Knowledge-enhanced Visual-Language Pretraining for Computational Pathology

In this paper, we consider the problem of visual representation learning for computational pathology, by exploiting large-scale image-text pairs gathered from public resources, along with the domain specific knowledge in pathology. Specifically, we make the following contributions: (i) We curate a pathology knowledge tree that consists of 50,470 informative attributes for 4,718 diseases requiring pathology diagnosis from 32 human tissues. To our knowledge, this is the first comprehensive structured pathology knowledge base; (ii) We develop a knowledge-enhanced visual-language pretraining approach, where we first project pathology-specific knowledge into latent embedding space via language model, and use it to guide the visual representation learning; (iii) We conduct thorough experiments to validate the effectiveness of our proposed components, demonstrating significant performance improvement on various downstream tasks, including cross-modal retrieval, zero-shot classification on pathology patches, and zero-shot tumor subtyping on whole slide images (WSIs). All codes, models and the pathology knowledge tree will be released to the research community

Anomaly Detection in Electrocardiograms: Advancing Clinical Diagnosis Through Self-Supervised Learning

The electrocardiogram (ECG) is an essential tool for diagnosing heart disease, with computer-aided systems improving diagnostic accuracy and reducing healthcare costs. Despite advancements, existing systems often miss rare cardiac anomalies that could be precursors to serious, life-threatening issues or alterations in the cardiac macro/microstructure. We address this gap by focusing on self-supervised anomaly detection (AD), training exclusively on normal ECGs to recognize deviations indicating anomalies. We introduce a novel self-supervised learning framework for ECG AD, utilizing a vast dataset of normal ECGs to autonomously detect and localize cardiac anomalies. It proposes a novel masking and restoration technique alongside a multi-scale cross-attention module, enhancing the model's ability to integrate global and local signal features. The framework emphasizes accurate localization of anomalies within ECG signals, ensuring the method's clinical relevance and reliability. To reduce the impact of individual variability, the approach further incorporates crucial patient-specific information from ECG reports, such as age and gender, thus enabling accurate identification of a broad spectrum of cardiac anomalies, including rare ones. Utilizing an extensive dataset of 478,803 ECG graphic reports from real-world clinical practice, our method has demonstrated exceptional effectiveness in AD across all tested conditions, regardless of their frequency of occurrence, significantly outperforming existing models. It achieved superior performance metrics, including an AUROC of 91.2%, an F1 score of 83.7%, a sensitivity rate of 84.2%, a specificity of 83.0%, and a precision of 75.6% with a fixed recall rate of 90%. It has also demonstrated robust localization capabilities, with an AUROC of 76.5% and a Dice coefficient of 65.3% for anomaly localization.

ReMamber: Referring Image Segmentation with Mamba Twister

Referring Image Segmentation (RIS) leveraging transformers has achieved great success on the interpretation of complex visual-language tasks. However, the quadratic computation cost makes it resource-consuming in capturing long-range visual-language dependencies. Fortunately, Mamba addresses this with efficient linear complexity in processing. However, directly applying Mamba to multi-modal interactions presents challenges, primarily due to inadequate channel interactions for the effective fusion of multi-modal data. In this paper, we propose ReMamber, a novel RIS architecture that integrates the power of Mamba with a multi-modal Mamba Twister block. The Mamba Twister explicitly models image-text interaction, and fuses textual and visual features through its unique channel and spatial twisting mechanism. We achieve the state-of-the-art on three challenging benchmarks. Moreover, we conduct thorough analyses of ReMamber and discuss other fusion designs using Mamba. These provide valuable perspectives for future research.

Adapting Visual-Language Models for Generalizable Anomaly Detection in Medical Images

Recent advancements in large-scale visual-language pre-trained models have led to significant progress in zero-/few-shot anomaly detection within natural image domains. However, the substantial domain divergence between natural and medical images limits the effectiveness of these methodologies in medical anomaly detection. This paper introduces a novel lightweight multi-level adaptation and comparison framework to repurpose the CLIP model for medical anomaly detection. Our approach integrates multiple residual adapters into the pre-trained visual encoder, enabling a stepwise enhancement of visual features across different levels. This multi-level adaptation is guided by multi-level, pixel-wise visual-language feature alignment loss functions, which recalibrate the model's focus from object semantics in natural imagery to anomaly identification in medical images. The adapted features exhibit improved generalization across various medical data types, even in zero-shot scenarios where the model encounters unseen medical modalities and anatomical regions during training. Our experiments on medical anomaly detection benchmarks demonstrate that our method significantly surpasses current state-of-the-art models, with an average AUC improvement of 6.24% and 7.33% for anomaly classification, 2.03% and 2.37% for anomaly segmentation, under the zero-shot and few-shot settings, respectively. Source code is available at: https://github.com/MediaBrain-SJTU/MVFA-AD

GetMesh: A Controllable Model for High-quality Mesh Generation and Manipulation

Mesh is a fundamental representation of 3D assets in various industrial applications, and is widely supported by professional softwares. However, due to its irregular structure, mesh creation and manipulation is often time-consuming and labor-intensive. In this paper, we propose a highly controllable generative model, GetMesh, for mesh generation and manipulation across different categories. By taking a varying number of points as the latent representation, and re-organizing them as triplane representation, GetMesh generates meshes with rich and sharp details, outperforming both single-category and multi-category counterparts. Moreover, it also enables fine-grained control over the generation process that previous mesh generative models cannot achieve, where changing global/local mesh topologies, adding/removing mesh parts, and combining mesh parts across categories can be intuitively, efficiently, and robustly accomplished by adjusting the number, positions or features of latent points. Project page is https://getmesh.github.io.

Audio-Visual Segmentation via Unlabeled Frame Exploitation

Audio-visual segmentation (AVS) aims to segment the sounding objects in video frames. Although great progress has been witnessed, we experimentally reveal that current methods reach marginal performance gain within the use of the unlabeled frames, leading to the underutilization issue. To fully explore the potential of the unlabeled frames for AVS, we explicitly divide them into two categories based on their temporal characteristics, i.e., neighboring frame (NF) and distant frame (DF). NFs, temporally adjacent to the labeled frame, often contain rich motion information that assists in the accurate localization of sounding objects. Contrary to NFs, DFs have long temporal distances from the labeled frame, which share semantic-similar objects with appearance variations. Considering their unique characteristics, we propose a versatile framework that effectively leverages them to tackle AVS. Specifically, for NFs, we exploit the motion cues as the dynamic guidance to improve the objectness localization. Besides, we exploit the semantic cues in DFs by treating them as valid augmentations to the labeled frames, which are then used to enrich data diversity in a self-training manner. Extensive experimental results demonstrate the versatility and superiority of our method, unleashing the power of the abundant unlabeled frames.

Graph Construction with Flexible Nodes for Traffic Demand Prediction

Graph neural networks (GNNs) have been widely applied in traffic demand prediction, and transportation modes can be divided into station-based mode and free-floating traffic mode. Existing research in traffic graph construction primarily relies on map matching to construct graphs based on the road network. However, the complexity and inhomogeneity of data distribution in free-floating traffic demand forecasting make road network matching inflexible. To tackle these challenges, this paper introduces a novel graph construction method tailored to free-floating traffic mode. We propose a novel density-based clustering algorithm (HDPC-L) to determine the flexible positioning of nodes in the graph, overcoming the computational bottlenecks of traditional clustering algorithms and enabling effective handling of large-scale datasets. Furthermore, we extract valuable information from ridership data to initialize the edge weights of GNNs. Comprehensive experiments on two real-world datasets, the Shenzhen bike-sharing dataset and the Haikou ride-hailing dataset, show that the method significantly improves the performance of the model. On average, our models show an improvement in accuracy of around 25\% and 19.5\% on the two datasets. Additionally, it significantly enhances computational efficiency, reducing training time by approximately 12% and 32.5% on the two datasets. We make our code available at https://github.com/houjinyan/HDPC-L-ODInit.

Towards Building Multilingual Language Model for Medicine

In this paper, we aim to develop an open-source, multilingual language model for medicine, that the benefits a wider, linguistically diverse audience from different regions. In general, we present the contribution from the following aspects: first, for multilingual medical-specific adaptation, we construct a new multilingual medical corpus, that contains approximately 25.5B tokens encompassing 6 main languages, termed as MMedC, that enables auto-regressive training for existing general LLMs. second, to monitor the development of multilingual LLMs in medicine, we propose a new multilingual medical multi-choice question-answering benchmark with rationale, termed as MMedBench; third, we have assessed a number of popular, opensource large language models (LLMs) on our benchmark, along with those further auto-regressive trained on MMedC, as a result, our final model, termed as MMedLM 2, with only 7B parameters, achieves superior performance compared to all other open-source models, even rivaling GPT-4 on MMedBench. We will make the resources publicly available, including code, model weights, and datasets.

DictLLM: Harnessing Key-Value Data Structures with Large Language Models for Enhanced Medical Diagnostics

Structured data offers a sophisticated mechanism for the organization of information. Existing methodologies for the text-serialization of structured data in the context of large language models fail to adequately address the heterogeneity inherent in key-value structured data. These methods are not ideal and frequently result in larger input sizes and poor adaptability to input changes. In this paper, we introduce DictLLM, an innovative framework designed to improve the modeling of key-value structured data, like medical laboratory reports, for generating medical diagnoses. DictLLM integrates three key components: (1) group positional encoding to maintain permutation invariance, (2) hierarchical attention bias to capture the inherent bias in structured data, and (3) an optimal transport alignment layer that aligns the embedding generated by the dictionary encoder with the LLM, thereby producing a sequence of fixed-length virtual tokens. We carry out experiments using various LLM models on a comprehensive real-world medical laboratory report dataset for automatic diagnosis generation, our findings illustrate that DictLLM significantly outperforms established baseline methods and few-shot GPT-4 implementations in terms of both Rouge-L and Knowledge F1 scores. Furthermore, our evaluation of the framework's scalability and robustness, through a series of experiments, underscores its exceptional capability in accurately modeling the complex key-value data structure of medical dictionary data.

Learning-based Bone Quality Classification Method for Spinal Metastasis

Spinal metastasis is the most common disease in bone metastasis and may cause pain, instability and neurological injuries. Early detection of spinal metastasis is critical for accurate staging and optimal treatment. The diagnosis is usually facilitated with Computed Tomography (CT) scans, which requires considerable efforts from well-trained radiologists. In this paper, we explore a learning-based automatic bone quality classification method for spinal metastasis based on CT images. We simultaneously take the posterolateral spine involvement classification task into account, and employ multi-task learning (MTL) technique to improve the performance. MTL acts as a form of inductive bias which helps the model generalize better on each task by sharing representations between related tasks. Based on the prior knowledge that the mixed type can be viewed as both blastic and lytic, we model the task of bone quality classification as two binary classification sub-tasks, i.e., whether blastic and whether lytic, and leverage a multiple layer perceptron to combine their predictions. In order to make the model more robust and generalize better, self-paced learning is adopted to gradually involve from easy to more complex samples into the training process. The proposed learning-based method is evaluated on a proprietary spinal metastasis CT dataset. At slice level, our method significantly outperforms an 121-layer DenseNet classifier in sensitivities by $+12.54\%$, $+7.23\%$ and $+29.06\%$ for blastic, mixed and lytic lesions, respectively, meanwhile $+12.33\%$, $+23.21\%$ and $+34.25\%$ at vertebrae level.