A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.
A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific prototypes at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). The key novelties in HComP-Net include a novel over-specificity loss to avoid learning over-specific prototypes, a novel discriminative loss to ensure prototypes at an internal node are absent in the contrasting set of species with different ancestry, and a novel masking module to allow for the exclusion of over-specific prototypes at higher levels of the tree without hampering classification performance. We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines.
In recent years, several Weakly Supervised Semantic Segmentation (WS3) methods have been proposed that use class activation maps (CAMs) generated by a classifier to produce pseudo-ground truths for training segmentation models. While CAMs are good at highlighting discriminative regions (DR) of an image, they are known to disregard regions of the object that do not contribute to the classifier's prediction, termed non-discriminative regions (NDR). In contrast, attribution methods such as saliency maps provide an alternative approach for assigning a score to every pixel based on its contribution to the classification prediction. This paper provides a comprehensive comparison between saliencies and CAMs for WS3. Our study includes multiple perspectives on understanding their similarities and dissimilarities. Moreover, we provide new evaluation metrics that perform a comprehensive assessment of WS3 performance of alternative methods w.r.t. CAMs. We demonstrate the effectiveness of saliencies in addressing the limitation of CAMs through our empirical studies on benchmark datasets. Furthermore, we propose random cropping as a stochastic aggregation technique that improves the performance of saliency, making it a strong alternative to CAM for WS3.
Swayam Rajat Mohanty, Moin Uddin Maruf, Vaibhav Singh et al.
Solar photovoltaic (PV) modules are prone to damage during manufacturing, installation and operation which reduces their power conversion efficiency. This diminishes their positive environmental impact over the lifecycle. Continuous monitoring of PV modules during operation via unmanned aerial vehicles is essential to ensure that defective panels are promptly replaced or repaired to maintain high power conversion efficiencies. Computer vision provides an automatic, non-destructive and cost-effective tool for monitoring defects in large-scale PV plants. We review the current landscape of deep learning-based computer vision techniques used for detecting defects in solar modules. We compare and evaluate the existing approaches at different levels, namely the type of images used, data collection and processing method, deep learning architectures employed, and model interpretability. Most approaches use convolutional neural networks together with data augmentation or generative adversarial network-based techniques. We evaluate the deep learning approaches by performing interpretability analysis on classification tasks. This analysis reveals that the model focuses on the darker regions of the image to perform the classification. We find clear gaps in the existing approaches while also laying out the groundwork for mitigating these challenges when building new models. We conclude with the relevant research gaps that need to be addressed and approaches for progress in this field: integrating geometric deep learning with existing approaches for building more robust and reliable models, leveraging physics-based neural networks that combine domain expertise of physical laws to build more domain-aware deep learning models, and incorporating interpretability as a factor for building models that can be trusted. The review points towards a clear roadmap for making this technology commercially relevant.
As applications of deep learning (DL) continue to seep into critical scientific use-cases, the importance of performing uncertainty quantification (UQ) with DL has become more pressing than ever before. In scientific applications, it is also important to inform the learning of DL models with knowledge of physics of the problem to produce physically consistent and generalized solutions. This is referred to as the emerging field of physics-informed deep learning (PIDL). We consider the problem of developing PIDL formulations that can also perform UQ. To this end, we propose a novel physics-informed GAN architecture, termed PID-GAN, where the knowledge of physics is used to inform the learning of both the generator and discriminator models, making ample use of unlabeled data instances. We show that our proposed PID-GAN framework does not suffer from imbalance of generator gradients from multiple loss terms as compared to state-of-the-art. We also empirically demonstrate the efficacy of our proposed framework on a variety of case studies involving benchmark physics-based PDEs as well as imperfect physics. All the code and datasets used in this study have been made available on this link : https://github.com/arkadaw9/PID-GAN.
The objective of unsupervised graph representation learning (GRL) is to learn a low-dimensional space of node embeddings that reflect the structure of a given unlabeled graph. Existing algorithms for this task rely on negative sampling objectives that maximize the similarity in node embeddings at nearby nodes (referred to as "cohesion") by maintaining positive and negative corpus of node pairs. While positive samples are drawn from node pairs that co-occur in short random walks, conventional approaches construct negative corpus by uniformly sampling random pairs, thus ignoring valuable information about structural dissimilarity among distant node pairs (referred to as "separation"). In this paper, we present a novel Distance-aware Negative Sampling (DNS) which maximizes the separation of distant node-pairs while maximizing cohesion at nearby node-pairs by setting the negative sampling probability proportional to the pair-wise shortest distances. Our approach can be used in conjunction with any GRL algorithm and we demonstrate the efficacy of our approach over baseline negative sampling methods over downstream node classification tasks on a number of benchmark datasets and GRL algorithms. All our codes and datasets are available at https://github.com/Distance-awareNS/DNS/.
Machine learning interatomic potentials (MLIPs) provide a computationally efficient alternative to quantum mechanical simulations for predicting material properties. Message-passing graph neural networks, commonly used in these MLIPs, rely on local descriptor-based symmetry functions to model atomic interactions. However, such local descriptor-based approaches struggle with systems exhibiting long-range interactions, charge transfer, and compositional heterogeneity. In this work, we develop a new equivariant MLIP incorporating long-range Coulomb interactions through explicit treatment of electronic degrees of freedom, specifically global charge distribution within the system. This is achieved using a charge equilibration scheme based on predicted atomic electronegativities. We systematically evaluate our model across a range of benchmark periodic and non-periodic datasets, demonstrating that it outperforms both short-range equivariant and long-range invariant MLIPs in energy and force predictions. Our approach enables more accurate and efficient simulations of systems with long-range interactions and charge heterogeneity, expanding the applicability of MLIPs in computational materials science.
Amartya Dutta, Kazi Sajeed Mehrab, Medha Sawhney et al.
Scene-Graph Generation (SGG) seeks to recognize objects in an image and distill their salient pairwise relationships. Most methods depend on dataset-specific supervision to learn the variety of interactions, restricting their usefulness in open-world settings, involving novel objects and/or relations. Even methods that leverage large Vision Language Models (VLMs) typically require benchmark-specific fine-tuning. We introduce Open-World SGG, a training-free, efficient, model-agnostic framework that taps directly into the pretrained knowledge of VLMs to produce scene graphs with zero additional learning. Casting SGG as a zero-shot structured-reasoning problem, our method combines multimodal prompting, embedding alignment, and a lightweight pair-refinement strategy, enabling inference over unseen object vocabularies and relation sets. To assess this setting, we formalize an Open-World evaluation protocol that measures performance when no SGG-specific data have been observed either in terms of objects and relations. Experiments on Visual Genome, Open Images V6, and the Panoptic Scene Graph (PSG) dataset demonstrate the capacity of pretrained VLMs to perform relational understanding without task-level training.
A central goal in deep learning is to learn compact representations of features at every layer of a neural network, which is useful for both unsupervised representation learning and structured network pruning. While there is a growing body of work in structured pruning, current state-of-the-art methods suffer from two key limitations: (i) instability during training, and (ii) need for an additional step of fine-tuning, which is resource-intensive. At the core of these limitations is the lack of a systematic approach that jointly prunes and refines weights during training in a single stage, and does not require any fine-tuning upon convergence to achieve state-of-the-art performance. We present a novel single-stage structured pruning method termed DiscriminAtive Masking (DAM). The key intuition behind DAM is to discriminatively prefer some of the neurons to be refined during the training process, while gradually masking out other neurons. We show that our proposed DAM approach has remarkably good performance over various applications, including dimensionality reduction, recommendation system, graph representation learning, and structured pruning for image classification. We also theoretically show that the learning objective of DAM is directly related to minimizing the L0 norm of the masking layer.
In this paper, we proposed the \textit{link injection}, a novel method that helps any differentiable graph machine learning models to go beyond observed connections from the input data in an end-to-end learning fashion. It finds out (weak) connections in favor of the current task that is not present in the input data via a parametric link injection layer. We evaluate our method on both node classification and link prediction tasks using a series of state-of-the-art graph convolution networks. Results show that the link injection helps a variety of models to achieve better performances on both applications. Further empirical analysis shows a great potential of this method in efficiently exploiting unseen connections from the injected links.