We introduce Fish-Visual Trait Analysis (Fish-Vista), the first organismal image dataset designed for the analysis of visual traits of aquatic species directly from images using machine learning and computer vision methods. Fish-Vista contains 69,269 annotated images spanning 4,316 fish species, curated and organized to serve three downstream tasks: species classification, trait identification, and trait segmentation. Our work makes two key contributions. First, we provide a fully reproducible data processing pipeline to process fish images sourced from various museum collections, contributing to the advancement of AI in biodiversity science. We annotate the images with carefully curated labels from biological databases and manual annotations to create an AI-ready dataset of visual traits. Second, our work offers fertile grounds for researchers to develop novel methods for a variety of problems in computer vision such as handling long-tailed distributions, out-of-distribution generalization, learning with weak labels, explainable AI, and segmenting small objects. Dataset and code for Fish-Vista are available at https://github.com/Imageomics/Fish-Vista

In subsurface imaging, learning the mapping from velocity maps to seismic waveforms (forward problem) and waveforms to velocity (inverse problem) is important for several applications. While traditional techniques for solving forward and inverse problems are computationally prohibitive, there is a growing interest to leverage recent advances in deep learning to learn the mapping between velocity maps and seismic waveform images directly from data. Despite the variety of architectures explored in previous works, several open questions still remain unanswered such as the effect of latent space sizes, the importance of manifold learning, the complexity of translation models, and the value of jointly solving forward and inverse problems. We propose a unified framework to systematically characterize prior research in this area termed the Generalized Forward-Inverse (GFI) framework, building on the assumption of manifolds and latent space translations. We show that GFI encompasses previous works in deep learning for subsurface imaging, which can be viewed as specific instantiations of GFI. We also propose two new model architectures within the framework of GFI: Latent U-Net and Invertible X-Net, leveraging the power of U-Nets for domain translation and the ability of IU-Nets to simultaneously learn forward and inverse translations, respectively. We show that our proposed models achieve state-of-the-art (SOTA) performance for forward and inverse problems on a wide range of synthetic datasets, and also investigate their zero-shot effectiveness on two real-world-like datasets. The code is available at https://github.com/KGML-lab/Generalized-Forward-Inverse-Framework-for-DL4SI

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. Our code is publicly accessible at Imageomics Institute Github site: https://github.com/Imageomics/HComPNet.

Abstract 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. (Model and code can be found at imageomics.github.io/phylo-diffusion )

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of $12$ state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of $469K$ question-answer pairs involving $30K$ images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images.

Despite the success of physics-informed neural networks (PINNs) in approximating partial differential equations (PDEs), PINNs can sometimes fail to converge to the correct solution in problems involving complicated PDEs. This is reflected in several recent studies on characterizing the "failure modes" of PINNs, although a thorough understanding of the connection between PINN failure modes and sampling strategies is missing. In this paper, we provide a novel perspective of failure modes of PINNs by hypothesizing that training PINNs relies on successful "propagation" of solution from initial and/or boundary condition points to interior points. We show that PINNs with poor sampling strategies can get stuck at trivial solutions if there are propagation failures, characterized by highly imbalanced PDE residual fields. To mitigate propagation failures, we propose a novel Retain-Resample-Release sampling (R3) algorithm that can incrementally accumulate collocation points in regions of high PDE residuals with little to no computational overhead. We provide an extension of R3 sampling to respect the principle of causality while solving time-dependent PDEs. We theoretically analyze the behavior of R3 sampling and empirically demonstrate its efficacy and efficiency in comparison with baselines on a variety of PDE problems.

Inferring the source information of greenhouse gases, such as methane, from spatially sparse sensor observations is an essential element in mitigating climate change. While it is well understood that the complex behavior of the atmospheric dispersion of such pollutants is governed by the Advection-Diffusion equation, it is difficult to directly apply the governing equations to identify the source location and magnitude (inverse problem) because of the spatially sparse and noisy observations, i.e., the pollution concentration is known only at the sensor locations and sensors sensitivity is limited. Here, we develop a multi-task learning framework that can provide high-fidelity reconstruction of the concentration field and identify emission characteristics of the pollution sources such as their location, emission strength, etc. from sparse sensor observations. We demonstrate that our proposed framework is able to achieve accurate reconstruction of the methane concentrations from sparse sensor measurements as well as precisely pin-point the location and emission strength of these pollution sources.

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.

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 a diverse range of applications in representation learning and structured pruning, 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 L_0 norm of the masking layer. All of our codes and datasets are available https://github.com/jayroxis/dam-pytorch.

To simultaneously address the rising need of expressing uncertainties in deep learning models along with producing model outputs which are consistent with the known scientific knowledge, we propose a novel physics-guided architecture (PGA) of neural networks in the context of lake temperature modeling where the physical constraints are hard coded in the neural network architecture. This allows us to integrate such models with state of the art uncertainty estimation approaches such as Monte Carlo (MC) Dropout without sacrificing the physical consistency of our results. We demonstrate the effectiveness of our approach in ensuring better generalizability as well as physical consistency in MC estimates over data collected from Lake Mendota in Wisconsin and Falling Creek Reservoir in Virginia, even with limited training data. We further show that our MC estimates correctly match the distribution of ground-truth observations, thus making the PGA paradigm amenable to physically grounded uncertainty quantification.