Kazuya Nishimura

Kaito Shiku, Ahtisham Fazeel Abbasi, Ryoma Bise et al.

Histology-based single-cell spatial transcriptomics (ST) estimation aims to predict gene expression for individual cells from histopathological images and cell locations, reducing the need for costly single-cell ST measurements. Unlike existing histology-to-ST methods that mainly predict spot-level profiles for local regions containing multiple cells, this task requires modeling cell-to-cell expression variability, which is strongly structured by cell type. We propose Genomics-Guided Cell-Type-Specific Mixture-of-Experts (GC-MoE), which estimates cell-type probabilities with a routing network and softly combines cell-type-specific experts for gene expression prediction. To further encode cell-type-dependent gene programs, we introduce the Cell-Type-Specific Co-Expression-Aware Predictor (CAP), together with a lightweight Cell-to-Cell Interaction Attention (C2CA) module for neighboring-cell context. Experiments and ablations on public single-cell ST datasets show consistent improvements over existing single-cell and adapted spot-level baselines.

Hyeonwoo Cho, Kazuya Nishimura, Kazuhide Watanabe et al.

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.

Yukinori Yamamoto, Kazuya Nishimura, Tsukasa Fukusato et al.

Deep learning-based 3D medical image segmentation methods relies on large-scale labeled datasets, yet acquiring such data is difficult due to privacy constraints and the high cost of expert annotation. Formula-Driven Supervised Learning (FDSL) offers an appealing alternative by generating training data and labels directly from mathematical formulas. However, existing voxel-based approaches are limited in geometric expressiveness and cannot synthesize realistic textures. We introduce Formula-Driven supervised learning with Implicit Functions (FDIF), a framework that enables scalable pre-training without using any real data and medical expert annotations. FDIF introduces an implicit-function representation based on signed distance functions (SDFs), enabling compact modeling of complex geometries while exploiting the surface representation of SDFs to support controllable synthesis of both geometric and intensity textures. Across three medical image segmentation benchmarks (AMOS, ACDC, and KiTS) and three architectures (SwinUNETR, nnUNet ResEnc-L, and nnUNet Primus-M), FDIF consistently improves over a formula-driven method, and achieves performance comparable to self-supervised approaches pre-trained on large-scale real datasets. We further show that FDIF pre-training also benefits 3D classification tasks, highlighting implicit-function-based formula supervision as a promising paradigm for data-free representation learning. Code is available at https://github.com/yamanoko/FDIF.

Kazuya Nishimura, Haruka Hirose, Ryoma Bise et al.

Gene expression estimation from pathology images has the potential to reduce the RNA sequencing cost. Point-wise loss functions have been widely used to minimize the discrepancy between predicted and absolute gene expression values. However, due to the complexity of the sequencing techniques and intrinsic variability across cells, the observed gene expression contains stochastic noise and batch effects, and estimating the absolute expression values accurately remains a significant challenge. To mitigate this, we propose a novel objective of learning relative expression patterns rather than absolute levels. We assume that the relative expression levels of genes exhibit consistent patterns across independent experiments, even when absolute expression values are affected by batch effects and stochastic noise in tissue samples. Based on the assumption, we model the relation and propose a novel loss function called STRank that is robust to noise and batch effects. Experiments using synthetic datasets and real datasets demonstrate the effectiveness of the proposed method. The code is available at https://github.com/naivete5656/STRank.

Kazuya Nishimura, Ryoma Bise, Shinnosuke Matsuo et al.

Estimating slide- and patch-level gene expression profiles from pathology images enables rapid and low-cost molecular analysis with broad clinical impact. Despite strong results, existing approaches treat gene expression as a mere slide- or spot-level signal and do not incorporate the fact that the measured expression arises from the aggregation of underlying cell-level expression. To explicitly introduce this missing cell-resolved guidance, we propose a Cell-type Prototype-informed Neural Network (CPNN) that leverages publicly available single-cell RNA-sequencing datasets. Since single-cell measurements are noisy and not paired with histology images, we first estimate cell-type prototypes-mean expression profiles that reflect stable gene-gene co-variation patterns.CPNN then learns cell-type compositional weights directly from images and models the relationship between prototypes and observed bulk or spatial expression, providing a biologically grounded and structurally regularized prediction framework. We evaluate CPNN on three slide-level datasets and three patch-level spatial transcriptomics datasets. Across all settings, CPNN achieves the highest performance in terms of Spearman correlation. Moreover, by visualizing the inferred compositional weights, our framework provides interpretable insights into which cell types drive the predicted expression. Code is publicly available at https://github.com/naivete5656/CPNN.

Kazuya Nishimura, Ami Katanaya, Shinichiro Chuma et al.

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.

Kaito Shiku, Kazuya Nishimura, Daiki Suehiro et al.

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.

Kazuya Nishimura, Ryoma Bise, Yasuhiro Kojima

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

Kazuya Nishimura, Hyeonwoo Cho, Ryoma Bise

Cell detection is the task of detecting the approximate positions of cell centroids from microscopy images. Recently, convolutional neural network-based approaches have achieved promising performance. However, these methods require a certain amount of annotation for each imaging condition. This annotation is a time-consuming and labor-intensive task. To overcome this problem, we propose a semi-supervised cell-detection method that effectively uses a time-lapse sequence with one labeled image and the other images unlabeled. First, we train a cell-detection network with a one-labeled image and estimate the unlabeled images with the trained network. We then select high-confidence positions from the estimations by tracking the detected cells from the labeled frame to those far from it. Next, we generate pseudo-labels from the tracking results and train the network by using pseudo-labels. We evaluated our method for seven conditions of public datasets, and we achieved the best results relative to other semi-supervised methods. Our code is available at https://github.com/naivete5656/SCDTC

Kazuya Nishimura, Junya Hayashida, Chenyang Wang et al.

We propose a weakly-supervised cell tracking method that can train a convolutional neural network (CNN) by using only the annotation of "cell detection" (i.e., the coordinates of cell positions) without association information, in which cell positions can be easily obtained by nuclear staining. First, we train co-detection CNN that detects cells in successive frames by using weak-labels. Our key assumption is that co-detection CNN implicitly learns association in addition to detection. To obtain the association, we propose a backward-and-forward propagation method that analyzes the correspondence of cell positions in the outputs of co-detection CNN. Experiments demonstrated that the proposed method can associate cells by analyzing co-detection CNN. Even though the method uses only weak supervision, the performance of our method was almost the same as the state-of-the-art supervised method. Code is publicly available in https://github.com/naivete5656/WSCTBFP

Kazuya Nishimura, Dai Fei Elmer Ker, Ryoma Bise

Cell shape analysis is important in biomedical research. Deep learning methods may perform to segment individual cells if they use sufficient training data that the boundary of each cell is annotated. However, it is very time-consuming for preparing such detailed annotation for many cell culture conditions. In this paper, we propose a weakly supervised method that can segment individual cell regions who touch each other with unclear boundaries in dense conditions without the training data for cell regions. We demonstrated the efficacy of our method using several data-set including multiple cell types captured by several types of microscopy. Our method achieved the highest accuracy compared with several conventional methods. In addition, we demonstrated that our method can perform without any annotation by using fluorescence images that cell nuclear were stained as training data. Code is publicly available in "https://github.com/naivete5656/WSISPDR".

Kazuya Nishimura, Ryoma Bise, Haruka Hirose et al.

Deep learning-based nuclei segmentation and classification in pathology images typically rely on large-scale pixel-level manual annotations, which are costly and difficult to obtain across diverse tissues and staining conditions. To address this limitation, we propose a framework that leverages spatial transcriptomics (ST) data as supervision for nuclei segmentation and classification. By incorporating cell-level ST data, we obtain gene expression profiles and corresponding nuclear masks from histopathological images. Gene expression profiles are converted into cell-type labels and used as training data for image-based classification. Because existing gene expression-based cell-type classification methods are not designed for image recognition, we introduce an image-oriented classification approach that bridges gene expression-based cell typing and image-based cell classification. To evaluate generalization, we conduct segmentation experiments on previously unseen organs and compare our method with conventional supervised models. Despite being trained on fewer organ types, our framework achieves higher segmentation accuracy, demonstrating strong transferability. Classification experiments further show consistent improvements over existing approaches.

Takumi Okuo, Kazuya Nishimura, Hiroaki Ito et al.

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.

Kaito Shiku, Kazuya Nishimura, Shinnosuke Matsuo et al.

Spatial transcriptomics (ST) is a novel technology that enables the observation of gene expression at the resolution of individual spots within pathological tissues. ST quantifies the expression of tens of thousands of genes in a tissue section; however, heavy observational noise is often introduced during measurement. In prior studies, to ensure meaningful assessment, both training and evaluation have been restricted to only a small subset of highly variable genes, and genes outside this subset have also been excluded from the training process. However, since there are likely co-expression relationships between genes, low-expression genes may still contribute to the estimation of the evaluation target. In this paper, we propose $Auxiliary \ Gene \ Learning$ (AGL) that utilizes the benefit of the ignored genes by reformulating their expression estimation as auxiliary tasks and training them jointly with the primary tasks. To effectively leverage auxiliary genes, we must select a subset of auxiliary genes that positively influence the prediction of the target genes. However, this is a challenging optimization problem due to the vast number of possible combinations. To overcome this challenge, we propose Prior-Knowledge-Based Differentiable Top-$k$ Gene Selection via Bi-level Optimization (DkGSB), a method that ranks genes by leveraging prior knowledge and relaxes the combinatorial selection problem into a differentiable top-$k$ selection problem. The experiments confirm the effectiveness of incorporating auxiliary genes and show that the proposed method outperforms conventional auxiliary task learning approaches.

Kazuma Fujii, Daiki Suehiro, Kazuya Nishimura et al.

Cell detection is an essential task in cell image analysis. Recent deep learning-based detection methods have achieved very promising results. In general, these methods require exhaustively annotating the cells in an entire image. If some of the cells are not annotated (imperfect annotation), the detection performance significantly degrades due to noisy labels. This often occurs in real collaborations with biologists and even in public data-sets. Our proposed method takes a pseudo labeling approach for cell detection from imperfect annotated data. A detection convolutional neural network (CNN) trained using such missing labeled data often produces over-detection. We treat partially labeled cells as positive samples and the detected positions except for the labeled cell as unlabeled samples. Then we select reliable pseudo labels from unlabeled data using recent machine learning techniques; positive-and-unlabeled (PU) learning and P-classification. Experiments using microscopy images for five different conditions demonstrate the effectiveness of the proposed method.

Hyeonwoo Cho, Kazuya Nishimura, Kazuhide Watanabe et al.

The domain shift problem is an important issue in automatic cell detection. A detection network trained with training data under a specific condition (source domain) may not work well in data under other conditions (target domain). We propose an unsupervised domain adaptation method for cell detection using the pseudo-cell-position heatmap, where a cell centroid becomes a peak with a Gaussian distribution in the map. In the prediction result for the target domain, even if a peak location is correct, the signal distribution around the peak often has anon-Gaussian shape. The pseudo-cell-position heatmap is re-generated using the peak positions in the predicted heatmap to have a clear Gaussian shape. Our method selects confident pseudo-cell-position heatmaps using a Bayesian network and adds them to the training data in the next iteration. The method can incrementally extend the domain from the source domain to the target domain in a semi-supervised manner. In the experiments using 8 combinations of domains, the proposed method outperformed the existing domain adaptation methods.

Kazuya Nishimura, Ryoma Bise

Automated mitotic detection in time-lapse phasecontrast microscopy provides us much information for cell behavior analysis, and thus several mitosis detection methods have been proposed. However, these methods still have two problems; 1) they cannot detect multiple mitosis events when there are closely placed. 2) they do not consider the annotation gaps, which may occur since the appearances of mitosis cells are very similar before and after the annotated frame. In this paper, we propose a novel mitosis detection method that can detect multiple mitosis events in a candidate sequence and mitigate the human annotation gap via estimating a spatiotemporal likelihood map by 3DCNN. In this training, the loss gradually decreases with the gap size between ground truth and estimation. This mitigates the annotation gaps. Our method outperformed the compared methods in terms of F1- score using a challenging dataset that contains the data under four different conditions.

Junya Hayashida, Kazuya Nishimura, Ryoma Bise

Conventional cell tracking methods detect multiple cells in each frame (detection) and then associate the detection results in successive time-frames (association). Most cell tracking methods perform the association task independently from the detection task. However, there is no guarantee of preserving coherence between these tasks, and lack of coherence may adversely affect tracking performance. In this paper, we propose the Motion and Position Map (MPM) that jointly represents both detection and association for not only migration but also cell division. It guarantees coherence such that if a cell is detected, the corresponding motion flow can always be obtained. It is a simple but powerful method for multi-object tracking in dense environments. We compared the proposed method with current tracking methods under various conditions in real biological images and found that it outperformed the state-of-the-art (+5.2\% improvement compared to the second-best).