First Place Solution of 2023 Global Artificial Intelligence Technology Innovation Competition Track 1

In this paper, we present our champion solution to the Global Artificial Intelligence Technology Innovation Competition Track 1: Medical Imaging Diagnosis Report Generation. We select CPT-BASE as our base model for the text generation task. During the pre-training stage, we delete the mask language modeling task of CPT-BASE and instead reconstruct the vocabulary, adopting a span mask strategy and gradually increasing the number of masking ratios to perform the denoising auto-encoder pre-training task. In the fine-tuning stage, we design iterative retrieval augmentation and noise-aware similarity bucket prompt strategies. The retrieval augmentation constructs a mini-knowledge base, enriching the input information of the model, while the similarity bucket further perceives the noise information within the mini-knowledge base, guiding the model to generate higher-quality diagnostic reports based on the similarity prompts. Surprisingly, our single model has achieved a score of 2.321 on leaderboard A, and the multiple model fusion scores are 2.362 and 2.320 on the A and B leaderboards respectively, securing first place in the rankings.

Automated Clinical Data Extraction with Knowledge Conditioned LLMs

The extraction of lung lesion information from clinical and medical imaging reports is crucial for research on and clinical care of lung-related diseases. Large language models (LLMs) can be effective at interpreting unstructured text in reports, but they often hallucinate due to a lack of domain-specific knowledge, leading to reduced accuracy and posing challenges for use in clinical settings. To address this, we propose a novel framework that aligns generated internal knowledge with external knowledge through in-context learning (ICL). Our framework employs a retriever to identify relevant units of internal or external knowledge and a grader to evaluate the truthfulness and helpfulness of the retrieved internal-knowledge rules, to align and update the knowledge bases. Our knowledge-conditioned approach also improves the accuracy and reliability of LLM outputs by addressing the extraction task in two stages: (i) lung lesion finding detection and primary structured field parsing, followed by (ii) further parsing of lesion description text into additional structured fields. Experiments with expert-curated test datasets demonstrate that this ICL approach can increase the F1 score for key fields (lesion size, margin and solidity) by an average of 12.9% over existing ICL methods.

Benchmarking Vision-Language Contrastive Methods for Medical Representation Learning

We perform a comprehensive benchmarking of contrastive frameworks for learning multimodal representations in the medical domain. Through this study, we aim to answer the following research questions: (i) How transferable are general-domain representations to the medical domain? (ii) Is multimodal contrastive training sufficient, or does it benefit from unimodal training as well? (iii) What is the impact of feature granularity on the effectiveness of multimodal medical representation learning? To answer these questions, we investigate eight contrastive learning approaches under identical training setups, and train them on 2.8 million image-text pairs from four datasets, and evaluate them on 25 downstream tasks, including classification (zero-shot and linear probing), image-to-text and text-to-image retrieval, and visual question-answering. Our findings suggest a positive answer to the first question, a negative answer to the second question, and the benefit of learning fine-grained features. Finally, we make our code publicly available.

Merlin: A Vision Language Foundation Model for 3D Computed Tomography

Over 85 million computed tomography (CT) scans are performed annually in the US, of which approximately one quarter focus on the abdomen. Given the current radiologist shortage, there is a large impetus to use artificial intelligence to alleviate the burden of interpreting these complex imaging studies. Prior state-of-the-art approaches for automated medical image interpretation leverage vision language models (VLMs). However, current medical VLMs are generally limited to 2D images and short reports, and do not leverage electronic health record (EHR) data for supervision. We introduce Merlin - a 3D VLM that we train using paired CT scans (6+ million images from 15,331 CTs), EHR diagnosis codes (1.8+ million codes), and radiology reports (6+ million tokens). We evaluate Merlin on 6 task types and 752 individual tasks. The non-adapted (off-the-shelf) tasks include zero-shot findings classification (31 findings), phenotype classification (692 phenotypes), and zero-shot cross-modal retrieval (image to findings and image to impressions), while model adapted tasks include 5-year disease prediction (6 diseases), radiology report generation, and 3D semantic segmentation (20 organs). We perform internal validation on a test set of 5,137 CTs, and external validation on 7,000 clinical CTs and on two public CT datasets (VerSe, TotalSegmentator). Beyond these clinically-relevant evaluations, we assess the efficacy of various network architectures and training strategies to depict that Merlin has favorable performance to existing task-specific baselines. We derive data scaling laws to empirically assess training data needs for requisite downstream task performance. Furthermore, unlike conventional VLMs that require hundreds of GPUs for training, we perform all training on a single GPU.

SAM-LAD: Segment Anything Model Meets Zero-Shot Logic Anomaly Detection

Visual anomaly detection is vital in real-world applications, such as industrial defect detection and medical diagnosis. However, most existing methods focus on local structural anomalies and fail to detect higher-level functional anomalies under logical conditions. Although recent studies have explored logical anomaly detection, they can only address simple anomalies like missing or addition and show poor generalizability due to being heavily data-driven. To fill this gap, we propose SAM-LAD, a zero-shot, plug-and-play framework for logical anomaly detection in any scene. First, we obtain a query image's feature map using a pre-trained backbone. Simultaneously, we retrieve the reference images and their corresponding feature maps via the nearest neighbor search of the query image. Then, we introduce the Segment Anything Model (SAM) to obtain object masks of the query and reference images. Each object mask is multiplied with the entire image's feature map to obtain object feature maps. Next, an Object Matching Model (OMM) is proposed to match objects in the query and reference images. To facilitate object matching, we further propose a Dynamic Channel Graph Attention (DCGA) module, treating each object as a keypoint and converting its feature maps into feature vectors. Finally, based on the object matching relations, an Anomaly Measurement Model (AMM) is proposed to detect objects with logical anomalies. Structural anomalies in the objects can also be detected. We validate our proposed SAM-LAD using various benchmarks, including industrial datasets (MVTec Loco AD, MVTec AD), and the logical dataset (DigitAnatomy). Extensive experimental results demonstrate that SAM-LAD outperforms existing SoTA methods, particularly in detecting logical anomalies.

Knowledge-grounded Adaptation Strategy for Vision-language Models: Building Unique Case-set for Screening Mammograms for Residents Training

A visual-language model (VLM) pre-trained on natural images and text pairs poses a significant barrier when applied to medical contexts due to domain shift. Yet, adapting or fine-tuning these VLMs for medical use presents considerable hurdles, including domain misalignment, limited access to extensive datasets, and high-class imbalances. Hence, there is a pressing need for strategies to effectively adapt these VLMs to the medical domain, as such adaptations would prove immensely valuable in healthcare applications. In this study, we propose a framework designed to adeptly tailor VLMs to the medical domain, employing selective sampling and hard-negative mining techniques for enhanced performance in retrieval tasks. We validate the efficacy of our proposed approach by implementing it across two distinct VLMs: the in-domain VLM (MedCLIP) and out-of-domain VLMs (ALBEF). We assess the performance of these models both in their original off-the-shelf state and after undergoing our proposed training strategies, using two extensive datasets containing mammograms and their corresponding reports. Our evaluation spans zero-shot, few-shot, and supervised scenarios. Through our approach, we observe a notable enhancement in Recall@K performance for the image-text retrieval task.

Developing an efficient corpus using Ensemble Data cleaning approach

Despite the observable benefit of Natural Language Processing (NLP) in processing a large amount of textual medical data within a limited time for information retrieval, a handful of research efforts have been devoted to uncovering novel data-cleaning methods. Data cleaning in NLP is at the centre point for extracting validated information. Another observed limitation in the NLP domain is having limited medical corpora that provide answers to a given medical question. Realising the limitations and challenges from two perspectives, this research aims to clean a medical dataset using ensemble techniques and to develop a corpus. The corpora expect that it will answer the question based on the semantic relationship of corpus sequences. However, the data cleaning method in this research suggests that the ensemble technique provides the highest accuracy (94%) compared to the single process, which includes vectorisation, exploratory data analysis, and feeding the vectorised data. The second aim of having an adequate corpus was realised by extracting answers from the dataset. This research is significant in machine learning, specifically data cleaning and the medical sector, but it also underscores the importance of NLP in the medical field, where accurate and timely information extraction can be a matter of life and death. It establishes text data processing using NLP as a powerful tool for extracting valuable information like image data.

Content-Based Image Retrieval for Multi-Class Volumetric Radiology Images: A Benchmark Study

While content-based image retrieval (CBIR) has been extensively studied in natural image retrieval, its application to medical images presents ongoing challenges, primarily due to the 3D nature of medical images. Recent studies have shown the potential use of pre-trained vision embeddings for CBIR in the context of radiology image retrieval. However, a benchmark for the retrieval of 3D volumetric medical images is still lacking, hindering the ability to objectively evaluate and compare the efficiency of proposed CBIR approaches in medical imaging. In this study, we extend previous work and establish a benchmark for region-based and multi-organ retrieval using the TotalSegmentator dataset (TS) with detailed multi-organ annotations. We benchmark embeddings derived from pre-trained supervised models on medical images against embeddings derived from pre-trained unsupervised models on non-medical images for 29 coarse and 104 detailed anatomical structures in volume and region levels. We adopt a late interaction re-ranking method inspired by text matching for image retrieval, comparing it against the original method proposed for volume and region retrieval achieving retrieval recall of 1.0 for diverse anatomical regions with a wide size range. The findings and methodologies presented in this paper provide essential insights and benchmarks for the development and evaluation of CBIR approaches in the context of medical imaging.

A Textbook Remedy for Domain Shifts: Knowledge Priors for Medical Image Analysis

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Factual Serialization Enhancement: A Key Innovation for Chest X-ray Report Generation

The automation of writing imaging reports is a valuable tool for alleviating the workload of radiologists. Crucial steps in this process involve the cross-modal alignment between medical images and reports, as well as the retrieval of similar historical cases. However, the presence of presentation-style vocabulary (e.g., sentence structure and grammar) in reports poses challenges for cross-modal alignment. Additionally, existing methods for similar historical cases retrieval face suboptimal performance owing to the modal gap issue. In response, this paper introduces a novel method, named Factual Serialization Enhancement (FSE), for chest X-ray report generation. FSE begins with the structural entities approach to eliminate presentation-style vocabulary in reports, providing specific input for our model. Then, uni-modal features are learned through cross-modal alignment between images and factual serialization in reports. Subsequently, we present a novel approach to retrieve similar historical cases from the training set, leveraging aligned image features. These features implicitly preserve semantic similarity with their corresponding reference reports, enabling us to calculate similarity solely among aligned features. This effectively eliminates the modal gap issue for knowledge retrieval without the requirement for disease labels. Finally, the cross-modal fusion network is employed to query valuable information from these cases, enriching image features and aiding the text decoder in generating high-quality reports. Experiments on MIMIC-CXR and IU X-ray datasets from both specific and general scenarios demonstrate the superiority of FSE over state-of-the-art approaches in both natural language generation and clinical efficacy metrics.