ChiENN: Embracing Molecular Chirality with Graph Neural Networks

Graph Neural Networks (GNNs) play a fundamental role in many deep learning problems, in particular in cheminformatics. However, typical GNNs cannot capture the concept of chirality, which means they do not distinguish between the 3D graph of a chemical compound and its mirror image (enantiomer). The ability to distinguish between enantiomers is important especially in drug discovery because enantiomers can have very distinct biochemical properties. In this paper, we propose a theoretically justified message-passing scheme, which makes GNNs sensitive to the order of node neighbors. We apply that general concept in the context of molecular chirality to construct Chiral Edge Neural Network (ChiENN) layer which can be appended to any GNN model to enable chirality-awareness. Our experiments show that adding ChiENN layers to a GNN outperforms current state-of-the-art methods in chiral-sensitive molecular property prediction tasks.

Fantastic Weights and How to Find Them: Where to Prune in Dynamic Sparse Training

Dynamic Sparse Training (DST) is a rapidly evolving area of research that seeks to optimize the sparse initialization of a neural network by adapting its topology during training. It has been shown that under specific conditions, DST is able to outperform dense models. The key components of this framework are the pruning and growing criteria, which are repeatedly applied during the training process to adjust the network's sparse connectivity. While the growing criterion's impact on DST performance is relatively well studied, the influence of the pruning criterion remains overlooked. To address this issue, we design and perform an extensive empirical analysis of various pruning criteria to better understand their effect on the dynamics of DST solutions. Surprisingly, we find that most of the studied methods yield similar results. The differences become more significant in the low-density regime, where the best performance is predominantly given by the simplest technique: magnitude-based pruning. The code is provided at https://github.com/alooow/fantastic_weights_paper

ProMIL: Probabilistic Multiple Instance Learning for Medical Imaging

Multiple Instance Learning (MIL) is a weakly-supervised problem in which one label is assigned to the whole bag of instances. An important class of MIL models is instance-based, where we first classify instances and then aggregate those predictions to obtain a bag label. The most common MIL model is when we consider a bag as positive if at least one of its instances has a positive label. However, this reasoning does not hold in many real-life scenarios, where the positive bag label is often a consequence of a certain percentage of positive instances. To address this issue, we introduce a dedicated instance-based method called ProMIL, based on deep neural networks and Bernstein polynomial estimation. An important advantage of ProMIL is that it can automatically detect the optimal percentage level for decision-making. We show that ProMIL outperforms standard instance-based MIL in real-world medical applications. We make the code available.

Augmentation-aware Self-supervised Learning with Guided Projector

Self-supervised learning (SSL) is a powerful technique for learning robust representations from unlabeled data. By learning to remain invariant to applied data augmentations, methods such as SimCLR and MoCo are able to reach quality on par with supervised approaches. However, this invariance may be harmful to solving some downstream tasks which depend on traits affected by augmentations used during pretraining, such as color. In this paper, we propose to foster sensitivity to such characteristics in the representation space by modifying the projector network, a common component of self-supervised architectures. Specifically, we supplement the projector with information about augmentations applied to images. In order for the projector to take advantage of this auxiliary guidance when solving the SSL task, the feature extractor learns to preserve the augmentation information in its representations. Our approach, coined Conditional Augmentation-aware Selfsupervised Learning (CASSLE), is directly applicable to typical joint-embedding SSL methods regardless of their objective functions. Moreover, it does not require major changes in the network architecture or prior knowledge of downstream tasks. In addition to an analysis of sensitivity towards different data augmentations, we conduct a series of experiments, which show that CASSLE improves over various SSL methods, reaching state-of-the-art performance in multiple downstream tasks.

MultiPlaneNeRF: Neural Radiance Field with Non-Trainable Representation

NeRF is a popular model that efficiently represents 3D objects from 2D images. However, vanilla NeRF has a few important limitations. NeRF must be trained on each object separately. The training time is long since we encode the object's shape and color in neural network weights. Moreover, NeRF does not generalize well to unseen data. In this paper, we present MultiPlaneNeRF -- a first model that simultaneously solves all the above problems. Our model works directly on 2D images. We project 3D points on 2D images to produce non-trainable representations. The projection step is not parametrized, and a very shallow decoder can efficiently process the representation. Using existing images as part of NeRF can significantly reduce the number of parameters since we train only a small implicit decoder. Furthermore, we can train MultiPlaneNeRF on a large data set and force our implicit decoder to generalize across many objects. Consequently, we can only replace the 2D images (without additional training) to produce a NeRF representation of the new object. In the experimental section, we demonstrate that MultiPlaneNeRF achieves comparable results to state-of-the-art models for synthesizing new views and has generalization properties.

r-softmax: Generalized Softmax with Controllable Sparsity Rate

Nowadays artificial neural network models achieve remarkable results in many disciplines. Functions mapping the representation provided by the model to the probability distribution are the inseparable aspect of deep learning solutions. Although softmax is a commonly accepted probability mapping function in the machine learning community, it cannot return sparse outputs and always spreads the positive probability to all positions. In this paper, we propose r-softmax, a modification of the softmax, outputting sparse probability distribution with controllable sparsity rate. In contrast to the existing sparse probability mapping functions, we provide an intuitive mechanism for controlling the output sparsity level. We show on several multi-label datasets that r-softmax outperforms other sparse alternatives to softmax and is highly competitive with the original softmax. We also apply r-softmax to the self-attention module of a pre-trained transformer language model and demonstrate that it leads to improved performance when fine-tuning the model on different natural language processing tasks.

Gaussian model for closed curves

Gaussian Mixture Models (GMM) do not adapt well to curved and strongly nonlinear data. However, we can use Gaussians in the curvilinear coordinate systems to solve this problem. Moreover, such a solution allows for the adaptation of clusters to the complicated shapes defined by the family of functions. But still, it is challenging to model clusters as closed curves (e.g., circles, ellipses, etc.). In this work, we propose a density representation of the closed curve, which can be used to detect the complicated templates in the data. For this purpose, we define a new probability distribution to model closed curves. Then we construct a mixture of such distributions and show that it can be effectively trained in the case of the one-dimensional closed curves.

NeRFlame: FLAME-based conditioning of NeRF for 3D face rendering

Traditional 3D face models are based on mesh representations with texture. One of the most important models is FLAME (Faces Learned with an Articulated Model and Expressions), which produces meshes of human faces that are fully controllable. Unfortunately, such models have problems with capturing geometric and appearance details. In contrast to mesh representation, the neural radiance field (NeRF) produces extremely sharp renders. But implicit methods are hard to animate and do not generalize well to unseen expressions. It is not trivial to effectively control NeRF models to obtain face manipulation. The present paper proposes a novel approach, named NeRFlame, which combines the strengths of both NeRF and FLAME methods. Our method enables high-quality rendering capabilities of NeRF while also offering complete control over the visual appearance, similar to FLAME. Unlike conventional NeRF-based architectures that utilize neural networks to model RGB colors and volume density, NeRFlame employs FLAME mesh as an explicit density volume. As a result, color values are non-zero only in the proximity of the FLAME mesh. This FLAME backbone is then integrated into the NeRF architecture to predict RGB colors, allowing NeRFlame to explicitly model volume density and implicitly model RGB colors.

Contrastive Hierarchical Clustering

Deep clustering has been dominated by flat models, which split a dataset into a predefined number of groups. Although recent methods achieve an extremely high similarity with the ground truth on popular benchmarks, the information contained in the flat partition is limited. In this paper, we introduce CoHiClust, a Contrastive Hierarchical Clustering model based on deep neural networks, which can be applied to typical image data. By employing a self-supervised learning approach, CoHiClust distills the base network into a binary tree without access to any labeled data. The hierarchical clustering structure can be used to analyze the relationship between clusters, as well as to measure the similarity between data points. Experiments demonstrate that CoHiClust generates a reasonable structure of clusters, which is consistent with our intuition and image semantics. Moreover, it obtains superior clustering accuracy on most of the image datasets compared to the state-of-the-art flat clustering models.