the learned SDF and radiance field using learnable mapping functions. Third, we design a method for estimating the ratio of incoming direct light represented via Spherical Gaussians reflected in a specular manner and then reconstruct the materials and direct illumination of the scene. Experimental results demonstrate that the proposed method outperforms the current state-of-the-art in recovering surfaces, materials, and lighting without relying on any additional data.

PET-NeuS: Positional Encoding Tri-Planes for Neural Surfaces

A signed distance function (SDF) parametrized by an MLP is a common ingredient of neural surface reconstruction. We build on the successful recent method NeuS to extend it by three new components. The first component is to borrow the tri-plane representation from EG3D and represent signed distance fields as a mixture of tri-planes and MLPs instead of representing it with MLPs only. Using tri-planes leads to a more expressive data structure but will also introduce noise in the reconstructed surface. The second component is to use a new type of positional encoding with learnable weights to combat noise in the reconstruction process. We divide the features in the tri-plane into multiple frequency scales and modulate them with sin and cos functions of different frequencies. The third component is to use learnable convolution operations on the tri-plane features using self-attention convolution to produce features with different frequency bands. The experiments show that PET-NeuS achieves high-fidelity surface reconstruction on standard datasets. Following previous work and using the Chamfer metric as the most important way to measure surface reconstruction quality, we are able to improve upon the NeuS baseline by 57% on Nerf-synthetic (0.84 compared to 1.97) and by 15.5% on DTU (0.71 compared to 0.84). The qualitative evaluation reveals how our method can better control the interference of high-frequency noise. Code available at \url{https://github.com/yiqun-wang/PET-NeuS}.

SDFReg: Learning Signed Distance Functions for Point Cloud Registration

Learning-based point cloud registration methods can handle clean point clouds well, while it is still challenging to generalize to noisy and partial point clouds. To this end, we propose a novel framework for noisy and partial point cloud registration. By introducing a neural implicit function representation, we replace the problem of rigid registration between point clouds with a registration problem between the point cloud and the neural implicit function. We then alternately optimize the implicit function representation and the registration between the implicit function and point cloud. In this way, point cloud registration can be performed in a coarse-to-fine manner. Since our method avoids computing point correspondences, it is robust to the noise and incompleteness of point clouds. Compared with the registration methods based on global features, our method can deal with surfaces with large density variations and achieve higher registration accuracy. Experimental results and comparisons demonstrate the effectiveness of the proposed framework.

Learning Harmonic Molecular Representations on Riemannian Manifold

Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the prevailing method in the geometric deep learning community. However, the equivariance constraints and message passing in Euclidean space may limit the network expressive power. In this work, we propose a Harmonic Molecular Representation learning (HMR) framework, which represents a molecule using the Laplace-Beltrami eigenfunctions of its molecular surface. HMR offers a multi-resolution representation of molecular geometric and chemical features on 2D Riemannian manifold. We also introduce a harmonic message passing method to realize efficient spectral message passing over the surface manifold for better molecular encoding. Our proposed method shows comparable predictive power to current models in small molecule property prediction, and outperforms the state-of-the-art deep learning models for ligand-binding protein pocket classification and the rigid protein docking challenge, demonstrating its versatility in molecular representation learning.

BlobGAN-3D: A Spatially-Disentangled 3D-Aware Generative Model for Indoor Scenes

3D-aware image synthesis has attracted increasing interest as it models the 3D nature of our real world. However, performing realistic object-level editing of the generated images in the multi-object scenario still remains a challenge. Recently, a 2D GAN termed BlobGAN has demonstrated great multi-object editing capabilities on real-world indoor scene datasets. In this work, we propose BlobGAN-3D, which is a 3D-aware improvement of the original 2D BlobGAN. We enable explicit camera pose control while maintaining the disentanglement for individual objects in the scene by extending the 2D blobs into 3D blobs. We keep the object-level editing capabilities of BlobGAN and in addition allow flexible control over the 3D location of the objects in the scene. We test our method on real-world indoor datasets and show that our method can achieve comparable image quality compared to the 2D BlobGAN and other 3D-aware GAN baselines while being able to enable camera pose control and object-level editing in the challenging multi-object real-world scenarios.

CroSel: Cross Selection of Confident Pseudo Labels for Partial-Label Learning

Partial-label learning (PLL) is an important weakly supervised learning problem, which allows each training example to have a candidate label set instead of a single ground-truth label. Identification-based methods have been widely explored to tackle label ambiguity issues in PLL, which regard the true label as a latent variable to be identified. However, identifying the true labels accurately and completely remains challenging, causing noise in pseudo labels during model training. In this paper, we propose a new method called CroSel, which leverages historical prediction information from models to identify true labels for most training examples. First, we introduce a cross selection strategy, which enables two deep models to select true labels of partially labeled data for each other. Besides, we propose a novel consistent regularization term called co-mix to avoid sample waste and tiny noise caused by false selection. In this way, CroSel can pick out the true labels of most examples with high precision. Extensive experiments demonstrate the superiority of CroSel, which consistently outperforms previous state-of-the-art methods on benchmark datasets. Additionally, our method achieves over 90\% accuracy and quantity for selecting true labels on CIFAR-type datasets under various settings.