LaPA: Latent Prompt Assist Model For Medical Visual Question Answering

Medical visual question answering (Med-VQA) aims to automate the prediction of correct answers for medical images and questions, thereby assisting physicians in reducing repetitive tasks and alleviating their workload. Existing approaches primarily focus on pre-training models using additional and comprehensive datasets, followed by fine-tuning to enhance performance in downstream tasks. However, there is also significant value in exploring existing models to extract clinically relevant information. In this paper, we propose the Latent Prompt Assist model (LaPA) for medical visual question answering. Firstly, we design a latent prompt generation module to generate the latent prompt with the constraint of the target answer. Subsequently, we propose a multi-modal fusion block with latent prompt fusion module that utilizes the latent prompt to extract clinical-relevant information from uni-modal and multi-modal features. Additionally, we introduce a prior knowledge fusion module to integrate the relationship between diseases and organs with the clinical-relevant information. Finally, we combine the final integrated information with image-language cross-modal information to predict the final answers. Experimental results on three publicly available Med-VQA datasets demonstrate that LaPA outperforms the state-of-the-art model ARL, achieving improvements of 1.83%, 0.63%, and 1.80% on VQA-RAD, SLAKE, and VQA-2019, respectively. The code is publicly available at https://github.com/GaryGuTC/LaPA_model.

How Much Data are Enough? Investigating Dataset Requirements for Patch-Based Brain MRI Segmentation Tasks

Training deep neural networks reliably requires access to large-scale datasets. However, obtaining such datasets can be challenging, especially in the context of neuroimaging analysis tasks, where the cost associated with image acquisition and annotation can be prohibitive. To mitigate both the time and financial costs associated with model development, a clear understanding of the amount of data required to train a satisfactory model is crucial. This paper focuses on an early stage phase of deep learning research, prior to model development, and proposes a strategic framework for estimating the amount of annotated data required to train patch-based segmentation networks. This framework includes the establishment of performance expectations using a novel Minor Boundary Adjustment for Threshold (MinBAT) method, and standardizing patch selection through the ROI-based Expanded Patch Selection (REPS) method. Our experiments demonstrate that tasks involving regions of interest (ROIs) with different sizes or shapes may yield variably acceptable Dice Similarity Coefficient (DSC) scores. By setting an acceptable DSC as the target, the required amount of training data can be estimated and even predicted as data accumulates. This approach could assist researchers and engineers in estimating the cost associated with data collection and annotation when defining a new segmentation task based on deep neural networks, ultimately contributing to their efficient translation to real-world applications.

Cross-domain Fiber Cluster Shape Analysis for Language Performance Cognitive Score Prediction

Shape plays an important role in computer graphics, offering informative features to convey an object's morphology and functionality. Shape analysis in brain imaging can help interpret structural and functionality correlations of the human brain. In this work, we investigate the shape of the brain's 3D white matter connections and its potential predictive relationship to human cognitive function. We reconstruct brain connections as sequences of 3D points using diffusion magnetic resonance imaging (dMRI) tractography. To describe each connection, we extract 12 shape descriptors in addition to traditional dMRI connectivity and tissue microstructure features. We introduce a novel framework, Shape--fused Fiber Cluster Transformer (SFFormer), that leverages a multi-head cross-attention feature fusion module to predict subject-specific language performance based on dMRI tractography. We assess the performance of the method on a large dataset including 1065 healthy young adults. The results demonstrate that both the transformer-based SFFormer model and its inter/intra feature fusion with shape, microstructure, and connectivity are informative, and together, they improve the prediction of subject-specific language performance scores. Overall, our results indicate that the shape of the brain's connections is predictive of human language function.

Exploiting Structural Consistency of Chest Anatomy for Unsupervised Anomaly Detection in Radiography Images

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. Exploiting this structured information could potentially ease the detection of anomalies from radiography images. To this end, we propose a Simple Space-Aware Memory Matrix for In-painting and Detecting anomalies from radiography images (abbreviated as SimSID). We formulate anomaly detection as an image reconstruction task, consisting of a space-aware memory matrix and an in-painting block in the feature space. During the training, SimSID can taxonomize the ingrained anatomical structures into recurrent visual patterns, and in the inference, it can identify anomalies (unseen/modified visual patterns) from the test image. Our SimSID surpasses the state of the arts in unsupervised anomaly detection by +8.0%, +5.0%, and +9.9% AUC scores on ZhangLab, COVIDx, and CheXpert benchmark datasets, respectively. Code: https://github.com/MrGiovanni/SimSID

Seeing Unseen: Discover Novel Biomedical Concepts via Geometry-Constrained Probabilistic Modeling

Machine learning holds tremendous promise for transforming the fundamental practice of scientific discovery by virtue of its data-driven nature. With the ever-increasing stream of research data collection, it would be appealing to autonomously explore patterns and insights from observational data for discovering novel classes of phenotypes and concepts. However, in the biomedical domain, there are several challenges inherently presented in the cumulated data which hamper the progress of novel class discovery. The non-i.i.d. data distribution accompanied by the severe imbalance among different groups of classes essentially leads to ambiguous and biased semantic representations. In this work, we present a geometry-constrained probabilistic modeling treatment to resolve the identified issues. First, we propose to parameterize the approximated posterior of instance embedding as a marginal von MisesFisher distribution to account for the interference of distributional latent bias. Then, we incorporate a suite of critical geometric properties to impose proper constraints on the layout of constructed embedding space, which in turn minimizes the uncontrollable risk for unknown class learning and structuring. Furthermore, a spectral graph-theoretic method is devised to estimate the number of potential novel classes. It inherits two intriguing merits compared to existent approaches, namely high computational efficiency and flexibility for taxonomy-adaptive estimation. Extensive experiments across various biomedical scenarios substantiate the effectiveness and general applicability of our method.

Multi-source-free Domain Adaptation via Uncertainty-aware Adaptive Distillation

Source-free domain adaptation (SFDA) alleviates the domain discrepancy among data obtained from domains without accessing the data for the awareness of data privacy. However, existing conventional SFDA methods face inherent limitations in medical contexts, where medical data are typically collected from multiple institutions using various equipment. To address this problem, we propose a simple yet effective method, named Uncertainty-aware Adaptive Distillation (UAD) for the multi-source-free unsupervised domain adaptation (MSFDA) setting. UAD aims to perform well-calibrated knowledge distillation from (i) model level to deliver coordinated and reliable base model initialisation and (ii) instance level via model adaptation guided by high-quality pseudo-labels, thereby obtaining a high-performance target domain model. To verify its general applicability, we evaluate UAD on two image-based diagnosis benchmarks among two multi-centre datasets, where our method shows a significant performance gain compared with existing works. The code will be available soon.

Learning to Generalize over Subpartitions for Heterogeneity-aware Domain Adaptive Nuclei Segmentation

Annotation scarcity and cross-modality/stain data distribution shifts are two major obstacles hindering the application of deep learning models for nuclei analysis, which holds a broad spectrum of potential applications in digital pathology. Recently, unsupervised domain adaptation (UDA) methods have been proposed to mitigate the distributional gap between different imaging modalities for unsupervised nuclei segmentation in histopathology images. However, existing UDA methods are built upon the assumption that data distributions within each domain should be uniform. Based on the over-simplified supposition, they propose to align the histopathology target domain with the source domain integrally, neglecting severe intra-domain discrepancy over subpartitions incurred by mixed cancer types and sampling organs. In this paper, for the first time, we propose to explicitly consider the heterogeneity within the histopathology domain and introduce open compound domain adaptation (OCDA) to resolve the crux. In specific, a two-stage disentanglement framework is proposed to acquire domain-invariant feature representations at both image and instance levels. The holistic design addresses the limitations of existing OCDA approaches which struggle to capture instance-wise variations. Two regularization strategies are specifically devised herein to leverage the rich subpartition-specific characteristics in histopathology images and facilitate subdomain decomposition. Moreover, we propose a dual-branch nucleus shape and structure preserving module to prevent nucleus over-generation and deformation in the synthesized images. Experimental results on both cross-modality and cross-stain scenarios over a broad range of diverse datasets demonstrate the superiority of our method compared with state-of-the-art UDA and OCDA methods.

A Deep Network for Explainable Prediction of Non-Imaging Phenotypes using Anatomical Multi-View Data

Large datasets often contain multiple distinct feature sets, or views, that offer complementary information that can be exploited by multi-view learning methods to improve results. We investigate anatomical multi-view data, where each brain anatomical structure is described with multiple feature sets. In particular, we focus on sets of white matter microstructure and connectivity features from diffusion MRI, as well as sets of gray matter area and thickness features from structural MRI. We investigate machine learning methodology that applies multi-view approaches to improve the prediction of non-imaging phenotypes, including demographics (age), motor (strength), and cognition (picture vocabulary). We present an explainable multi-view network (EMV-Net) that can use different anatomical views to improve prediction performance. In this network, each individual anatomical view is processed by a view-specific feature extractor and the extracted information from each view is fused using a learnable weight. This is followed by a wavelet transform-based module to obtain complementary information across views which is then applied to calibrate the view-specific information. Additionally, the calibrator produces an attention-based calibration score to indicate anatomical structures' importance for interpretation.

Complex Organ Mask Guided Radiology Report Generation

The goal of automatic report generation is to generate a clinically accurate and coherent phrase from a single given X-ray image, which could alleviate the workload of traditional radiology reporting. However, in a real-world scenario, radiologists frequently face the challenge of producing extensive reports derived from numerous medical images, thereby medical report generation from multi-image perspective is needed. In this paper, we propose the Complex Organ Mask Guided (termed as COMG) report generation model, which incorporates masks from multiple organs (e.g., bones, lungs, heart, and mediastinum), to provide more detailed information and guide the model's attention to these crucial body regions. Specifically, we leverage prior knowledge of the disease corresponding to each organ in the fusion process to enhance the disease identification phase during the report generation process. Additionally, cosine similarity loss is introduced as target function to ensure the convergence of cross-modal consistency and facilitate model optimization.Experimental results on two public datasets show that COMG achieves a 11.4% and 9.7% improvement in terms of BLEU@4 scores over the SOTA model KiUT on IU-Xray and MIMIC, respectively. The code is publicly available at https://github.com/GaryGuTC/COMG_model.

ODM3D: Alleviating Foreground Sparsity for Semi-Supervised Monocular 3D Object Detection

Monocular 3D object detection (M3OD) is a significant yet inherently challenging task in autonomous driving due to absence of explicit depth cues in a single RGB image. In this paper, we strive to boost currently underperforming monocular 3D object detectors by leveraging an abundance of unlabelled data via semi-supervised learning. Our proposed ODM3D framework entails cross-modal knowledge distillation at various levels to inject LiDAR-domain knowledge into a monocular detector during training. By identifying foreground sparsity as the main culprit behind existing methods' suboptimal training, we exploit the precise localisation information embedded in LiDAR points to enable more foreground-attentive and efficient distillation via the proposed BEV occupancy guidance mask, leading to notably improved knowledge transfer and M3OD performance. Besides, motivated by insights into why existing cross-modal GT-sampling techniques fail on our task at hand, we further design a novel cross-modal object-wise data augmentation strategy for effective RGB-LiDAR joint learning. Our method ranks 1st in both KITTI validation and test benchmarks, significantly surpassing all existing monocular methods, supervised or semi-supervised, on both BEV and 3D detection metrics.