Jie Hu

Yihang Du, Jiaying Hu, Suyang Hou et al.

Spatial labeling assigns labels to specific spatial locations to characterize their spatial properties and relationships, with broad applications in scientific research and practice. Measuring the similarity between two spatial labelings is essential for understanding their differences and the contributing factors, such as changes in location properties or labeling methods. An adequate and unbiased measurement of spatial labeling similarity should consider the number of matched labels (label agreement), the topology of spatial label distribution, and the heterogeneous impacts of mismatched labels. However, existing methods often fail to account for all these aspects. To address this gap, we propose a methodological framework to guide the development of methods that meet these requirements. Given two spatial labelings, the framework transforms them into graphs based on location organization, labels, and attributes (e.g., location significance). The distributions of their graph attributes are then extracted, enabling an efficient computation of distributional discrepancy to reflect the dissimilarity level between the two labelings. We further provide a concrete implementation of this framework, termed Spatial Labeling Analogy Metric (SLAM), along with an analysis of its theoretical foundation, for evaluating spatial labeling results in spatial transcriptomics (ST) \textit{as per} their similarity with ground truth labeling. Through a series of carefully designed experimental cases involving both simulated and real ST data, we demonstrate that SLAM provides a comprehensive and accurate reflection of labeling quality compared to other well-established evaluation metrics. Our code is available at https://github.com/YihDu/SLAM.

Jie Hu, Junwei Zheng, Jiale Wei et al.

Recent advancements in the Mamba architecture, with its linear computational complexity, being a promising alternative to transformer architectures suffering from quadratic complexity. While existing works primarily focus on adapting Mamba as vision encoders, the critical role of task-specific Mamba decoders remains under-explored, particularly for distortion-prone dense prediction tasks. This paper addresses two interconnected challenges: (1) The design of a Mamba-based decoder that seamlessly adapts to various architectures (e.g., CNN-, Transformer-, and Mamba-based backbones), and (2) The performance degradation in decoders lacking distortion-aware capability when processing wide-FoV images (e.g., 180° fisheye and 360° panoramic settings). We propose the Deformable Mamba Decoder, an efficient distortion-aware decoder that integrates Mamba's computational efficiency with adaptive distortion awareness. Comprehensive experiments on five wide-FoV segmentation benchmarks validate its effectiveness. Notably, our decoder achieves a +2.5% performance improvement on the 360° Stanford2D3D segmentation benchmark while reducing 72% parameters and 97% FLOPs, as compared to the widely-used decoder heads.

Jinfan Frank Hu

Tokenization plays a critical role in processing agglutinative languages, where a single word can encode multiple morphemes carrying syntactic and semantic information. This study evaluates the impact of various tokenization strategies - word-level, character-level, n-gram, and Byte Pair Encoding (BPE) - on the quality of static word embeddings generated by Word2Vec for Turkish and Finnish. Using a 10,000-article Wikipedia corpus, we trained models under low-resource conditions and evaluated them on a Named Entity Recognition (NER) task. Despite the theoretical appeal of subword segmentation, word-level tokenization consistently outperformed all alternatives across all tokenization strategies tested. These findings suggest that in agglutinative, low-resource contexts, preserving boundaries via word-level tokenization may yield better embedding performance than complex statistical methods. This has practical implications for developing NLP pipelines for under-resourced languages where annotated data and computing power are limited.

Hongkang Song, Zihui Zhang, Yanpeng Zhou et al. · oxford

Spinal cord tumors significantly contribute to neurological morbidity and mortality. Precise morphometric quantification, encompassing the size, location, and type of such tumors, holds promise for optimizing treatment planning strategies. Although recent methods have demonstrated excellent performance in medical image segmentation, they primarily focus on discerning shapes with relatively large morphology such as brain tumors, ignoring the challenging problem of identifying spinal cord tumors which tend to have tiny sizes, diverse locations, and shapes. To tackle this hard problem of multiclass spinal cord tumor segmentation, we propose a new method, called BATseg, to learn a tumor surface distance field by applying our new multiclass boundary-aware loss function. To verify the effectiveness of our approach, we also introduce the first and large-scale spinal cord tumor dataset. It comprises gadolinium-enhanced T1-weighted 3D MRI scans from 653 patients and contains the four most common spinal cord tumor types: astrocytomas, ependymomas, hemangioblastomas, and spinal meningiomas. Extensive experiments on our dataset and another public kidney tumor segmentation dataset show that our proposed method achieves superior performance for multiclass tumor segmentation.

Xiaoli Liu, Pan Hu, Zhi Mao et al.

Background: Elderly patients with MODS have high risk of death and poor prognosis. The performance of current scoring systems assessing the severity of MODS and its mortality remains unsatisfactory. This study aims to develop an interpretable and generalizable model for early mortality prediction in elderly patients with MODS. Methods: The MIMIC-III, eICU-CRD and PLAGH-S databases were employed for model generation and evaluation. We used the eXtreme Gradient Boosting model with the SHapley Additive exPlanations method to conduct early and interpretable predictions of patients' hospital outcome. Three types of data source combinations and five typical evaluation indexes were adopted to develop a generalizable model. Findings: The interpretable model, with optimal performance developed by using MIMIC-III and eICU-CRD datasets, was separately validated in MIMIC-III, eICU-CRD and PLAGH-S datasets (no overlapping with training set). The performances of the model in predicting hospital mortality as validated by the three datasets were: AUC of 0.858, sensitivity of 0.834 and specificity of 0.705; AUC of 0.849, sensitivity of 0.763 and specificity of 0.784; and AUC of 0.838, sensitivity of 0.882 and specificity of 0.691, respectively. Comparisons of AUC between this model and baseline models with MIMIC-III dataset validation showed superior performances of this model; In addition, comparisons in AUC between this model and commonly used clinical scores showed significantly better performance of this model. Interpretation: The interpretable machine learning model developed in this study using fused datasets with large sample sizes was robust and generalizable. This model outperformed the baseline models and several clinical scores for early prediction of mortality in elderly ICU patients. The interpretative nature of this model provided clinicians with the ranking of mortality risk features.