Gla-AI4BioMed at RRG24: Visual Instruction-tuned Adaptation for Radiology Report Generation

We introduce a radiology-focused visual language model designed to generate radiology reports from chest X-rays. Building on previous findings that large language models (LLMs) can acquire multimodal capabilities when aligned with pretrained vision encoders, we demonstrate similar potential with chest X-ray images. This integration enhances the ability of model to understand and describe chest X-ray images. Our model combines an image encoder with a fine-tuned LLM based on the Vicuna-7B architecture, enabling it to generate different sections of a radiology report with notable accuracy. The training process involves a two-stage approach: (i) initial alignment of chest X-ray features with the LLM (ii) followed by fine-tuning for radiology report generation.

TSUBF-Net: Trans-Spatial UNet-like Network with Bi-direction Fusion for Segmentation of Adenoid Hypertrophy in CT

Adenoid hypertrophy stands as a common cause of obstructive sleep apnea-hypopnea syndrome in children. It is characterized by snoring, nasal congestion, and growth disorders. Computed Tomography (CT) emerges as a pivotal medical imaging modality, utilizing X-rays and advanced computational techniques to generate detailed cross-sectional images. Within the realm of pediatric airway assessments, CT imaging provides an insightful perspective on the shape and volume of enlarged adenoids. Despite the advances of deep learning methods for medical imaging analysis, there remains an emptiness in the segmentation of adenoid hypertrophy in CT scans. To address this research gap, we introduce TSUBF-Nett (Trans-Spatial UNet-like Network based on Bi-direction Fusion), a 3D medical image segmentation framework. TSUBF-Net is engineered to effectively discern intricate 3D spatial interlayer features in CT scans and enhance the extraction of boundary-blurring features. Notably, we propose two innovative modules within the U-shaped network architecture:the Trans-Spatial Perception module (TSP) and the Bi-directional Sampling Collaborated Fusion module (BSCF).These two modules are in charge of operating during the sampling process and strategically fusing down-sampled and up-sampled features, respectively. Furthermore, we introduce the Sobel loss term, which optimizes the smoothness of the segmentation results and enhances model accuracy. Extensive 3D segmentation experiments are conducted on several datasets. TSUBF-Net is superior to the state-of-the-art methods with the lowest HD95: 7.03, IoU:85.63, and DSC: 92.26 on our own AHSD dataset. The results in the other two public datasets also demonstrate that our methods can robustly and effectively address the challenges of 3D segmentation in CT scans.

Libra: Leveraging Temporal Images for Biomedical Radiology Analysis

Radiology report generation (RRG) is a challenging task, as it requires a thorough understanding of medical images, integration of multiple temporal inputs, and accurate report generation. Effective interpretation of medical images, such as chest X-rays (CXRs), demands sophisticated visual-language reasoning to map visual findings to structured reports. Recent studies have shown that multimodal large language models (MLLMs) can acquire multimodal capabilities by aligning with pre-trained vision encoders. However, current approaches predominantly focus on single-image analysis or utilise rule-based symbolic processing to handle multiple images, thereby overlooking the essential temporal information derived from comparing current images with prior ones. To overcome this critical limitation, we introduce Libra, a temporal-aware MLLM tailored for CXR report generation using temporal images. Libra integrates a radiology-specific image encoder with a MLLM and utilises a novel Temporal Alignment Connector to capture and synthesise temporal information of images across different time points with unprecedented precision. Extensive experiments show that Libra achieves new state-of-the-art performance among the same parameter scale MLLMs for RRG tasks on the MIMIC-CXR. Specifically, Libra improves the RadCliQ metric by 12.9% and makes substantial gains across all lexical metrics compared to previous models.

Learning Optimal Lattice Vector Quantizers for End-to-end Neural Image Compression

It is customary to deploy uniform scalar quantization in the end-to-end optimized Neural image compression methods, instead of more powerful vector quantization, due to the high complexity of the latter. Lattice vector quantization (LVQ), on the other hand, presents a compelling alternative, which can exploit inter-feature dependencies more effectively while keeping computational efficiency almost the same as scalar quantization. However, traditional LVQ structures are designed/optimized for uniform source distributions, hence nonadaptive and suboptimal for real source distributions of latent code space for Neural image compression tasks. In this paper, we propose a novel learning method to overcome this weakness by designing the rate-distortion optimal lattice vector quantization (OLVQ) codebooks with respect to the sample statistics of the latent features to be compressed. By being able to better fit the LVQ structures to any given latent sample distribution, the proposed OLVQ method improves the rate-distortion performances of the existing quantization schemes in neural image compression significantly, while retaining the amenability of uniform scalar quantization.

Trajectory Flow Matching with Applications to Clinical Time Series Modeling

Modeling stochastic and irregularly sampled time series is a challenging problem found in a wide range of applications, especially in medicine. Neural stochastic differential equations (Neural SDEs) are an attractive modeling technique for this problem, which parameterize the drift and diffusion terms of an SDE with neural networks. However, current algorithms for training Neural SDEs require backpropagation through the SDE dynamics, greatly limiting their scalability and stability. To address this, we propose Trajectory Flow Matching (TFM), which trains a Neural SDE in a simulation-free manner, bypassing backpropagation through the dynamics. TFM leverages the flow matching technique from generative modeling to model time series. In this work we first establish necessary conditions for TFM to learn time series data. Next, we present a reparameterization trick which improves training stability. Finally, we adapt TFM to the clinical time series setting, demonstrating improved performance on three clinical time series datasets both in terms of absolute performance and uncertainty prediction.

Feint and Attack: Attention-Based Strategies for Jailbreaking and Protecting LLMs

Jailbreak attack can be used to access the vulnerabilities of Large Language Models (LLMs) by inducing LLMs to generate the harmful content. And the most common method of the attack is to construct semantically ambiguous prompts to confuse and mislead the LLMs. To access the security and reveal the intrinsic relation between the input prompt and the output for LLMs, the distribution of attention weight is introduced to analyze the underlying reasons. By using statistical analysis methods, some novel metrics are defined to better describe the distribution of attention weight, such as the Attention Intensity on Sensitive Words (Attn_SensWords), the Attention-based Contextual Dependency Score (Attn_DepScore) and Attention Dispersion Entropy (Attn_Entropy). By leveraging the distinct characteristics of these metrics, the beam search algorithm and inspired by the military strategy "Feint and Attack", an effective jailbreak attack strategy named as Attention-Based Attack (ABA) is proposed. In the ABA, nested attack prompts are employed to divert the attention distribution of the LLMs. In this manner, more harmless parts of the input can be used to attract the attention of the LLMs. In addition, motivated by ABA, an effective defense strategy called as Attention-Based Defense (ABD) is also put forward. Compared with ABA, the ABD can be used to enhance the robustness of LLMs by calibrating the attention distribution of the input prompt. Some comparative experiments have been given to demonstrate the effectiveness of ABA and ABD. Therefore, both ABA and ABD can be used to access the security of the LLMs. The comparative experiment results also give a logical explanation that the distribution of attention weight can bring great influence on the output for LLMs.

CCDepth: A Lightweight Self-supervised Depth Estimation Network with Enhanced Interpretability

Self-supervised depth estimation, which solely requires monocular image sequence as input, has become increasingly popular and promising in recent years. Current research primarily focuses on enhancing the prediction accuracy of the models. However, the excessive number of parameters impedes the universal deployment of the model on edge devices. Moreover, the emerging neural networks, being black-box models, are difficult to analyze, leading to challenges in understanding the rationales for performance improvements. To mitigate these issues, this study proposes a novel hybrid self-supervised depth estimation network, CCDepth, comprising convolutional neural networks (CNNs) and the white-box CRATE (Coding RAte reduction TransformEr) network. This novel network uses CNNs and the CRATE modules to extract local and global information in images, respectively, thereby boosting learning efficiency and reducing model size. Furthermore, incorporating the CRATE modules into the network enables a mathematically interpretable process in capturing global features. Extensive experiments on the KITTI dataset indicate that the proposed CCDepth network can achieve performance comparable with those state-of-the-art methods, while the model size has been significantly reduced. In addition, a series of quantitative and qualitative analyses on the inner features in the CCDepth network further confirm the effectiveness of the proposed method.

Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

Fast Point Cloud Geometry Compression with Context-based Residual Coding and INR-based Refinement

Compressing a set of unordered points is far more challenging than compressing images/videos of regular sample grids, because of the difficulties in characterizing neighboring relations in an irregular layout of points. Many researchers resort to voxelization to introduce regularity, but this approach suffers from quantization loss. In this research, we use the KNN method to determine the neighborhoods of raw surface points. This gives us a means to determine the spatial context in which the latent features of 3D points are compressed by arithmetic coding. As such, the conditional probability model is adaptive to local geometry, leading to significant rate reduction. Additionally, we propose a dual-layer architecture where a non-learning base layer reconstructs the main structures of the point cloud at low complexity, while a learned refinement layer focuses on preserving fine details. This design leads to reductions in model complexity and coding latency by two orders of magnitude compared to SOTA methods. Moreover, we incorporate an implicit neural representation (INR) into the refinement layer, allowing the decoder to sample points on the underlying surface at arbitrary densities. This work is the first to effectively exploit content-aware local contexts for compressing irregular raw point clouds, achieving high rate-distortion performance, low complexity, and the ability to function as an arbitrary-scale upsampling network simultaneously.

Beyond Entity Alignment: Towards Complete Knowledge Graph Alignment via Entity-Relation Synergy

Knowledge Graph Alignment (KGA) aims to integrate knowledge from multiple sources to address the limitations of individual Knowledge Graphs (KGs) in terms of coverage and depth. However, current KGA models fall short in achieving a ``complete'' knowledge graph alignment. Existing models primarily emphasize the linkage of cross-graph entities but overlook aligning relations across KGs, thereby providing only a partial solution to KGA. The semantic correlations embedded in relations are largely overlooked, potentially restricting a comprehensive understanding of cross-KG signals. In this paper, we propose to conceptualize relation alignment as an independent task and conduct KGA by decomposing it into two distinct but highly correlated sub-tasks: entity alignment and relation alignment. To capture the mutually reinforcing correlations between these objectives, we propose a novel Expectation-Maximization-based model, EREM, which iteratively optimizes both sub-tasks. Experimental results on real-world datasets demonstrate that EREM consistently outperforms state-of-the-art models in both entity alignment and relation alignment tasks.