arXiv subjects

Bishesh Khanal

Publications and source records attributed to Bishesh Khanal.

At least 19 recordsLinked to original sources

arXiv2026

Large-Scale Pretraining for Improving Deep Learning-Based Geometric Distortion Correction of Diffusion-Weighted Imaging

Diffusion-weighted imaging (DWI) is widely used in clinical settings but remains vulnerable to geometric distortion. Conventional correction methods often require additional acquisitions or vendor-specific solutions, limiting their feasibility in high-throughput, resource-constrained settings. This study investigates whether large-scale pretraining strategies can improve deep learning-based distortion correction for single-phase-encoding DWI. We formulate the task as image reconstruction, and compare a non-pretrained baseline against a self-supervised and a generative pretrained model, evaluated using both quantitative image-similarity metrics and qualitative expert assessment. The best-performing model was further tested for transferability on data collected in an LMIC setting with acquisition shift. Pretrained models outperformed the non-pretrained baseline, with cWDM achieving the strongest results across both quantitative and qualitative evaluation. However, application to LMIC data revealed transferability challenges, including contrast alteration and over-reliance on T1-weighted anatomical structure. Registering images to a common standard space improved predictions, suggesting that harmonized preprocessing may enhance cross-domain deployment.

cs.CV↗

arXiv2026

Topology-Driven Fusion of nnU-Net and MedNeXt for Accurate Brain Tumor Segmentation on Sub-Saharan Africa Dataset

Accurate automatic brain tumor segmentation in Low and Middle-Income (LMIC) countries is challenging due to the lack of defined national imaging protocols, diverse imaging data, extensive use of low-field Magnetic Resonance Imaging (MRI) scanners and limited health-care resources. As part of the Brain Tumor Segmentation (BraTS) Africa 2025 Challenge, we applied topology refinement to the state-of-the-art segmentation models like nnU-Net, MedNeXt, and a combination of both. Since the BraTS-Africa dataset has low MRI image quality, we incorporated the BraTS 2025 challenge data of pre-treatment adult glioma (Task 1) to pre-train the segmentation model and use it to fine-tune on the BraTS-Africa dataset. We added an extra topology refinement module to address the issue of deformation in prediction that arose due to topological error. With the introduction of this module, we achieved a better Normalized Surface Distance (NSD) of 0.810, 0.829, and 0.895 on Surrounding Non-Enhancing FLAIR Hyperintensity (SNFH) , Non-Enhancing Tumor Core (NETC) and Enhancing tumor (ET).

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arXiv2026

Automated Quality Assessment of Blind Sweep Obstetric Ultrasound for Improved Diagnosis

Blind Sweep Obstetric Ultrasound (BSOU) enables scalable fetal imaging in low-resource settings by allowing minimally trained operators to acquire standardized sweep videos for automated Artificial Intelligence(AI) interpretation. However, the reliability of such AI systems depends critically on the quality of the acquired sweeps, and little is known about how deviations from the intended protocol affect downstream predictions. In this work, we present a systematic evaluation of BSOU quality and its impact on three key AI tasks: sweep-tag classification, fetal presentation classification, and placenta-location classification. We simulate plausible acquisition deviations, including reversed sweep direction, probe inversion, and incomplete sweeps, to quantify model robustness, and we develop automated quality-assessment models capable of detecting these perturbations. To approximate real-world deployment, we simulate a feedback loop in which flagged sweeps are re-acquired, showing that such correction improves downstream task performance. Our findings highlight the sensitivity of BSOU-based AI models to acquisition variability and demonstrate that automated quality assessment can play a central role in building reliable, scalable AI-assisted prenatal ultrasound workflows, particularly in low-resource environments.

cs.CV↗

arXiv2026

Evaluating Large Language Models' Responses to Sexual and Reproductive Health Queries in Nepali

As Large Language Models (LLMs) become integrated into daily life, they are increasingly used for personal queries, including Sexual and Reproductive Health (SRH), allowing users to chat anonymously without fear of judgment. However, current evaluation methods primarily focus on accuracy, often for objective queries in high-resource languages, and lack criteria to assess usability and safety, especially for low-resource languages and culturally sensitive domains like SRH. This paper introduces LLM Evaluation Framework (LEAF), that conducts assessments across multiple criteria: accuracy, language, usability gaps (including relevance, adequacy, and cultural appropriateness), and safety gaps (safety, sensitivity, and confidentiality). Using the LEAF framework, we assessed 14K SRH queries in Nepali from over 9K users. Responses were manually annotated by SRH experts according to the framework. Results revealed that only 35.1% of the responses were "proper", meaning they were accurate, adequate and had no major usability or safety related gaps. Insights include differences in performance between ChatGPT versions, such as similar accuracy but varying usability and safety aspects. This evaluation highlights significant limitations of current LLMs and underscores the need for improvement. The LEAF Framework is adaptable across domains and languages, particularly where usability and safety are critical, offering a pathway to better address sensitive topics.

cs.CL↗

arXiv2026

The AI Pyramid A Conceptual Framework for Workforce Capability in the Age of AI

Artificial intelligence (AI) represents a qualitative shift in technological change by extending cognitive labor itself rather than merely automating routine tasks. Recent evidence shows that generative AI disproportionately affects highly educated, white collar work, challenging existing assumptions about workforce vulnerability and rendering traditional approaches to digital or AI literacy insufficient. This paper introduces the concept of AI Nativity, the capacity to integrate AI fluidly into everyday reasoning, problem solving, and decision making, and proposes the AI Pyramid, a conceptual framework for organizing human capability in an AI mediated economy. The framework distinguishes three interdependent capability layers: AI Native capability as a universal baseline for participation in AI augmented environments; AI Foundation capability for building, integrating, and sustaining AI enabled systems; and AI Deep capability for advancing frontier AI knowledge and applications. Crucially, the pyramid is not a career ladder but a system level distribution of capabilities required at scale. Building on this structure, the paper argues that effective AI workforce development requires treating capability formation as infrastructure rather than episodic training, centered on problem based learning embedded in work contexts and supported by dynamic skill ontologies and competency based measurement. The framework has implications for organizations, education systems, and governments seeking to align learning, measurement, and policy with the evolving demands of AI mediated work, while addressing productivity, resilience, and inequality at societal scale.

cs.AI↗

arXiv2025

From Development to Deployment of AI-assisted Telehealth and Screening for Vision- and Hearing-threatening diseases in resource-constrained settings: Field Observations, Challenges and Way Forward

Vision- and hearing-threatening diseases cause preventable disability, especially in resource-constrained settings(RCS) with few specialists and limited screening setup. Large scale AI-assisted screening and telehealth has potential to expand early detection, but practical deployment is challenging in paper-based workflows and limited documented field experience exist to build upon. We provide insights on challenges and ways forward in development to adoption of scalable AI-assisted Telehealth and screening in such settings. Specifically, we find that iterative, interdisciplinary collaboration through early prototyping, shadow deployment and continuous feedback is important to build shared understanding as well as reduce usability hurdles when transitioning from paper-based to AI-ready workflows. We find public datasets and AI models highly useful despite poor performance due to domain shift. In addition, we find the need for automated AI-based image quality check to capture gradable images for robust screening in high-volume camps. Our field learning stress the importance of treating AI development and workflow digitization as an end-to-end, iterative co-design process. By documenting these practical challenges and lessons learned, we aim to address the gap in contextual, actionable field knowledge for building real-world AI-assisted telehealth and mass-screening programs in RCS.

cs.CV↗

arXiv2025

Multimodal Latent Fusion of ECG Leads for Early Assessment of Pulmonary Hypertension

Recent advancements in early assessment of pulmonary hypertension (PH) primarily focus on applying machine learning methods to centralized diagnostic modalities, such as 12-lead electrocardiogram (12L-ECG). Despite their potential, these approaches fall short in decentralized clinical settings, e.g., point-of-care and general practice, where handheld 6-lead ECG (6L-ECG) can offer an alternative but is limited by the scarcity of labeled data for developing reliable models. To address this, we propose a lead-specific electrocardiogram multimodal variational autoencoder (\textsc{LS-EMVAE}), which incorporates a hierarchical modality expert (HiME) fusion mechanism and a latent representation alignment loss. HiME combines mixture-of-experts and product-of-experts to enable flexible, adaptive latent fusion, while the alignment loss improves coherence among lead-specific and shared representations. To alleviate data scarcity and enhance representation learning, we adopt a transfer learning strategy: the model is first pre-trained on a large unlabeled 12L-ECG dataset and then fine-tuned on smaller task-specific labeled 6L-ECG datasets. We validate \textsc{LS-EMVAE} across two retrospective cohorts in a 6L-ECG setting: 892 subjects from the ASPIRE registry for (1) PH detection and (2) phenotyping pre-/post-capillary PH, and 16,416 subjects from UK Biobank for (3) predicting elevated pulmonary atrial wedge pressure, where it consistently outperforms unimodal and multimodal baseline methods and demonstrates strong generalizability and interpretability. The code is available at https://github.com/Shef-AIRE/LS-EMVAE.

eess.SP↗

arXiv2024

Parameter-efficient Fine-tuning for improved Convolutional Baseline for Brain Tumor Segmentation in Sub-Saharan Africa Adult Glioma Dataset

Automating brain tumor segmentation using deep learning methods is an ongoing challenge in medical imaging. Multiple lingering issues exist including domain-shift and applications in low-resource settings which brings a unique set of challenges including scarcity of data. As a step towards solving these specific problems, we propose Convolutional adapter-inspired Parameter-efficient Fine-tuning (PEFT) of MedNeXt architecture. To validate our idea, we show our method performs comparable to full fine-tuning with the added benefit of reduced training compute using BraTS-2021 as pre-training dataset and BraTS-Africa as the fine-tuning dataset. BraTS-Africa consists of a small dataset (60 train / 35 validation) from the Sub-Saharan African population with marked shift in the MRI quality compared to BraTS-2021 (1251 train samples). We first show that models trained on BraTS-2021 dataset do not generalize well to BraTS-Africa as shown by 20% reduction in mean dice on BraTS-Africa validation samples. Then, we show that PEFT can leverage both the BraTS-2021 and BraTS-Africa dataset to obtain mean dice of 0.8 compared to 0.72 when trained only on BraTS-Africa. Finally, We show that PEFT (0.80 mean dice) results in comparable performance to full fine-tuning (0.77 mean dice) which may show PEFT to be better on average but the boxplots show that full finetuning results is much lesser variance in performance. Nevertheless, on disaggregation of the dice metrics, we find that the model has tendency to oversegment as shown by high specificity (0.99) compared to relatively low sensitivity(0.75). The source code is available at https://github.com/CAMERA-MRI/SPARK2024/tree/main/PEFT_MedNeXt

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arXiv2024

NLPineers@ NLU of Devanagari Script Languages 2025: Hate Speech Detection using Ensembling of BERT-based models

This paper explores hate speech detection in Devanagari-scripted languages, focusing on Hindi and Nepali, for Subtask B of the CHIPSAL@COLING 2025 Shared Task. Using a range of transformer-based models such as XLM-RoBERTa, MURIL, and IndicBERT, we examine their effectiveness in navigating the nuanced boundary between hate speech and free expression. Our best performing model, implemented as ensemble of multilingual BERT models achieve Recall of 0.7762 (Rank 3/31 in terms of recall) and F1 score of 0.6914 (Rank 17/31). To address class imbalance, we used backtranslation for data augmentation, and cosine similarity to preserve label consistency after augmentation. This work emphasizes the need for hate speech detection in Devanagari-scripted languages and presents a foundation for further research.

cs.CL↗

arXiv2024

TuneVLSeg: Prompt Tuning Benchmark for Vision-Language Segmentation Models

Vision-Language Models (VLMs) have shown impressive performance in vision tasks, but adapting them to new domains often requires expensive fine-tuning. Prompt tuning techniques, including textual, visual, and multimodal prompting, offer efficient alternatives by leveraging learnable prompts. However, their application to Vision-Language Segmentation Models (VLSMs) and evaluation under significant domain shifts remain unexplored. This work presents an open-source benchmarking framework, TuneVLSeg, to integrate various unimodal and multimodal prompt tuning techniques into VLSMs, making prompt tuning usable for downstream segmentation datasets with any number of classes. TuneVLSeg includes $6$ prompt tuning strategies on various prompt depths used in $2$ VLSMs totaling of $8$ different combinations. We test various prompt tuning on $8$ diverse medical datasets, including $3$ radiology datasets (breast tumor, echocardiograph, chest X-ray pathologies) and $5$ non-radiology datasets (polyp, ulcer, skin cancer), and two natural domain segmentation datasets. Our study found that textual prompt tuning struggles under significant domain shifts, from natural-domain images to medical data. Furthermore, visual prompt tuning, with fewer hyperparameters than multimodal prompt tuning, often achieves performance competitive to multimodal approaches, making it a valuable first attempt. Our work advances the understanding and applicability of different prompt-tuning techniques for robust domain-specific segmentation. The source code is available at https://github.com/naamiinepal/tunevlseg.

cs.CV↗

arXiv2024

AI-Assisted Cervical Cancer Screening

Visual Inspection with Acetic Acid (VIA) remains the most feasible cervical cancer screening test in resource-constrained settings of low- and middle-income countries (LMICs), which are often performed screening camps or primary/community health centers by nurses instead of the preferred but unavailable expert Gynecologist. To address the highly subjective nature of the test, various handheld devices integrating cameras or smartphones have been recently explored to capture cervical images during VIA and aid decision-making via telemedicine or AI models. Most studies proposing AI models retrospectively use a relatively small number of already collected images from specific devices, digital cameras, or smartphones; the challenges and protocol for quality image acquisition during VIA in resource-constrained camp settings, challenges in getting gold standard, data imbalance, etc. are often overlooked. We present a novel approach and describe the end-to-end design process to build a robust smartphone-based AI-assisted system that does not require buying a separate integrated device: the proposed protocol for quality image acquisition in resource-constrained settings, dataset collected from 1,430 women during VIA performed by nurses in screening camps, preprocessing pipeline, and training and evaluation of a deep-learning-based classification model aimed to identify (pre)cancerous lesions. Our work shows that the readily available smartphones and a suitable protocol can capture the cervix images with the required details for the VIA test well; the deep-learning-based classification model provides promising results to assist nurses in VIA screening; and provides a direction for large-scale data collection and validation in resource-constrained settings.

eess.IV↗

arXiv2024

Deep-learning Assisted Detection and Quantification of (oo)cysts of Giardia and Cryptosporidium on Smartphone Microscopy Images

The consumption of microbial-contaminated food and water is responsible for the deaths of millions of people annually. Smartphone-based microscopy systems are portable, low-cost, and more accessible alternatives for the detection of Giardia and Cryptosporidium than traditional brightfield microscopes. However, the images from smartphone microscopes are noisier and require manual cyst identification by trained technicians, usually unavailable in resource-limited settings. Automatic detection of (oo)cysts using deep-learning-based object detection could offer a solution for this limitation. We evaluate the performance of four state-of-the-art object detectors to detect (oo)cysts of Giardia and Cryptosporidium on a custom dataset that includes both smartphone and brightfield microscopic images from vegetable samples. Faster RCNN, RetinaNet, You Only Look Once (YOLOv8s), and Deformable Detection Transformer (Deformable DETR) deep-learning models were employed to explore their efficacy and limitations. Our results show that while the deep-learning models perform better with the brightfield microscopy image dataset than the smartphone microscopy image dataset, the smartphone microscopy predictions are still comparable to the prediction performance of non-experts. Also, we publicly release brightfield and smartphone microscopy datasets with the benchmark results for the detection of Giardia and Cryptosporidium, independently captured on reference (or standard lab setting) and vegetable samples. Our code and dataset are available at https://github.com/naamiinepal/smartphone_microscopy and https://doi.org/10.5281/zenodo.7813183, respectively.

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arXiv2024

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.

cs.CY↗

arXiv2024

VLSM-Adapter: Finetuning Vision-Language Segmentation Efficiently with Lightweight Blocks

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

cs.CV↗

arXiv2024

Exploring Transfer Learning in Medical Image Segmentation using Vision-Language Models

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated $11$ datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

cs.CV↗

arXiv2024

Investigating the Robustness of Vision Transformers against Label Noise in Medical Image Classification

Label noise in medical image classification datasets significantly hampers the training of supervised deep learning methods, undermining their generalizability. The test performance of a model tends to decrease as the label noise rate increases. Over recent years, several methods have been proposed to mitigate the impact of label noise in medical image classification and enhance the robustness of the model. Predominantly, these works have employed CNN-based architectures as the backbone of their classifiers for feature extraction. However, in recent years, Vision Transformer (ViT)-based backbones have replaced CNNs, demonstrating improved performance and a greater ability to learn more generalizable features, especially when the dataset is large. Nevertheless, no prior work has rigorously investigated how transformer-based backbones handle the impact of label noise in medical image classification. In this paper, we investigate the architectural robustness of ViT against label noise and compare it to that of CNNs. We use two medical image classification datasets -- COVID-DU-Ex, and NCT-CRC-HE-100K -- both corrupted by injecting label noise at various rates. Additionally, we show that pretraining is crucial for ensuring ViT's improved robustness against label noise in supervised training.

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arXiv2024

How does self-supervised pretraining improve robustness against noisy labels across various medical image classification datasets?

Noisy labels can significantly impact medical image classification, particularly in deep learning, by corrupting learned features. Self-supervised pretraining, which doesn't rely on labeled data, can enhance robustness against noisy labels. However, this robustness varies based on factors like the number of classes, dataset complexity, and training size. In medical images, subtle inter-class differences and modality-specific characteristics add complexity. Previous research hasn't comprehensively explored the interplay between self-supervised learning and robustness against noisy labels in medical image classification, considering all these factors. In this study, we address three key questions: i) How does label noise impact various medical image classification datasets? ii) Which types of medical image datasets are more challenging to learn and more affected by label noise? iii) How do different self-supervised pretraining methods enhance robustness across various medical image datasets? Our results show that DermNet, among five datasets (Fetal plane, DermNet, COVID-DU-Ex, MURA, NCT-CRC-HE-100K), is the most challenging but exhibits greater robustness against noisy labels. Additionally, contrastive learning stands out among the eight self-supervised methods as the most effective approach to enhance robustness against noisy labels.

eess.IV↗

arXiv2023

Benchmarking Encoder-Decoder Architectures for Biplanar X-ray to 3D Shape Reconstruction

Various deep learning models have been proposed for 3D bone shape reconstruction from two orthogonal (biplanar) X-ray images. However, it is unclear how these models compare against each other since they are evaluated on different anatomy, cohort and (often privately held) datasets. Moreover, the impact of the commonly optimized image-based segmentation metrics such as dice score on the estimation of clinical parameters relevant in 2D-3D bone shape reconstruction is not well known. To move closer toward clinical translation, we propose a benchmarking framework that evaluates tasks relevant to real-world clinical scenarios, including reconstruction of fractured bones, bones with implants, robustness to population shift, and error in estimating clinical parameters. Our open-source platform provides reference implementations of 8 models (many of whose implementations were not publicly available), APIs to easily collect and preprocess 6 public datasets, and the implementation of automatic clinical parameter and landmark extraction methods. We present an extensive evaluation of 8 2D-3D models on equal footing using 6 public datasets comprising images for four different anatomies. Our results show that attention-based methods that capture global spatial relationships tend to perform better across all anatomies and datasets; performance on clinically relevant subgroups may be overestimated without disaggregated reporting; ribs are substantially more difficult to reconstruct compared to femur, hip and spine; and the dice score improvement does not always bring a corresponding improvement in the automatic estimation of clinically relevant parameters.

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