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.

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.

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.

Rethinking the Importance of Sampling in Physics-informed Neural Networks

Physics-informed neural networks (PINNs) have emerged as a powerful tool for solving partial differential equations (PDEs) in a variety of domains. While previous research in PINNs has mainly focused on constructing and balancing loss functions during training to avoid poor minima, the effect of sampling collocation points on the performance of PINNs has largely been overlooked. In this work, we find that the performance of PINNs can vary significantly with different sampling strategies, and using a fixed set of collocation points can be quite detrimental to the convergence of PINNs to the correct solution. In particular, (1) we hypothesize that training of PINNs rely on successful "propagation" of solution from initial and/or boundary condition points to interior points, and PINNs with poor sampling strategies can get stuck at trivial solutions if there are \textit{propagation failures}. (2) We demonstrate that propagation failures are characterized by highly imbalanced PDE residual fields where very high residuals are observed over very narrow regions. (3) To mitigate propagation failure, we propose a novel \textit{evolutionary sampling} (Evo) method that can incrementally accumulate collocation points in regions of high PDE residuals. We further provide an extension of Evo to respect the principle of causality while solving time-dependent PDEs. We empirically demonstrate the efficacy and efficiency of our proposed methods in a variety of PDE problems.

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.

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.

Beyond Observed Connections : Link Injection

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.

Physics-Guided Architecture (PGA) of Neural Networks for Quantifying Uncertainty in Lake Temperature Modeling

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.