Krishna Agarwal

Suyog Jadhav, Dilip K. Prasad, Krishna Agarwal

The morphological analysis of mitochondria in fluorescence microscopy (FM) is crucial for understanding cellular health, energy production, and metabolic regulation. While foundation models like the Segment Anything Model (SAM) have revolutionized natural image segmentation, their direct application to FM is hindered by a significant domain shift characterized by diffraction-limited resolution, low contrast, and complex overlapping organelle networks. Furthermore, the development of robust models is bottlenecked by a severe lack of high-quality, manually annotated instance segmentation datasets for mitochondria. In this paper, we propose a scalable solution to this data scarcity by finetuning SAM exclusively on synthetically generated FM data. We simulate realistic mitochondria data and emulate the optical properties of fluorescence microscopes to create a large-scale annotated dataset. We evaluate our fine-tuned model on a curated dataset of real, manually annotated FM images. Qualitative and quantitative analyses demonstrate that our synthetically fine-tuned model improves precision and average dice score over strong baselines. This work establishes the potential of simulation-assisted training for FM instance segmentation.

Abhinanda R. Punnakkal, Suyog S Jadhav, Alexander Horsch et al.

Fluorescence microscopy is a quintessential tool for observing cells and understanding the underlying mechanisms of life-sustaining processes of all living organisms. The problem of extracting 3D shape of mitochondria from fluorescence microscopy images remains unsolved due to the complex and varied shapes expressed by mitochondria and the poor resolving capacity of these microscopes. We propose an approach to bridge this gap by learning a shape prior for mitochondria termed as MiShape, by leveraging high-resolution electron microscopy data. MiShape is a generative model learned using implicit representations of mitochondrial shapes. It provides a shape distribution that can be used to generate infinite realistic mitochondrial shapes. We demonstrate the representation power of MiShape and its utility for 3D shape reconstruction given a single 2D fluorescence image or a small 3D stack of 2D slices. We also showcase applications of our method by deriving simulated fluorescence microscope datasets that have realistic 3D ground truths for the problem of 2D segmentation and microscope-to-microscope transformation.

Krishna Agarwal, Muhamad Rizka Maulana, Vamsi Addanki et al.

Modern datacenter switches share packet buffers across ports to boost overall throughput and reduce packet loss. However, as buffer availability per-port-per-bandwidth unit continues to decrease, existing buffer-sharing strategies face increasing performance challenges. Recent efforts have attempted to integrate Buffer Management (BM) with Active Queue Management (AQM) to harness the advantages of both BM and AQM approaches to improve performance. While these hybrid solutions show promise, their complexity of dynamically calculating multiple factors for integration hinders generalization and efficiency. This paper presents BShare, a simple buffer sharing mechanism that uses packet queueing delay. BShare requires only a single operator-configurable parameter. Our simulation results show that BSHARE improves the flow completion time (FCT) performance of advanced transport protocols, such as PowerTCP, by up to 45.07% compared to ABM, particularly under burst-heavy datacenter workloads.

S. R. Eshwar, Aniruddha Mukherjee, Kintan Saha et al.

In a recent work, we proposed Reliable Policy Iteration (RPI), that restores policy iteration's monotonicity-of-value-estimates property to the function approximation setting. Here, we assess the robustness of RPI's empirical performance on two classical control tasks -- CartPole and Inverted Pendulum -- under changes to neural network and environmental parameters. Relative to DQN, Double DQN, DDPG, TD3, and PPO, RPI reaches near-optimal performance early and sustains this policy as training proceeds. Because deep RL methods are often hampered by sample inefficiency, training instability, and hyperparameter sensitivity, our results highlight RPI's promise as a more reliable alternative.

Rohit Agarwal, Arijit Das, Alexander Horsch et al.

The domain of online learning has experienced multifaceted expansion owing to its prevalence in real-life applications. Nonetheless, this progression operates under the assumption that the input feature space of the streaming data remains constant. In this survey paper, we address the topic of online learning in the context of haphazard inputs, explicitly foregoing such an assumption. We discuss, classify, evaluate, and compare the methodologies that are adept at modeling haphazard inputs, additionally providing the corresponding code implementations and their carbon footprint. Moreover, we classify the datasets related to the field of haphazard inputs and introduce evaluation metrics specifically designed for datasets exhibiting imbalance. The code of each methodology can be found at https://github.com/Rohit102497/HaphazardInputsReview

Rohit Agarwal, Aryan Dessai, Arif Ahmed Sekh et al.

The field of varying feature space in online learning settings, also known as haphazard inputs, is very prominent nowadays due to its applicability in various fields. However, the current solutions to haphazard inputs are model-dependent and cannot benefit from the existing advanced deep-learning methods, which necessitate inputs of fixed dimensions. Therefore, we propose to transform the varying feature space in an online learning setting to a fixed-dimension image representation on the fly. This simple yet novel approach is model-agnostic, allowing any vision-based models to be applicable for haphazard inputs, as demonstrated using ResNet and ViT. The image representation handles the inconsistent input data seamlessly, making our proposed approach scalable and robust. We show the efficacy of our method on four publicly available datasets. The code is available at https://github.com/Rohit102497/HaphazardInputsAsImages.

Rohit Agarwal, Karaka Prasanth Naidu, Alexander Horsch et al.

We study the online learning problem characterized by the varying input feature space of streaming data. Although LSTMs have been employed to effectively capture the temporal nature of streaming data, they cannot handle the dimension-varying streams in an online learning setting. Therefore, we propose a dynamic LSTM-based novel method, called packetLSTM, to model the dimension-varying streams. The packetLSTM's dynamic framework consists of an evolving packet of LSTMs, each dedicated to processing one input feature. Each LSTM retains the local information of its corresponding feature, while a shared common memory consolidates global information. This configuration facilitates continuous learning and mitigates the issue of forgetting, even when certain features are absent for extended time periods. The idea of utilizing one LSTM per feature coupled with a dimension-invariant operator for information aggregation enhances the dynamic nature of packetLSTM. This dynamic nature is evidenced by the model's ability to activate, deactivate, and add new LSTMs as required, thus seamlessly accommodating varying input dimensions. The packetLSTM achieves state-of-the-art results on five datasets, and its underlying principle is extended to other RNN types, like GRU and vanilla RNN.

Zicheng Liu, Mayank Roy, Dilip K. Prasad et al.

Solving electromagnetic inverse scattering problems (ISPs) is challenging due to the intrinsic nonlinearity, ill-posedness, and expensive computational cost. Recently, deep neural network (DNN) techniques have been successfully applied on ISPs and shown potential of superior imaging over conventional methods. In this paper, we analyse the analogy between DNN solvers and traditional iterative algorithms and discuss how important physical phenomena cannot be effectively incorporated in the training process. We show the importance of including near-field priors in the learning process of DNNs. To this end, we propose new designs of loss functions which incorporate multiple-scattering based near-field quantities (such as scattered fields or induced currents within domain of interest). Effects of physics-guided loss functions are studied using a variety of numerical experiments. Pros and cons of the investigated ISP solvers with different loss functions are summarized.

Rohit Agarwal, Arif Ahmed Sekh, Krishna Agarwal et al.

Streaming classification methods assume the number of input features is fixed and always received. But in many real-world scenarios demand is some input features are reliable while others are unreliable or inconsistent. In this paper, we propose a novel deep learning-based model called Auxiliary Network (Aux-Net), which is scalable and agile. It employs a weighted ensemble of classifiers to give a final outcome. The Aux-Net model is based on the hedging algorithm and online gradient descent. It employs a model of varying depth in an online setting using single pass learning. Aux-Net is a foundational work towards scalable neural network model for a dynamic complex environment requiring ad hoc or inconsistent input data. The efficacy of Aux-Net is shown on public dataset.

Arif Ahmed Sekh, Ida S. Opstad, Rohit Agarwal et al.

In many real-world scientific problems, generating ground truth (GT) for supervised learning is almost impossible. The causes include limitations imposed by scientific instrument, physical phenomenon itself, or the complexity of modeling. Performing artificial intelligence (AI) tasks such as segmentation, tracking, and analytics of small sub-cellular structures such as mitochondria in microscopy videos of living cells is a prime example. The 3D blurring function of microscope, digital resolution from pixel size, optical resolution due to the character of light, noise characteristics, and complex 3D deformable shapes of mitochondria, all contribute to making this problem GT hard. Manual segmentation of 100s of mitochondria across 1000s of frames and then across many such videos is not only herculean but also physically inaccurate because of the instrument and phenomena imposed limitations. Unsupervised learning produces less than optimal results and accuracy is important if inferences relevant to therapy are to be derived. In order to solve this unsurmountable problem, we bring modeling and deep learning to a nexus. We show that accurate physics based modeling of microscopy data including all its limitations can be the solution for generating simulated training datasets for supervised learning. We show here that our simulation-supervised segmentation approach is a great enabler for studying mitochondrial states and behaviour in heart muscle cells, where mitochondria have a significant role to play in the health of the cells. We report unprecedented mean IoU score of 91% for binary segmentation (19% better than the best performing unsupervised approach) of mitochondria in actual microscopy videos of living cells. We further demonstrate the possibility of performing multi-class classification, tracking, and morphology associated analytics at the scale of individual mitochondrion.