arXiv subjects

Anuj Karpatne

Publications and source records attributed to Anuj Karpatne.

At least 37 records · Page 2Linked to original sources

arXiv2024

A Simple Interpretable Transformer for Fine-Grained Image Classification and Analysis

We present a novel usage of Transformers to make image classification interpretable. Unlike mainstream classifiers that wait until the last fully connected layer to incorporate class information to make predictions, we investigate a proactive approach, asking each class to search for itself in an image. We realize this idea via a Transformer encoder-decoder inspired by DEtection TRansformer (DETR). We learn "class-specific" queries (one for each class) as input to the decoder, enabling each class to localize its patterns in an image via cross-attention. We name our approach INterpretable TRansformer (INTR), which is fairly easy to implement and exhibits several compelling properties. We show that INTR intrinsically encourages each class to attend distinctively; the cross-attention weights thus provide a faithful interpretation of the prediction. Interestingly, via "multi-head" cross-attention, INTR could identify different "attributes" of a class, making it particularly suitable for fine-grained classification and analysis, which we demonstrate on eight datasets. Our code and pre-trained models are publicly accessible at the Imageomics Institute GitHub site: https://github.com/Imageomics/INTR.

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arXiv2024

Knowledge-guided Machine Learning: Current Trends and Future Prospects

This paper presents an overview of scientific modeling and discusses the complementary strengths and weaknesses of ML methods for scientific modeling in comparison to process-based models. It also provides an introduction to the current state of research in the emerging field of scientific knowledge-guided machine learning (KGML) that aims to use both scientific knowledge and data in ML frameworks to achieve better generalizability, scientific consistency, and explainability of results. We discuss different facets of KGML research in terms of the type of scientific knowledge used, the form of knowledge-ML integration explored, and the method for incorporating scientific knowledge in ML. We also discuss some of the common categories of use cases in environmental sciences where KGML methods are being developed, using illustrative examples in each category.

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arXiv2023

MEMTRACK: A Deep Learning-Based Approach to Microrobot Tracking in Dense and Low-Contrast Environments

Tracking microrobots is challenging, considering their minute size and high speed. As the field progresses towards developing microrobots for biomedical applications and conducting mechanistic studies in physiologically relevant media (e.g., collagen), this challenge is exacerbated by the dense surrounding environments with feature size and shape comparable to microrobots. Herein, we report Motion Enhanced Multi-level Tracker (MEMTrack), a robust pipeline for detecting and tracking microrobots using synthetic motion features, deep learning-based object detection, and a modified Simple Online and Real-time Tracking (SORT) algorithm with interpolation for tracking. Our object detection approach combines different models based on the object's motion pattern. We trained and validated our model using bacterial micro-motors in collagen (tissue phantom) and tested it in collagen and aqueous media. We demonstrate that MEMTrack accurately tracks even the most challenging bacteria missed by skilled human annotators, achieving precision and recall of 77% and 48% in collagen and 94% and 35% in liquid media, respectively. Moreover, we show that MEMTrack can quantify average bacteria speed with no statistically significant difference from the laboriously-produced manual tracking data. MEMTrack represents a significant contribution to microrobot localization and tracking, and opens the potential for vision-based deep learning approaches to microrobot control in dense and low-contrast settings. All source code for training and testing MEMTrack and reproducing the results of the paper have been made publicly available https://github.com/sawhney-medha/MEMTrack.

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arXiv2023

Neuro-Visualizer: An Auto-encoder-based Loss Landscape Visualization Method

In recent years, there has been a growing interest in visualizing the loss landscape of neural networks. Linear landscape visualization methods, such as principal component analysis, have become widely used as they intuitively help researchers study neural networks and their training process. However, these linear methods suffer from limitations and drawbacks due to their lack of flexibility and low fidelity at representing the high dimensional landscape. In this paper, we present a novel auto-encoder-based non-linear landscape visualization method called Neuro-Visualizer that addresses these shortcoming and provides useful insights about neural network loss landscapes. To demonstrate its potential, we run experiments on a variety of problems in two separate applications of knowledge-guided machine learning (KGML). Our findings show that Neuro-Visualizer outperforms other linear and non-linear baselines and helps corroborate, and sometime challenge, claims proposed by machine learning community. All code and data used in the experiments of this paper are available at an anonymous link https://anonymous.4open.science/r/NeuroVisualizer-FDD6

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arXiv2023

Beyond Discriminative Regions: Saliency Maps as Alternatives to CAMs for Weakly Supervised Semantic Segmentation

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.

cs.CV↗

arXiv2023

Mitigating Propagation Failures in Physics-informed Neural Networks using Retain-Resample-Release (R3) Sampling

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.

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arXiv2023

Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

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arXiv2023

Let There Be Order: Rethinking Ordering in Autoregressive Graph Generation

Conditional graph generation tasks involve training a model to generate a graph given a set of input conditions. Many previous studies employ autoregressive models to incrementally generate graph components such as nodes and edges. However, as graphs typically lack a natural ordering among their components, converting a graph into a sequence of tokens is not straightforward. While prior works mostly rely on conventional heuristics or graph traversal methods like breadth-first search (BFS) or depth-first search (DFS) to convert graphs to sequences, the impact of ordering on graph generation has largely been unexplored. This paper contributes to this problem by: (1) highlighting the crucial role of ordering in autoregressive graph generation models, (2) proposing a novel theoretical framework that perceives ordering as a dimensionality reduction problem, thereby facilitating a deeper understanding of the relationship between orderings and generated graph accuracy, and (3) introducing "latent sort," a learning-based ordering scheme to perform dimensionality reduction of graph tokens. Our experimental results showcase the effectiveness of latent sort across a wide range of graph generation tasks, encouraging future works to further explore and develop learning-based ordering schemes for autoregressive graph generation.

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arXiv2022

Adjoint-Matching Neural Network Surrogates for Fast 4D-Var Data Assimilation

Data assimilation is the process of fusing information from imperfect computer simulations with noisy, sparse measurements of reality to obtain improved estimates of the state or parameters of a dynamical system of interest. The data assimilation procedures used in many geoscience applications, such as numerical weather forecasting, are variants of the our-dimensional variational (4D-Var) algorithm. The cost of solving the underlying 4D-Var optimization problem is dominated by the cost of repeated forward and adjoint model runs. This motivates substituting the evaluations of the physical model and its adjoint by fast, approximate surrogate models. Neural networks offer a promising approach for the data-driven creation of surrogate models. The accuracy of the surrogate 4D-Var solution depends on the accuracy with each the surrogate captures both the forward and the adjoint model dynamics. We formulate and analyze several approaches to incorporate adjoint information into the construction of neural network surrogates. The resulting networks are tested on unseen data and in a sequential data assimilation problem using the Lorenz-63 system. Surrogates constructed using adjoint information demonstrate superior performance on the 4D-Var data assimilation problem compared to a standard neural network surrogate that uses only forward dynamics information.

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arXiv2022

Multi-task Learning for Source Attribution and Field Reconstruction for Methane Monitoring

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.

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arXiv2022

Physics-Guided Problem Decomposition for Scaling Deep Learning of High-dimensional Eigen-Solvers: The Case of Schrödinger's Equation

Given their ability to effectively learn non-linear mappings and perform fast inference, deep neural networks (NNs) have been proposed as a viable alternative to traditional simulation-driven approaches for solving high-dimensional eigenvalue equations (HDEs), which are the foundation for many scientific applications. Unfortunately, for the learned models in these scientific applications to achieve generalization, a large, diverse, and preferably annotated dataset is typically needed and is computationally expensive to obtain. Furthermore, the learned models tend to be memory- and compute-intensive primarily due to the size of the output layer. While generalization, especially extrapolation, with scarce data has been attempted by imposing physical constraints in the form of physics loss, the problem of model scalability has remained. In this paper, we alleviate the compute bottleneck in the output layer by using physics knowledge to decompose the complex regression task of predicting the high-dimensional eigenvectors into multiple simpler sub-tasks, each of which are learned by a simple "expert" network. We call the resulting architecture of specialized experts Physics-Guided Mixture-of-Experts (PG-MoE). We demonstrate the efficacy of such physics-guided problem decomposition for the case of the Schrödinger's Equation in Quantum Mechanics. Our proposed PG-MoE model predicts the ground-state solution, i.e., the eigenvector that corresponds to the smallest possible eigenvalue. The model is 150x smaller than the network trained to learn the complex task while being competitive in generalization. To improve the generalization of the PG-MoE, we also employ a physics-guided loss function based on variational energy, which by quantum mechanics principles is minimized iff the output is the ground-state solution.

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arXiv2021

CoPhy-PGNN: Learning Physics-guided Neural Networks with Competing Loss Functions for Solving Eigenvalue Problems

Physics-guided Neural Networks (PGNNs) represent an emerging class of neural networks that are trained using physics-guided (PG) loss functions (capturing violations in network outputs with known physics), along with the supervision contained in data. Existing work in PGNNs has demonstrated the efficacy of adding single PG loss functions in the neural network objectives, using constant trade-off parameters, to ensure better generalizability. However, in the presence of multiple PG functions with competing gradient directions, there is a need to adaptively tune the contribution of different PG loss functions during the course of training to arrive at generalizable solutions. We demonstrate the presence of competing PG losses in the generic neural network problem of solving for the lowest (or highest) eigenvector of a physics-based eigenvalue equation, which is commonly encountered in many scientific problems. We present a novel approach to handle competing PG losses and demonstrate its efficacy in learning generalizable solutions in two motivating applications of quantum mechanics and electromagnetic propagation. All the code and data used in this work is available at https://github.com/jayroxis/Cophy-PGNN.

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arXiv2021

Physics-Informed Machine Learning for Optical Modes in Composites

We demonstrate that embedding physics-driven constraints into machine learning process can dramatically improve accuracy and generalizability of the resulting model. Physics-informed learning is illustrated on the example of analysis of optical modes propagating through a spatially periodic composite. The approach presented can be readily utilized in other situations mapped onto an eigenvalue problem, a known bottleneck of computational electrodynamics. Physics-informed learning can be used to improve machine-learning-driven design, optimization, and characterization, in particular in situations where exact solutions are scarce or are slow to come up with.

physics.comp-ph↗

arXiv2021

Learning Compact Representations of Neural Networks using DiscriminAtive Masking (DAM)

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.

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arXiv2021

Physics-guided Neural Networks (PGNN): An Application in Lake Temperature Modeling

This paper introduces a framework for combining scientific knowledge of physics-based models with neural networks to advance scientific discovery. This framework, termed physics-guided neural networks (PGNN), leverages the output of physics-based model simulations along with observational features in a hybrid modeling setup to generate predictions using a neural network architecture. Further, this framework uses physics-based loss functions in the learning objective of neural networks to ensure that the model predictions not only show lower errors on the training set but are also scientifically consistent with the known physics on the unlabeled set. We illustrate the effectiveness of PGNN for the problem of lake temperature modeling, where physical relationships between the temperature, density, and depth of water are used to design a physics-based loss function. By using scientific knowledge to guide the construction and learning of neural networks, we are able to show that the proposed framework ensures better generalizability as well as scientific consistency of results. All the code and datasets used in this study have been made available on this link \url{https://github.com/arkadaw9/PGNN}.

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arXiv2021

PID-GAN: A GAN Framework based on a Physics-informed Discriminator for Uncertainty Quantification with Physics

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.

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arXiv2021

GCNNMatch: Graph Convolutional Neural Networks for Multi-Object Tracking via Sinkhorn Normalization

This paper proposes a novel method for online Multi-Object Tracking (MOT) using Graph Convolutional Neural Network (GCNN) based feature extraction and end-to-end feature matching for object association. The Graph based approach incorporates both appearance and geometry of objects at past frames as well as the current frame into the task of feature learning. This new paradigm enables the network to leverage the "context" information of the geometry of objects and allows us to model the interactions among the features of multiple objects. Another central innovation of our proposed framework is the use of the Sinkhorn algorithm for end-to-end learning of the associations among objects during model training. The network is trained to predict object associations by taking into account constraints specific to the MOT task. Experimental results demonstrate the efficacy of the proposed approach in achieving top performance on the MOT '15, '16, '17 and '20 Challenges among state-of-the-art online approaches. The code is available at https://github.com/IPapakis/GCNNMatch.

cs.CV↗

arXiv2021

A Data-Driven Approach to Full-Field Damage and Failure Pattern Prediction in Microstructure-Dependent Composites using Deep Learning

An image-based deep learning framework is developed in this paper to predict damage and failure in microstructure-dependent composite materials. The work is motivated by the complexity and computational cost of high-fidelity simulations of such materials. The proposed deep learning framework predicts the post-failure full-field stress distribution and crack pattern in two-dimensional representations of the composites based on the geometry of microstructures. The material of interest is selected to be a high-performance unidirectional carbon fiber-reinforced polymer composite. The deep learning framework contains two stacked fully-convolutional networks, namely, Generator 1 and Generator 2, trained sequentially. First, Generator 1 learns to translate the microstructural geometry to the full-field post-failure stress distribution. Then, Generator 2 learns to translate the output of Generator 1 to the failure pattern. A physics-informed loss function is also designed and incorporated to further improve the performance of the proposed framework and facilitate the validation process. In order to provide a sufficiently large data set for training and validating the deep learning framework, 4500 microstructural representations are synthetically generated and simulated in an efficient finite element framework. It is shown that the proposed deep learning approach can effectively predict the composites' post-failure full-field stress distribution and failure pattern, two of the most complex phenomena to simulate in computational solid mechanics.

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