Safal Thapaliya

Safal Thapaliya, Jiatan Huang, Chuxu Zhang

Node classification on graphs often requires labeled nodes, yet obtaining labels at graph scale is expensive. When node attributes contain semantic content, such as paper abstracts, web pages, or product descriptions, large language models (LLMs) can provide low-cost supervision by annotating a small subset of nodes. However, these LLM-generated labels are noisy, and existing label-free graph learning methods usually treat this noise as either global or class-conditional. We find that LLM annotation errors are not only class-dependent but also region-dependent: within the same class, reliability can vary sharply across feature-space clusters. In light of this, we propose Cluster-Aware Noise Estimation (CANE), a label-free learning framework that estimates cluster-conditional LLM reliability without ground truth labels, and uses this estimate to decide which pseudo-labels to trust, and which labels to correct. Across various graph benchmarks and GNN backbones, CANE improves over the strongest label-free baselines, with the largest gains on datasets exhibiting stronger cluster-conditional noise.

Suprim Nakarmi, Sanam Pudasaini, Safal Thapaliya et al.

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.

Kanchan Poudel, Manish Dhakal, Prasiddha Bhandari et al.

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.

Rabin Adhikari, Manish Dhakal, Safal Thapaliya et al.

Accurate segmentation is essential for echocardiography-based assessment of cardiovascular diseases (CVDs). However, the variability among sonographers and the inherent challenges of ultrasound images hinder precise segmentation. By leveraging the joint representation of image and text modalities, Vision-Language Segmentation Models (VLSMs) can incorporate rich contextual information, potentially aiding in accurate and explainable segmentation. However, the lack of readily available data in echocardiography hampers the training of VLSMs. In this study, we explore using synthetic datasets from Semantic Diffusion Models (SDMs) to enhance VLSMs for echocardiography segmentation. We evaluate results for two popular VLSMs (CLIPSeg and CRIS) using seven different kinds of language prompts derived from several attributes, automatically extracted from echocardiography images, segmentation masks, and their metadata. Our results show improved metrics and faster convergence when pretraining VLSMs on SDM-generated synthetic images before finetuning on real images. The code, configs, and prompts are available at https://github.com/naamiinepal/synthetic-boost.

Rabin Adhikari, Safal Thapaliya, Nirajan Basnet et al.

Billions of people across the globe have been using social media platforms in their local languages to voice their opinions about the various topics related to the COVID-19 pandemic. Several organizations, including the World Health Organization, have developed automated social media analysis tools that classify COVID-19-related tweets into various topics. However, these tools that help combat the pandemic are limited to very few languages, making several countries unable to take their benefit. While multi-lingual or low-resource language-specific tools are being developed, they still need to expand their coverage, such as for the Nepali language. In this paper, we identify the eight most common COVID-19 discussion topics among the Twitter community using the Nepali language, set up an online platform to automatically gather Nepali tweets containing the COVID-19-related keywords, classify the tweets into the eight topics, and visualize the results across the period in a web-based dashboard. We compare the performance of two state-of-the-art multi-lingual language models for Nepali tweet classification, one generic (mBERT) and the other Nepali language family-specific model (MuRIL). Our results show that the models' relative performance depends on the data size, with MuRIL doing better for a larger dataset. The annotated data, models, and the web-based dashboard are open-sourced at https://github.com/naamiinepal/covid-tweet-classification.

Safal Thapaliya, Zehong Wang, Jiazheng Li et al.

Graph-structured data exhibit substantial heterogeneity in where their predictive signals originate: in some domains, node-level semantics dominate, while in others, structural patterns play a central role. This structure-semantics heterogeneity implies that no graph learning model with a fixed inductive bias can generalize optimally across diverse graph domains. However, most existing methods address this challenge from the model side by incrementally injecting new inductive biases, which remains fundamentally limited given the open-ended diversity of real-world graphs. In this work, we take a data-centric perspective and treat node semantics as a task-adaptive variable. We propose a Data-Adaptive Semantic Refinement framework DAS for graph representation learning, which couples a fixed graph neural network (GNN) and a large language model (LLM) in a closed feedback loop. The GNN provides implicit supervisory signals to guide the semantic refinement of LLM, and the refined semantics are fed back to update the same graph learner. We evaluate our approach on both text-rich and text-free graphs. Results show consistent improvements on structure-dominated graphs while remaining competitive on semantics-rich graphs, demonstrating the effectiveness of data-centric semantic adaptation under structure-semantics heterogeneity.

Manish Dhakal, Rabin Adhikari, Safal Thapaliya et al.

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.