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Researcher profile

Anirban Mukhopadhyay

Anirban Mukhopadhyay contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer VisionMachine Learningeess.IVmath.NTcs.CYeess.SPGraphicsHuman-Computer InteractionMolecular Networks

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Published work

23 published item(s)

preprint2026arXiv

SWoMo: Neuro-Symbolic World Model for Cataract Surgery Simulation

Realistic surgical simulation plays a crucial role in training novice surgeons and in the development of autonomous agents. World models can scale such simulation environments to realistic and diverse procedures by predicting future patient states conditioned on current observations and surgical actions. However, current state-of-the-art approaches often fail to satisfy key criteria required for clinical applicability, including visual realism, physically grounded interactions, and the ability to simulate scenarios beyond the training distribution. Hence, we introduce SWoMo, a neuro-symbolic world model for cataract surgery simulation that decouples motion generation from visual realism. The symbolic component, consisting of a rule-based simulator and scene graph representations, models motion dynamics and tool-tissue interactions, while a diffusion model produces realistic visual appearance, including textures and tissue deformations. We propose an inverse pairing strategy that reconstructs real surgical videos in the simulator to obtain paired simulated and real videos, which are then used to train our video diffusion model for the reverse objective of sim-to-real translation. Our experiments show both qualitative and quantitative improvements over prior work. We demonstrate that our simulator further satisfies the key criteria, including generalisation to unseen interaction geometries, improvements in downstream phase detection, and unsupervised video style transfer. The code, data, and model weights are available at: https://ssharvienkumar.github.io/SWoMo/

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

The state-of-the-art 3D anisotropic intracranial hemorrhage segmentation on non-contrast head CT: The INSTANCE challenge

Automatic intracranial hemorrhage segmentation in 3D non-contrast head CT (NCCT) scans is significant in clinical practice. Existing hemorrhage segmentation methods usually ignores the anisotropic nature of the NCCT, and are evaluated on different in-house datasets with distinct metrics, making it highly challenging to improve segmentation performance and perform objective comparisons among different methods. The INSTANCE 2022 was a grand challenge held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). It is intended to resolve the above-mentioned problems and promote the development of both intracranial hemorrhage segmentation and anisotropic data processing. The INSTANCE released a training set of 100 cases with ground-truth and a validation set with 30 cases without ground-truth labels that were available to the participants. A held-out testing set with 70 cases is utilized for the final evaluation and ranking. The methods from different participants are ranked based on four metrics, including Dice Similarity Coefficient (DSC), Hausdorff Distance (HD), Relative Volume Difference (RVD) and Normalized Surface Dice (NSD). A total of 13 teams submitted distinct solutions to resolve the challenges, making several baseline models, pre-processing strategies and anisotropic data processing techniques available to future researchers. The winner method achieved an average DSC of 0.6925, demonstrating a significant growth over our proposed baseline method. To the best of our knowledge, the proposed INSTANCE challenge releases the first intracranial hemorrhage segmentation benchmark, and is also the first challenge that intended to resolve the anisotropic problem in 3D medical image segmentation, which provides new alternatives in these research fields.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Continual Hippocampus Segmentation with Transformers

In clinical settings, where acquisition conditions and patient populations change over time, continual learning is key for ensuring the safe use of deep neural networks. Yet most existing work focuses on convolutional architectures and image classification. Instead, radiologists prefer to work with segmentation models that outline specific regions-of-interest, for which Transformer-based architectures are gaining traction. The self-attention mechanism of Transformers could potentially mitigate catastrophic forgetting, opening the way for more robust medical image segmentation. In this work, we explore how recently-proposed Transformer mechanisms for semantic segmentation behave in sequential learning scenarios, and analyse how best to adapt continual learning strategies for this setting. Our evaluation on hippocampus segmentation shows that Transformer mechanisms mitigate catastrophic forgetting for medical image segmentation compared to purely convolutional architectures, and demonstrates that regularising ViT modules should be done with caution.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Correlation of multiplicative functions over function fields

In this article we study the asymptotic behaviour of the correlation functions over polynomial ring $\mathbb{F}_q[x]$. Let $\mathcal{M}_{n, q}$ and $\mathcal{P}_{n, q}$ be the set of all monic polynomials and monic irreducible polynomials of degree $n$ over $\mathbb{F}_q$ respectively. For multiplicative functions $ψ_1$ and $ψ_2$ on $\mathbb{F}_q[x]$, we obtain asymptotic formula for the following correlation functions for a fixed $q$ and $n\to \infty$ \begin{align*} &S_{2}(n, q):=\displaystyle\sum_{f\in \mathcal{M}_{n, q}}ψ_1(f+h_1) ψ_2(f+h_2), \\ &R_2(n, q):=\displaystyle\sum_{P\in \mathcal{P}_{n, q}}ψ_1(P+h_1)ψ_2(P+h_2), \end{align*} where $h_1, h_2$ are fixed polynomials of degree $<n$ over $\mathbb{F}_q$. As a consequence, for real valued additive functions $\tilde{ψ_1}$ and $\tilde{ψ_2}$ on $\mathbb{F}_q[x]$ we show that for a fixed $q$ and $n\to \infty$, the following distribution functions \begin{align*} &\frac{1}{|\mathcal{M}_{n, q}|}\Big|\{f\in \mathcal{M}_{n, q} : \tilde{ψ_1}(f+h_1)+\tilde{ψ_2}(f+h_2)\leq x\}\Big|,\\ & \frac{1}{|\mathcal{P}_{n, q}|}\Big|\{P\in \mathcal{P}_{n, q} : \tilde{ψ_1}(P+h_1)+\tilde{ψ_2}(P+h_2)\leq x\}\Big| \end{align*} converges weakly towards a limit distribution.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Disentanglement enables cross-domain Hippocampus Segmentation

Limited amount of labelled training data are a common problem in medical imaging. This makes it difficult to train a well-generalised model and therefore often leads to failure in unknown domains. Hippocampus segmentation from magnetic resonance imaging (MRI) scans is critical for the diagnosis and treatment of neuropsychatric disorders. Domain differences in contrast or shape can significantly affect segmentation. We address this issue by disentangling a T1-weighted MRI image into its content and domain. This separation enables us to perform a domain transfer and thus convert data from new sources into the training domain. This step thus simplifies the segmentation problem, resulting in higher quality segmentations. We achieve the disentanglement with the proposed novel methodology &#39;Content Domain Disentanglement GAN&#39;, and we propose to retrain the UNet on the transformed outputs to deal with GAN-specific artefacts. With these changes, we are able to improve performance on unseen domains by 6-13% and outperform state-of-the-art domain transfer methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Distance-based detection of out-of-distribution silent failures for Covid-19 lung lesion segmentation

Automatic segmentation of ground glass opacities and consolidations in chest computer tomography (CT) scans can potentially ease the burden of radiologists during times of high resource utilisation. However, deep learning models are not trusted in the clinical routine due to failing silently on out-of-distribution (OOD) data. We propose a lightweight OOD detection method that leverages the Mahalanobis distance in the feature space and seamlessly integrates into state-of-the-art segmentation pipelines. The simple approach can even augment pre-trained models with clinically relevant uncertainty quantification. We validate our method across four chest CT distribution shifts and two magnetic resonance imaging applications, namely segmentation of the hippocampus and the prostate. Our results show that the proposed method effectively detects far- and near-OOD samples across all explored scenarios.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

On the explicit Galois group of $\mathbb{Q}(\sqrt{a_{1}}, \sqrt{a_{2}}, \dots, \sqrt{a_{n}}, ζ_{d})$ over $\mathbb{Q}$

Let $S= \{ a_{1}, a_{2}, \dots, a_{n} \}$ be a finite set of non-zero integers. In \cite{KBAM21}, Karthick Babu and Anirban Mukhopadhyay calculated the explicit structure of the Galois group of multi-quadratic field $\mathbb{Q}(\sqrt{a_{1}}, \sqrt{a_{2}}, \dots, \sqrt{a_{n}})$ over $\mathbb{Q}$. For a positive integer $d \geq 3$, $ζ_{d}$ denotes the primitive $d$-th root of unity. In this paper, we calculate the explicit structure of the Galois group of $\mathbb{Q}(\sqrt{a_{1}}, \sqrt{a_{2}}, \dots, \sqrt{a_{n}}, ζ_{d})$ over $\mathbb{Q}$ in terms of its action on $ζ_{d}$ and $\sqrt{a_{i}}$ for $1 \leq i \leq n$.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Task-agnostic Continual Hippocampus Segmentation for Smooth Population Shifts

Most continual learning methods are validated in settings where task boundaries are clearly defined and task identity information is available during training and testing. We explore how such methods perform in a task-agnostic setting that more closely resembles dynamic clinical environments with gradual population shifts. We propose ODEx, a holistic solution that combines out-of-distribution detection with continual learning techniques. Validation on two scenarios of hippocampus segmentation shows that our proposed method reliably maintains performance on earlier tasks without losing plasticity.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

A survey on shape-constraint deep learning for medical image segmentation

Since the advent of U-Net, fully convolutional deep neural networks and its many variants have completely changed the modern landscape of deep learning based medical image segmentation. However, the over dependence of these methods on pixel level classification and regression has been identified early on as a problem. Especially when trained on medical databases with sparse available annotation, these methods are prone to generate segmentation artifacts such as fragmented structures, topological inconsistencies and islands of pixel. These artefacts are especially problematic in medical imaging since segmentation is almost always a pre-processing step for some downstream evaluation. The range of possible downstream evaluations is rather big, for example surgical planning, visualization, shape analysis, prognosis, treatment planning etc. However, one common thread across all these downstream tasks is the demand of anatomical consistency. To ensure the segmentation result is anatomically consistent, approaches based on Markov/ Conditional Random Fields, Statistical Shape Models are becoming increasingly popular over the past 5 years. In this review paper, a broad overview of recent literature on bringing anatomical constraints for medical image segmentation is given, the shortcomings and opportunities of the proposed methods are thoroughly discussed and potential future work is elaborated. We review the most relevant papers published until the submission date. For quick access, important details such as the underlying method, datasets and performance are tabulated.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

CycleGAN for Interpretable Online EMT Compensation

Purpose: Electromagnetic Tracking (EMT) can partially replace X-ray guidance in minimally invasive procedures, reducing radiation in the OR. However, in this hybrid setting, EMT is disturbed by metallic distortion caused by the X-ray device. We plan to make hybrid navigation clinical reality to reduce radiation exposure for patients and surgeons, by compensating EMT error. Methods: Our online compensation strategy exploits cycle-consistent generative adversarial neural networks (CycleGAN). 3D positions are translated from various bedside environments to their bench equivalents. Domain-translated points are fine-tuned to reduce error in the bench domain. We evaluate our compensation approach in a phantom experiment. Results: Since the domain-translation approach maps distorted points to their lab equivalents, predictions are consistent among different C-arm environments. Error is successfully reduced in all evaluation environments. Our qualitative phantom experiment demonstrates that our approach generalizes well to an unseen C-arm environment. Conclusion: Adversarial, cycle-consistent training is an explicable, consistent and thus interpretable approach for online error compensation. Qualitative assessment of EMT error compensation gives a glimpse to the potential of our method for rotational error compensation.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation

Purpose: Segmentation of surgical instruments in endoscopic videos is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods: We introduce a teacher-student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the erroneous learning problem of the current consistency-based unsupervised domain adaptation framework. Results: Empirical results on three datasets highlight the effectiveness of the proposed framework over current approaches for the endoscopic instrument segmentation task. Additionally, we provide analysis of major factors affecting the performance on all datasets to highlight the strengths and failure modes of our approach. Conclusion: We show that our proposed approach can successfully exploit the unlabeled real endoscopic video frames and improve generalization performance over pure simulation-based training and the previous state-of-the-art. This takes us one step closer to effective segmentation of surgical tools in the annotation scarce setting.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

AutoSNAP: Automatically Learning Neural Architectures for Instrument Pose Estimation

Despite recent successes, the advances in Deep Learning have not yet been fully translated to Computer Assisted Intervention (CAI) problems such as pose estimation of surgical instruments. Currently, neural architectures for classification and segmentation tasks are adopted ignoring significant discrepancies between CAI and these tasks. We propose an automatic framework (AutoSNAP) for instrument pose estimation problems, which discovers and learns the architectures for neural networks. We introduce 1)~an efficient testing environment for pose estimation, 2)~a powerful architecture representation based on novel Symbolic Neural Architecture Patterns (SNAPs), and 3)~an optimization of the architecture using an efficient search scheme. Using AutoSNAP, we discover an improved architecture (SNAPNet) which outperforms both the hand-engineered i3PosNet and the state-of-the-art architecture search method DARTS.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Bounded gaps between product of two primes in imaginary quadratic number fields

We study the gaps between products of two primes in imaginary quadratic number fields using a combination of the methods of Goldston-Graham-Pintz-Yildirim \cite{GGPY}, and Maynard \cite{MAY}. An important consequence of our main theorem is existence of infinitely many pairs $α_1, α_2$ which are product of two primes in the imaginary quadratic field $K$ such that $|σ(α_1-α_2)|\leq 2$ for all embedding $σ$ of $K$ if the class number of $K$ is one and $|σ(α_1-α_2)|\leq 8$ for all embedding $σ$ of $K$ if the class number of $K$ is two.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation

Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis&#39;15 dataset) highlight the effectiveness of the proposed \emph{Endo-Sim2Real} method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

EXCLUVIS: A MATLAB GUI Software for Comparative Study of Clustering and Visualization of Gene Expression Data

Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its input parameters which can substantially affect the behavior of the algorithm. Cluster validity indices determine the partitioning that best fits the underlying data. In bioinformatics, microarray gene expression technology has made it possible to measure the gene expression levels of thousands of genes simultaneously. Many genomic studies, which aim to analyze the functions of some genes, highly rely on some clustering technique for grouping similarly expressed genes in one cluster or partitioning tissue samples based on similar expression values of genes. In this work, an application package called EXCLUVIS (gene EXpression data CLUstering and VISualization) has been developed using MATLAB Graphical User Interface (GUI) environment for analyzing the performances of different clustering algorithms on gene expression datasets. In this application package, the user needs to select a number of parameters such as internal validity indices, external validity indices and number of clusters from the active windows for evaluating the performance of the clustering algorithms. EXCLUVIS compares the performances of K-means, fuzzy C-means, hierarchical clustering and multiobjective evolutionary clustering algorithms. Heatmap and cluster profile plots are used for visualizing the results. EXCLUVIS allows the users to easily find the goodness of clustering solutions as well as provides visual representations of the clustering outcomes.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

i3PosNet: Instrument Pose Estimation from X-Ray in temporal bone surgery

Purpose: Accurate estimation of the position and orientation (pose) of surgical instruments is crucial for delicate minimally invasive temporal bone surgery. Current techniques lack in accuracy and/or line-of-sight constraints (conventional tracking systems) or expose the patient to prohibitive ionizing radiation (intra-operative CT). A possible solution is to capture the instrument with a c-arm at irregular intervals and recover the pose from the image. Methods: i3PosNet infers the position and orientation of instruments from images using a pose estimation network. Said framework considers localized patches and outputs pseudo-landmarks. The pose is reconstructed from pseudo-landmarks by geometric considerations. Results: We show i3PosNet reaches errors less than 0.05mm. It outperforms conventional image registration-based approaches reducing average and maximum errors by at least two thirds. i3PosNet trained on synthetic images generalizes to real x-rays without any further adaptation. Conclusion: The translation of Deep Learning based methods to surgical applications is difficult, because large representative datasets for training and testing are not available. This work empirically shows sub-millimeter pose estimation trained solely based on synthetic training data.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Leveraging Spatial Uncertainty for Online Error Compensation in EMT

Purpose: Electromagnetic Tracking (EMT) can potentially complement fluoroscopic navigation, reducing radiation exposure in a hybrid setting. Due to the susceptibility to external distortions, systematic error in EMT needs to be compensated algorithmically. Compensation algorithms for EMT in guidewire procedures are only practical in an online setting. Methods: We collect positional data and train a symmetric Artificial Neural Network (ANN) architecture for compensating navigation error. The results are evaluated in both online and offline scenarios and are compared to polynomial fits. We assess spatial uncertainty of the compensation proposed by the ANN. Simulations based on real data show how this uncertainty measure can be utilized to improve accuracy and limit radiation exposure in hybrid navigation. Results: ANNs compensate unseen distortions by more than 70%, outperforming polynomial regression. Working on known distortions, ANNs outperform polynomials as well. We empirically demonstrate a linear relationship between tracking accuracy and model uncertainty. The effectiveness of hybrid tracking is shown in a simulation experiment. Conclusion: ANNs are suitable for EMT error compensation and can generalize across unseen distortions. Model uncertainty needs to be assessed when spatial error compensation algorithms are developed, so that training data collection can be optimized. Finally, we find that error compensation in EMT reduces the need for x-ray images in hybrid navigation.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

M3d-CAM: A PyTorch library to generate 3D data attention maps for medical deep learning

M3d-CAM is an easy to use library for generating attention maps of CNN-based PyTorch models improving the interpretability of model predictions for humans. The attention maps can be generated with multiple methods like Guided Backpropagation, Grad-CAM, Guided Grad-CAM and Grad-CAM++. These attention maps visualize the regions in the input data that influenced the model prediction the most at a certain layer. Furthermore, M3d-CAM supports 2D and 3D data for the task of classification as well as for segmentation. A key feature is also that in most cases only a single line of code is required for generating attention maps for a model making M3d-CAM basically plug and play.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Predicting potential drug targets and repurposable drugs for COVID-19 via a deep generative model for graphs

Coronavirus Disease 2019 (COVID-19) has been creating a worldwide pandemic situation. Repurposing drugs, already shown to be free of harmful side effects, for the treatment of COVID-19 patients is an important option in launching novel therapeutic strategies. Therefore, reliable molecule interaction data are a crucial basis, where drug-/protein-protein interaction networks establish invaluable, year-long carefully curated data resources. However, these resources have not yet been systematically exploited using high-performance artificial intelligence approaches. Here, we combine three networks, two of which are year-long curated, and one of which, on SARS-CoV-2-human host-virus protein interactions, was published only most recently (30th of April 2020), raising a novel network that puts drugs, human and virus proteins into mutual context. We apply Variational Graph AutoEncoders (VGAEs), representing most advanced deep learning based methodology for the analysis of data that are subject to network constraints. Reliable simulations confirm that we operate at utmost accuracy in terms of predicting missing links. We then predict hitherto unknown links between drugs and human proteins against which virus proteins preferably bind. The corresponding therapeutic agents present splendid starting points for exploring novel host-directed therapy (HDT) options.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Detection and Characterization of Intrinsic Symmetry

A comprehensive framework for detection and characterization of overlapping intrinsic symmetry over 3D shapes is proposed. To identify prominent symmetric regions which overlap in space and vary in form, the proposed framework is decoupled into a Correspondence Space Voting procedure followed by a Transformation Space Mapping procedure. In the correspondence space voting procedure, significant symmetries are first detected by identifying surface point pairs on the input shape that exhibit local similarity in terms of their intrinsic geometry while simultaneously maintaining an intrinsic distance structure at a global level. Since different point pairs can share a common point, the detected symmetric shape regions can potentially overlap. To this end, a global intrinsic distance-based voting technique is employed to ensure the inclusion of only those point pairs that exhibit significant symmetry. In the transformation space mapping procedure, the Functional Map framework is employed to generate the final map of symmetries between point pairs. The transformation space mapping procedure ensures the retrieval of the underlying dense correspondence map throughout the 3D shape that follows a particular symmetry. Additionally, the formulation of a novel cost matrix enables the inner product to succesfully indicate the complexity of the underlying symmetry transformation. The proposed transformation space mapping procedure is shown to result in the formulation of a semi-metric symmetry space where each point in the space represents a specific symmetry transformation and the distance between points represents the complexity between the corresponding transformations. Experimental results show that the proposed framework can successfully process complex 3D shapes that possess rich symmetries.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Morphological Analusis Of The Left Ventricular Eendocardial Surface Using A Bag-Of-Features Descriptor

The limitations of conventional imaging techniques have hitherto precluded a thorough and formal investigation of the complex morphology of the left ventricular (LV) endocardial surface and its relation to the severity of Coronary Artery Disease (CAD). Recent developments in high-resolution Multirow-Detector Computed Tomography (MDCT) scanner technology have enabled the imaging of LV endocardial surface morphology in a single heart beat. Analysis of high-resolution Computed Tomography (CT) images from a 320-MDCT scanner allows the study of the relationship between percent Diameter Stenosis (DS) of the major coronary arteries and localization of the cardiac segments affected by coronary arterial stenosis. In this paper a novel approach for the analysis using a combination of rigid transformation-invariant shape descriptors and a more generalized isometry-invariant Bag-of-Features (BoF) descriptor, is proposed and implemented. The proposed approach is shown to be successful in identifying, localizing and quantifying the incidence and extent of CAD and thus, is seen to have a potentially significant clinical impact. Specifically, the association between the incidence and extent of CAD, determined via the percent DS measurements of the major coronary arteries, and the alterations in the endocardial surface morphology is formally quantified. A multivariate regression test performed on a strict leave-one-out basis are shown to exhibit a distinct pattern in terms of the correlation coefficient within the cardiac segments where the incidence of coronary arterial stenosis is localized.

0 citations0 reviewsNo code linkedOpen access