Xin Chen

Liangwei Nathan Zheng, Chang George Dong, Wei Emma Zhang et al.

Drug-drug interaction (DDI) identification is a crucial aspect of pharmacology research. There are many DDI types (hundreds), and they are not evenly distributed with equal chance to occur. Some of the rarely occurred DDI types are often high risk and could be life-critical if overlooked, exemplifying the long-tailed distribution problem. Existing models falter against this distribution challenge and overlook the multi-faceted nature of drugs in DDI prediction. In this paper, a novel multi-modal deep learning-based framework, namely TFDM, is introduced to leverage multiple properties of a drug to achieve DDI classification. The proposed framework fuses multimodal features of drugs, including graph-based, molecular structure, Target and Enzyme, for DDI identification. To tackle the challenge posed by the distribution skewness across categories, a novel loss function called Tailed Focal Loss is introduced, aimed at further enhancing the model performance and address gradient vanishing problem of focal loss in extremely long-tailed dataset. Intensive experiments over 4 challenging long-tailed dataset demonstrate that the TFMD outperforms the most recent SOTA methods in long-tailed DDI classification tasks. The source code is released to reproduce our experiment results: https://github.com/IcurasLW/TFMD_Longtailed_DDI.git

Yue Li, Qing Xu, Yixuan Zhang et al.

The Segment Anything Model 2 (SAM2) demonstrates remarkable universal segmentation capabilities on natural images. However, its performance on ultrasound images is significantly degraded due to domain disparities. This limitation raises two critical challenges: how to efficiently adapt SAM2 to ultrasound imaging while maintaining parameter efficiency, and how to deploy the adapted model effectively in resource-constrained clinical environments. To address these issues, we propose UniUltra for universal ultrasound segmentation. Specifically, we first introduce a novel context-edge hybrid adapter (CH-Adapter) that enhances fine-grained perception across diverse ultrasound imaging modalities while achieving parameter-efficient fine-tuning. To further improve clinical applicability, we develop a deep-supervised knowledge distillation (DSKD) technique that transfers knowledge from the large image encoder of the fine-tuned SAM2 to a super lightweight encoder, substantially reducing computational requirements without compromising performance. Extensive experiments demonstrate that UniUltra outperforms state-of-the-arts with superior generalization capabilities. Notably, our framework achieves competitive performance using only 8.91% of SAM2's parameters during fine-tuning, and the final compressed model reduces the parameter count by 94.08% compared to the original SAM2, making it highly suitable for practical clinical deployment. The source code is available at https://github.com/xq141839/UniUltra.

Zhendi Gong, Susan Francis, Eleanor Cox et al.

Multi-organ segmentation holds paramount significance in many clinical tasks. In practice, compared to large fully annotated datasets, multiple small datasets are often more accessible and organs are not labelled consistently. Normally, an individual model is trained for each of these datasets, which is not an effective way of using data for model learning. It remains challenging to train a single model that can robustly learn from several partially labelled datasets due to label conflict and data imbalance problems. We propose MO-CTranS: a single model that can overcome such problems. MO-CTranS contains a CNN-based encoder and a Transformer-based decoder, which are connected in a multi-resolution manner. Task-specific tokens are introduced in the decoder to help differentiate label discrepancies. Our method was evaluated and compared to several baseline models and state-of-the-art (SOTA) solutions on abdominal MRI datasets that were acquired in different views (i.e. axial and coronal) and annotated for different organs (i.e. liver, kidney, spleen). Our method achieved better performance (most were statistically significant) than the compared methods. Github link: https://github.com/naisops/MO-CTranS.

Yanbiao Ji, Chang Liu, Xin Chen et al.

Enabling large language models (LLMs) to effectively process and reason with graph-structured data remains a significant challenge despite their remarkable success in natural language tasks. Current approaches either convert graph structures into verbose textual descriptions, consuming substantial computational resources, or employ complex graph neural networks as tokenizers, which introduce significant training overhead. To bridge this gap, we present NT-LLM, a novel framework with an anchor-based positional encoding scheme for graph representation. Our approach strategically selects reference nodes as anchors and encodes each node's position relative to these anchors, capturing essential topological information without the computational burden of existing methods. Notably, we identify and address a fundamental issue: the inherent misalignment between discrete hop-based distances in graphs and continuous distances in embedding spaces. By implementing a rank-preserving objective for positional encoding pretraining, NT-LLM achieves superior performance across diverse graph tasks ranging from basic structural analysis to complex reasoning scenarios. Our comprehensive evaluation demonstrates that this lightweight yet powerful approach effectively enhances LLMs' ability to understand and reason with graph-structured information, offering an efficient solution for graph-based applications of language models.

Jing Li, Zhijie Sun, Xuan He et al.

The Mixtures-of-Experts (MoE) model is a widespread distributed and integrated learning method for large language models (LLM), which is favored due to its ability to sparsify and expand models efficiently. However, the performance of MoE is limited by load imbalance and high latency of All-to-All communication, along with relatively redundant computation owing to large expert capacity. Load imbalance may result from existing routing policies that consistently tend to select certain experts. The frequent inter-node communication in the All-to-All procedure also significantly prolongs the training time. To alleviate the above performance problems, we propose a novel routing strategy that combines load balance and locality by converting partial inter-node communication to that of intra-node. Notably, we elucidate that there is a minimum threshold for expert capacity, calculated through the maximal angular deviation between the gating weights of the experts and the assigned tokens. We port these modifications on the PanGu-Sigma model based on the MindSpore framework with multi-level routing and conduct experiments on Ascend clusters. The experiment results demonstrate that the proposed LocMoE reduces training time per epoch by 12.68% to 22.24% compared to classical routers, such as hash router and switch router, without impacting the model accuracy.

Ning Zhang, Susan Francis, Rayaz Malik et al.

Semantic image segmentation is one of the most important tasks in medical image analysis. Most state-of-the-art deep learning methods require a large number of accurately annotated examples for model training. However, accurate annotation is difficult to obtain especially in medical applications. In this paper, we propose a spatially constrained deep convolutional neural network (DCNN) to achieve smooth and robust image segmentation using inaccurately annotated labels for training. In our proposed method, image segmentation is formulated as a graph optimization problem that is solved by a DCNN model learning process. The cost function to be optimized consists of a unary term that is calculated by cross entropy measurement and a pairwise term that is based on enforcing a local label consistency. The proposed method has been evaluated based on corneal confocal microscopic (CCM) images for nerve fiber segmentation, where accurate annotations are extremely difficult to be obtained. Based on both the quantitative result of a synthetic dataset and qualitative assessment of a real dataset, the proposed method has achieved superior performance in producing high quality segmentation results even with inaccurate labels for training.

Xianxu Hou, Jingxin Liu, Bolei Xu et al.

Supervised semantic segmentation normally assumes the test data being in a similar data domain as the training data. However, in practice, the domain mismatch between the training and unseen data could lead to a significant performance drop. Obtaining accurate pixel-wise label for images in different domains is tedious and labor intensive, especially for histopathology images. In this paper, we propose a dual adaptive pyramid network (DAPNet) for histopathological gland segmentation adapting from one stain domain to another. We tackle the domain adaptation problem on two levels: 1) the image-level considers the differences of image color and style; 2) the feature-level addresses the spatial inconsistency between two domains. The two components are implemented as domain classifiers with adversarial training. We evaluate our new approach using two gland segmentation datasets with H&E and DAB-H stains respectively. The extensive experiments and ablation study demonstrate the effectiveness of our approach on the domain adaptive segmentation task. We show that the proposed approach performs favorably against other state-of-the-art methods.