Philip Chikontwe

Philip Chikontwe, Soo Jeong Nam, Heounjeong Go et al.

Whole slide image (WSI) classification is a fundamental task for the diagnosis and treatment of diseases; but, curation of accurate labels is time-consuming and limits the application of fully-supervised methods. To address this, multiple instance learning (MIL) is a popular method that poses classification as a weakly supervised learning task with slide-level labels only. While current MIL methods apply variants of the attention mechanism to re-weight instance features with stronger models, scant attention is paid to the properties of the data distribution. In this work, we propose to re-calibrate the distribution of a WSI bag (instances) by using the statistics of the max-instance (critical) feature. We assume that in binary MIL, positive bags have larger feature magnitudes than negatives, thus we can enforce the model to maximize the discrepancy between bags with a metric feature loss that models positive bags as out-of-distribution. To achieve this, unlike existing MIL methods that use single-batch training modes, we propose balanced-batch sampling to effectively use the feature loss i.e., (+/-) bags simultaneously. Further, we employ a position encoding module (PEM) to model spatial/morphological information, and perform pooling by multi-head self-attention (PSMA) with a Transformer encoder. Experimental results on existing benchmark datasets show our approach is effective and improves over state-of-the-art MIL methods.

Philip Chikontwe, Soopil Kim, Sang Hyun Park

Few-shot classification is a challenging problem that aims to learn a model that can adapt to unseen classes given a few labeled samples. Recent approaches pre-train a feature extractor, and then fine-tune for episodic meta-learning. Other methods leverage spatial features to learn pixel-level correspondence while jointly training a classifier. However, results using such approaches show marginal improvements. In this paper, inspired by the transformer style self-attention mechanism, we propose a strategy to cross-attend and re-weight discriminative features for few-shot classification. Given a base representation of support and query images after global pooling, we introduce a single shared module that projects features and cross-attends in two aspects: (i) query to support, and (ii) support to query. The module computes attention scores between features to produce an attention pooled representation of features in the same class that is later added to the original representation followed by a projection head. This effectively re-weights features in both aspects (i & ii) to produce features that better facilitate improved metric-based meta-learning. Extensive experiments on public benchmarks show our approach outperforms state-of-the-art methods by 3%~5%.

Qian Da, Yijiang Chen, Min Ju et al.

Recent breakthroughs in artificial intelligence through foundation models and agents have accelerated the evolution of computational pathology. Demonstrated performance gains reported across academia in benchmarking datasets in predictive tasks such as diagnosis, prognosis, and treatment response have ignited substantial enthusiasm for clinical application. Despite this development momentum, real world adoption has lagged, as implementation faces economic, technical, and administrative challenges. Beyond existing discussions of technical architectures and comparative performance, this review considers how these emerging AI systems can be responsibly integrated into medical practice by connecting deployable clinical relevance with downstream analytical capabilities and their technical maturity, operational readiness, and economic and regulatory context. Drawing on perspectives from an international group, we provide a practical assessment of current capabilities and barriers to adoption in patient care settings.

Sion An, Myeongkyun Kang, Soopil Kim et al.

Electroencephalography (EEG) motor imagery (MI) classification is a fundamental, yet challenging task due to the variation of signals between individuals i.e., inter-subject variability. Previous approaches try to mitigate this using task-specific (TS) EEG signals from the target subject in training. However, recording TS EEG signals requires time and limits its applicability in various fields. In contrast, resting state (RS) EEG signals are a viable alternative due to ease of acquisition with rich subject information. In this paper, we propose a novel subject-adaptive transfer learning strategy that utilizes RS EEG signals to adapt models on unseen subject data. Specifically, we disentangle extracted features into task- and subject-dependent features and use them to calibrate RS EEG signals for obtaining task information while preserving subject characteristics. The calibrated signals are then used to adapt the model to the target subject, enabling the model to simulate processing TS EEG signals of the target subject. The proposed method achieves state-of-the-art accuracy on three public benchmarks, demonstrating the effectiveness of our method in cross-subject EEG MI classification. Our findings highlight the potential of leveraging RS EEG signals to advance practical brain-computer interface systems. The code is available at https://github.com/SionAn/MICCAI2024-ResTL.

Soopil Kim, Sion An, Philip Chikontwe et al.

Logical anomalies (LA) refer to data violating underlying logical constraints e.g., the quantity, arrangement, or composition of components within an image. Detecting accurately such anomalies requires models to reason about various component types through segmentation. However, curation of pixel-level annotations for semantic segmentation is both time-consuming and expensive. Although there are some prior few-shot or unsupervised co-part segmentation algorithms, they often fail on images with industrial object. These images have components with similar textures and shapes, and a precise differentiation proves challenging. In this study, we introduce a novel component segmentation model for LA detection that leverages a few labeled samples and unlabeled images sharing logical constraints. To ensure consistent segmentation across unlabeled images, we employ a histogram matching loss in conjunction with an entropy loss. As segmentation predictions play a crucial role, we propose to enhance both local and global sample validity detection by capturing key aspects from visual semantics via three memory banks: class histograms, component composition embeddings and patch-level representations. For effective LA detection, we propose an adaptive scaling strategy to standardize anomaly scores from different memory banks in inference. Extensive experiments on the public benchmark MVTec LOCO AD reveal our method achieves 98.1% AUROC in LA detection vs. 89.6% from competing methods.

Soopil Kim, Philip Chikontwe, Sang Hyun Park

Few shot segmentation (FSS) aims to learn pixel-level classification of a target object in a query image using only a few annotated support samples. This is challenging as it requires modeling appearance variations of target objects and the diverse visual cues between query and support images with limited information. To address this problem, we propose a semi-supervised FSS strategy that leverages additional prototypes from unlabeled images with uncertainty guided pseudo label refinement. To obtain reliable prototypes from unlabeled images, we meta-train a neural network to jointly predict segmentation and estimate the uncertainty of predictions. We employ the uncertainty estimates to exclude predictions with high degrees of uncertainty for pseudo label construction to obtain additional prototypes based on the refined pseudo labels. During inference, query segmentation is predicted using prototypes from both support and unlabeled images including low-level features of the query images. Our approach is end-to-end and can easily supplement existing approaches without the requirement of additional training to employ unlabeled samples. Extensive experiments on PASCAL-$5^i$ and COCO-$20^i$ demonstrate that our model can effectively remove unreliable predictions to refine pseudo labels and significantly improve upon state-of-the-art performances.

Myeongkyun Kang, Dongkyu Won, Miguel Luna et al.

Models trained on datasets with texture bias usually perform poorly on out-of-distribution samples since biased representations are embedded into the model. Recently, various image translation and debiasing methods have attempted to disentangle texture biased representations for downstream tasks, but accurately discarding biased features without altering other relevant information is still challenging. In this paper, we propose a novel framework that leverages image translation to generate additional training images using the content of a source image and the texture of a target image with a different bias property to explicitly mitigate texture bias when training a model on a target task. Our model ensures texture similarity between the target and generated images via a texture co-occurrence loss while preserving content details from source images with a spatial self-similarity loss. Both the generated and original training images are combined to train improved classification or segmentation models robust to inconsistent texture bias. Evaluation on five classification- and two segmentation-datasets with known texture biases demonstrates the utility of our method, and reports significant improvements over recent state-of-the-art methods in all cases.

Dongkyu Won, Euijin Jung, Sion An et al.

Recently, Self-supervised learning methods able to perform image denoising without ground truth labels have been proposed. These methods create low-quality images by adding random or Gaussian noise to images and then train a model for denoising. Ideally, it would be beneficial if one can generate high-quality CT images with only a few training samples via self-supervision. However, the performance of CT denoising is generally limited due to the complexity of CT noise. To address this problem, we propose a novel self-supervised learning-based CT denoising method. In particular, we train pre-train CT denoising and noise models that can predict CT noise from Low-dose CT (LDCT) using available LDCT and Normal-dose CT (NDCT) pairs. For a given test LDCT, we generate Pseudo-LDCT and NDCT pairs using the pre-trained denoising and noise models and then update the parameters of the denoising model using these pairs to remove noise in the test LDCT. To make realistic Pseudo LDCT, we train multiple noise models from individual images and generate the noise using the ensemble of noise models. We evaluate our method on the 2016 AAPM Low-Dose CT Grand Challenge dataset. The proposed ensemble noise model can generate realistic CT noise, and thus our method significantly improves the denoising performance existing denoising models trained by supervised- and self-supervised learning.

Myeongkyun Kang, Philip Chikontwe, Miguel Luna et al.

Following the pandemic outbreak, several works have proposed to diagnose COVID-19 with deep learning in computed tomography (CT); reporting performance on-par with experts. However, models trained/tested on the same in-distribution data may rely on the inherent data biases for successful prediction, failing to generalize on out-of-distribution samples or CT with different scanning protocols. Early attempts have partly addressed bias-mitigation and generalization through augmentation or re-sampling, but are still limited by collection costs and the difficulty of quantifying bias in medical images. In this work, we propose Mixing-AdaSIN; a bias mitigation method that uses a generative model to generate de-biased images by mixing texture information between different labeled CT scans with semantically similar features. Here, we use Adaptive Structural Instance Normalization (AdaSIN) to enhance de-biasing generation quality and guarantee structural consistency. Following, a classifier trained with the generated images learns to correctly predict the label without bias and generalizes better. To demonstrate the efficacy of our method, we construct a biased COVID-19 vs. bacterial pneumonia dataset based on CT protocols and compare with existing state-of-the-art de-biasing methods. Our experiments show that classifiers trained with de-biased generated images report improved in-distribution performance and generalization on an external COVID-19 dataset.

Soopil Kim, Sion An, Philip Chikontwe et al.

Segmentation of organs of interest in 3D medical images is necessary for accurate diagnosis and longitudinal studies. Though recent advances using deep learning have shown success for many segmentation tasks, large datasets are required for high performance and the annotation process is both time consuming and labor intensive. In this paper, we propose a 3D few shot segmentation framework for accurate organ segmentation using limited training samples of the target organ annotation. To achieve this, a U-Net like network is designed to predict segmentation by learning the relationship between 2D slices of support data and a query image, including a bidirectional gated recurrent unit (GRU) that learns consistency of encoded features between adjacent slices. Also, we introduce a transfer learning method to adapt the characteristics of the target image and organ by updating the model before testing with arbitrary support and query data sampled from the support data. We evaluate our proposed model using three 3D CT datasets with annotations of different organs. Our model yielded significantly improved performance over state-of-the-art few shot segmentation models and was comparable to a fully supervised model trained with more target training data.

Sion An, Soopil Kim, Philip Chikontwe et al.

Brain-Computer Interfaces (BCI) based on Electroencephalography (EEG) signals, in particular motor imagery (MI) data have received a lot of attention and show the potential towards the design of key technologies both in healthcare and other industries. MI data is generated when a subject imagines movement of limbs and can be used to aid rehabilitation as well as in autonomous driving scenarios. Thus, classification of MI signals is vital for EEG-based BCI systems. Recently, MI EEG classification techniques using deep learning have shown improved performance over conventional techniques. However, due to inter-subject variability, the scarcity of unseen subject data, and low signal-to-noise ratio, extracting robust features and improving accuracy is still challenging. In this context, we propose a novel two-way few shot network that is able to efficiently learn how to learn representative features of unseen subject categories and how to classify them with limited MI EEG data. The pipeline includes an embedding module that learns feature representations from a set of samples, an attention mechanism for key signal feature discovery, and a relation module for final classification based on relation scores between a support set and a query signal. In addition to the unified learning of feature similarity and a few shot classifier, our method leads to emphasize informative features in support data relevant to the query data, which generalizes better on unseen subjects. For evaluation, we used the BCI competition IV 2b dataset and achieved an 9.3% accuracy improvement in the 20-shot classification task with state-of-the-art performance. Experimental results demonstrate the effectiveness of employing attention and the overall generality of our method.