arXiv subjects

Ryoma Bise

Publications and source records attributed to Ryoma Bise.

At least 37 records · Page 2Linked to original sources

arXiv2025

Adaptive Pseudo Label Selection for Individual Unlabeled Data by Positive and Unlabeled Learning

This paper proposes a novel pseudo-labeling method for medical image segmentation that can perform learning on ``individual images'' to select effective pseudo-labels. We introduce Positive and Unlabeled Learning (PU learning), which uses only positive and unlabeled data for binary classification problems, to obtain the appropriate metric for discriminating foreground and background regions on each unlabeled image. Our PU learning makes us easy to select pseudo-labels for various background regions. The experimental results show the effectiveness of our method.

cs.CV↗

arXiv2025

Weakly-Supervised Domain Adaptation with Proportion-Constrained Pseudo-Labeling

Domain shift is a significant challenge in machine learning, particularly in medical applications where data distributions differ across institutions due to variations in data collection practices, equipment, and procedures. This can degrade performance when models trained on source domain data are applied to the target domain. Domain adaptation methods have been widely studied to address this issue, but most struggle when class proportions between the source and target domains differ. In this paper, we propose a weakly-supervised domain adaptation method that leverages class proportion information from the target domain, which is often accessible in medical datasets through prior knowledge or statistical reports. Our method assigns pseudo-labels to the unlabeled target data based on class proportion (called proportion-constrained pseudo-labeling), improving performance without the need for additional annotations. Experiments on two endoscopic datasets demonstrate that our method outperforms semi-supervised domain adaptation techniques, even when 5% of the target domain is labeled. Additionally, the experimental results with noisy proportion labels highlight the robustness of our method, further demonstrating its effectiveness in real-world application scenarios.

cs.LG↗

arXiv2025

Towards Spatial Transcriptomics-guided Pathological Image Recognition with Batch-Agnostic Encoder

Spatial transcriptomics (ST) is a novel technique that simultaneously captures pathological images and gene expression profiling with spatial coordinates. Since ST is closely related to pathological features such as disease subtypes, it may be valuable to augment image representation with pathological information. However, there are no attempts to leverage ST for image recognition ({\it i.e,} patch-level classification of subtypes of pathological image.). One of the big challenges is significant batch effects in spatial transcriptomics that make it difficult to extract pathological features of images from ST. In this paper, we propose a batch-agnostic contrastive learning framework that can extract consistent signals from gene expression of ST in multiple patients. To extract consistent signals from ST, we utilize the batch-agnostic gene encoder that is trained in a variational inference manner. Experiments demonstrated the effectiveness of our framework on a publicly available dataset. Code is publicly available at https://github.com/naivete5656/TPIRBAE

cs.CV↗

arXiv2025

Instance-wise Supervision-level Optimization in Active Learning

Active learning (AL) is a label-efficient machine learning paradigm that focuses on selectively annotating high-value instances to maximize learning efficiency. Its effectiveness can be further enhanced by incorporating weak supervision, which uses rough yet cost-effective annotations instead of exact (i.e., full) but expensive annotations. We introduce a novel AL framework, Instance-wise Supervision-Level Optimization (ISO), which not only selects the instances to annotate but also determines their optimal annotation level within a fixed annotation budget. Its optimization criterion leverages the value-to-cost ratio (VCR) of each instance while ensuring diversity among the selected instances. In classification experiments, ISO consistently outperforms traditional AL methods and surpasses a state-of-the-art AL approach that combines full and weak supervision, achieving higher accuracy at a lower overall cost. This code is available at https://github.com/matsuo-shinnosuke/ISOAL.

cs.CV↗

arXiv2025

Guidance-base Diffusion Models for Improving Photoacoustic Image Quality

Photoacoustic(PA) imaging is a non-destructive and non-invasive technology for visualizing minute blood vessel structures in the body using ultrasonic sensors. In PA imaging, the image quality of a single-shot image is poor, and it is necessary to improve the image quality by averaging many single-shot images. Therefore, imaging the entire subject requires high imaging costs. In our study, we propose a method to improve the quality of PA images using diffusion models. In our method, we improve the reverse diffusion process using sensor information of PA imaging and introduce a guidance method using imaging condition information to generate high-quality images.

cs.CV↗

arXiv2024

Ordinal Multiple-instance Learning for Ulcerative Colitis Severity Estimation with Selective Aggregated Transformer

Patient-level diagnosis of severity in ulcerative colitis (UC) is common in real clinical settings, where the most severe score in a patient is recorded. However, previous UC classification methods (i.e., image-level estimation) mainly assumed the input was a single image. Thus, these methods can not utilize severity labels recorded in real clinical settings. In this paper, we propose a patient-level severity estimation method by a transformer with selective aggregator tokens, where a severity label is estimated from multiple images taken from a patient, similar to a clinical setting. Our method can effectively aggregate features of severe parts from a set of images captured in each patient, and it facilitates improving the discriminative ability between adjacent severity classes. Experiments demonstrate the effectiveness of the proposed method on two datasets compared with the state-of-the-art MIL methods. Moreover, we evaluated our method in real clinical settings and confirmed that our method outperformed the previous image-level methods. The code is publicly available at https://github.com/Shiku-Kaito/Ordinal-Multiple-instance-Learning-for-Ulcerative-Colitis-Severity-Estimation.

cs.CV↗

arXiv2024

Deep Bayesian Active Learning-to-Rank with Relative Annotation for Estimation of Ulcerative Colitis Severity

Automatic image-based severity estimation is an important task in computer-aided diagnosis. Severity estimation by deep learning requires a large amount of training data to achieve a high performance. In general, severity estimation uses training data annotated with discrete (i.e., quantized) severity labels. Annotating discrete labels is often difficult in images with ambiguous severity, and the annotation cost is high. In contrast, relative annotation, in which the severity between a pair of images is compared, can avoid quantizing severity and thus makes it easier. We can estimate relative disease severity using a learning-to-rank framework with relative annotations, but relative annotation has the problem of the enormous number of pairs that can be annotated. Therefore, the selection of appropriate pairs is essential for relative annotation. In this paper, we propose a deep Bayesian active learning-to-rank that automatically selects appropriate pairs for relative annotation. Our method preferentially annotates unlabeled pairs with high learning efficiency from the model uncertainty of the samples. We prove the theoretical basis for adapting Bayesian neural networks to pairwise learning-to-rank and demonstrate the efficiency of our method through experiments on endoscopic images of ulcerative colitis on both private and public datasets. We also show that our method achieves a high performance under conditions of significant class imbalance because it automatically selects samples from the minority classes.

cs.CV↗

arXiv2024

Theoretical Proportion Label Perturbation for Learning from Label Proportions in Large Bags

Learning from label proportions (LLP) is a kind of weakly supervised learning that trains an instance-level classifier from label proportions of bags, which consist of sets of instances without using instance labels. A challenge in LLP arises when the number of instances in a bag (bag size) is numerous, making the traditional LLP methods difficult due to GPU memory limitations. This study aims to develop an LLP method capable of learning from bags with large sizes. In our method, smaller bags (mini-bags) are generated by sampling instances from large-sized bags (original bags), and these mini-bags are used in place of the original bags. However, the proportion of a mini-bag is unknown and differs from that of the original bag, leading to overfitting. To address this issue, we propose a perturbation method for the proportion labels of sampled mini-bags to mitigate overfitting to noisy label proportions. This perturbation is added based on the multivariate hypergeometric distribution, which is statistically modeled. Additionally, loss weighting is implemented to reduce the negative impact of proportions sampled from the tail of the distribution. Experimental results demonstrate that the proportion label perturbation and loss weighting achieve classification accuracy comparable to that obtained without sampling. Our codes are available at https://github.com/stainlessnight/LLP-LargeBags.

cs.LG↗

arXiv2024

Learning from Partial Label Proportions for Whole Slide Image Segmentation

In this paper, we address the segmentation of tumor subtypes in whole slide images (WSI) by utilizing incomplete label proportions. Specifically, we utilize `partial' label proportions, which give the proportions among tumor subtypes but do not give the proportion between tumor and non-tumor. Partial label proportions are recorded as the standard diagnostic information by pathologists, and we, therefore, want to use them for realizing the segmentation model that can classify each WSI patch into one of the tumor subtypes or non-tumor. We call this problem ``learning from partial label proportions (LPLP)'' and formulate the problem as a weakly supervised learning problem. Then, we propose an efficient algorithm for this challenging problem by decomposing it into two weakly supervised learning subproblems: multiple instance learning (MIL) and learning from label proportions (LLP). These subproblems are optimized efficiently in the end-to-end manner. The effectiveness of our algorithm is demonstrated through experiments conducted on two WSI datasets.

cs.CV↗

arXiv2024

Proportion Estimation by Masked Learning from Label Proportion

The PD-L1 rate, the number of PD-L1 positive tumor cells over the total number of all tumor cells, is an important metric for immunotherapy. This metric is recorded as diagnostic information with pathological images. In this paper, we propose a proportion estimation method with a small amount of cell-level annotation and proportion annotation, which can be easily collected. Since the PD-L1 rate is calculated from only `tumor cells' and not using `non-tumor cells', we first detect tumor cells with a detection model. Then, we estimate the PD-L1 proportion by introducing a masking technique to `learning from label proportion.' In addition, we propose a weighted focal proportion loss to address data imbalance problems. Experiments using clinical data demonstrate the effectiveness of our method. Our method achieved the best performance in comparisons.

cs.CV↗

arXiv2024

Counting Network for Learning from Majority Label

The paper proposes a novel problem in multi-class Multiple-Instance Learning (MIL) called Learning from the Majority Label (LML). In LML, the majority class of instances in a bag is assigned as the bag's label. LML aims to classify instances using bag-level majority classes. This problem is valuable in various applications. Existing MIL methods are unsuitable for LML due to aggregating confidences, which may lead to inconsistency between the bag-level label and the label obtained by counting the number of instances for each class. This may lead to incorrect instance-level classification. We propose a counting network trained to produce the bag-level majority labels estimated by counting the number of instances for each class. This led to the consistency of the majority class between the network outputs and one obtained by counting the number of instances. Experimental results show that our counting network outperforms conventional MIL methods on four datasets The code is publicly available at https://github.com/Shiku-Kaito/Counting-Network-for-Learning-from-Majority-Label.

cs.CV↗

arXiv2024

Cell Tracking in C. elegans with Cell Position Heatmap-Based Alignment and Pairwise Detection

3D cell tracking in a living organism has a crucial role in live cell image analysis. Cell tracking in C. elegans has two difficulties. First, cell migration in a consecutive frame is large since they move their head during scanning. Second, cell detection is often inconsistent in consecutive frames due to touching cells and low-contrast images, and these inconsistent detections affect the tracking performance worse. In this paper, we propose a cell tracking method to address these issues, which has two main contributions. First, we introduce cell position heatmap-based non-rigid alignment with test-time fine-tuning, which can warp the detected points to near the positions at the next frame. Second, we propose a pairwise detection method, which uses the information of detection results at the previous frame for detecting cells at the current frame. The experimental results demonstrate the effectiveness of each module, and the proposed method achieved the best performance in comparison.

cs.CV↗

arXiv2023

MixBag: Bag-Level Data Augmentation for Learning from Label Proportions

Learning from label proportions (LLP) is a promising weakly supervised learning problem. In LLP, a set of instances (bag) has label proportions, but no instance-level labels are given. LLP aims to train an instance-level classifier by using the label proportions of the bag. In this paper, we propose a bag-level data augmentation method for LLP called MixBag, based on the key observation from our preliminary experiments; that the instance-level classification accuracy improves as the number of labeled bags increases even though the total number of instances is fixed. We also propose a confidence interval loss designed based on statistical theory to use the augmented bags effectively. To the best of our knowledge, this is the first attempt to propose bag-level data augmentation for LLP. The advantage of MixBag is that it can be applied to instance-level data augmentation techniques and any LLP method that uses the proportion loss. Experimental results demonstrate this advantage and the effectiveness of our method.

cs.CV↗

arXiv2023

Mitosis Detection from Partial Annotation by Dataset Generation via Frame-Order Flipping

Detection of mitosis events plays an important role in biomedical research. Deep-learning-based mitosis detection methods have achieved outstanding performance with a certain amount of labeled data. However, these methods require annotations for each imaging condition. Collecting labeled data involves time-consuming human labor. In this paper, we propose a mitosis detection method that can be trained with partially annotated sequences. The base idea is to generate a fully labeled dataset from the partial labels and train a mitosis detection model with the generated dataset. First, we generate an image pair not containing mitosis events by frame-order flipping. Then, we paste mitosis events to the image pair by alpha-blending pasting and generate a fully labeled dataset. We demonstrate the performance of our method on four datasets, and we confirm that our method outperforms other comparisons which use partially labeled sequences.

cs.CV↗

arXiv2023

Mixing Data Augmentation with Preserving Foreground Regions in Medical Image Segmentation

The development of medical image segmentation using deep learning can significantly support doctors' diagnoses. Deep learning needs large amounts of data for training, which also requires data augmentation to extend diversity for preventing overfitting. However, the existing methods for data augmentation of medical image segmentation are mainly based on models which need to update parameters and cost extra computing resources. We proposed data augmentation methods designed to train a high accuracy deep learning network for medical image segmentation. The proposed data augmentation approaches are called KeepMask and KeepMix, which can create medical images by better identifying the boundary of the organ with no more parameters. Our methods achieved better performance and obtained more precise boundaries for medical image segmentation on datasets. The dice coefficient of our methods achieved 94.15% (3.04% higher than baseline) on CHAOS and 74.70% (5.25% higher than baseline) on MSD spleen with Unet.

eess.IV↗

arXiv2023

Cluster Entropy: Active Domain Adaptation in Pathological Image Segmentation

The domain shift in pathological segmentation is an important problem, where a network trained by a source domain (collected at a specific hospital) does not work well in the target domain (from different hospitals) due to the different image features. Due to the problems of class imbalance and different class prior of pathology, typical unsupervised domain adaptation methods do not work well by aligning the distribution of source domain and target domain. In this paper, we propose a cluster entropy for selecting an effective whole slide image (WSI) that is used for semi-supervised domain adaptation. This approach can measure how the image features of the WSI cover the entire distribution of the target domain by calculating the entropy of each cluster and can significantly improve the performance of domain adaptation. Our approach achieved competitive results against the prior arts on datasets collected from two hospitals.

cs.CV↗

arXiv2023

Effective Pseudo-Labeling based on Heatmap for Unsupervised Domain Adaptation in Cell Detection

Cell detection is an important task in biomedical research. Recently, deep learning methods have made it possible to improve the performance of cell detection. However, a detection network trained with training data under a specific condition (source domain) may not work well on data under other conditions (target domains), which is called the domain shift problem. In particular, cells are cultured under different conditions depending on the purpose of the research. Characteristics, e.g., the shapes and density of the cells, change depending on the conditions, and such changes may cause domain shift problems. Here, we propose an unsupervised domain adaptation method for cell detection using a pseudo-cell-position heatmap, where the cell centroid is at the peak of a Gaussian distribution in the map and selective pseudo-labeling. In the prediction result for the target domain, even if the peak location is correct, the signal distribution around the peak often has a non-Gaussian shape. The pseudo-cell-position heatmap is thus re-generated using the peak positions in the predicted heatmap to have a clear Gaussian shape. Our method selects confident pseudo-cell-position heatmaps based on uncertainty and curriculum learning. We conducted numerous experiments showing that, compared with the existing methods, our method improved detection performance under different conditions.

cs.CV↗

arXiv2023

Cluster-Guided Semi-Supervised Domain Adaptation for Imbalanced Medical Image Classification

Semi-supervised domain adaptation is a technique to build a classifier for a target domain by modifying a classifier in another (source) domain using many unlabeled samples and a small number of labeled samples from the target domain. In this paper, we develop a semi-supervised domain adaptation method, which has robustness to class-imbalanced situations, which are common in medical image classification tasks. For robustness, we propose a weakly-supervised clustering pipeline to obtain high-purity clusters and utilize the clusters in representation learning for domain adaptation. The proposed method showed state-of-the-art performance in the experiment using severely class-imbalanced pathological image patches.

cs.CV↗