Xi Long

Marc Aubreville, Nikolas Stathonikos, Christof A. Bertram et al.

The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. Recognition of mitotic figures by pathologists is known to be subject to a strong inter-rater bias, which limits the prognostic value. State-of-the-art deep learning methods can support the expert in this assessment but are known to strongly deteriorate when applied in a different clinical environment than was used for training. One decisive component in the underlying domain shift has been identified as the variability caused by using different whole slide scanners. The goal of the MICCAI MIDOG 2021 challenge has been to propose and evaluate methods that counter this domain shift and derive scanner-agnostic mitosis detection algorithms. The challenge used a training set of 200 cases, split across four scanning systems. As a test set, an additional 100 cases split across four scanning systems, including two previously unseen scanners, were given. The best approaches performed on an expert level, with the winning algorithm yielding an F_1 score of 0.748 (CI95: 0.704-0.781). In this paper, we evaluate and compare the approaches that were submitted to the challenge and identify methodological factors contributing to better performance.

Xi Long, Christy Boscardin, Lauren A. Maggio et al.

Knowledge syntheses (literature reviews) are essential to health professions education (HPE), consolidating findings to advance theory and practice. However, they are labor-intensive, especially during data extraction. Artificial Intelligence (AI)-assisted extraction promises efficiency but raises concerns about accuracy, making it critical to distinguish AI 'hallucinations' (fabricated content) from legitimate interpretive differences. We developed an extraction platform using large language models (LLMs) to automate data extraction and compared AI to human responses across 187 publications and 17 extraction questions from a published scoping review. AI-human, human-human, and AI-AI consistencies were measured using interrater reliability (categorical) and thematic similarity ratings (open-ended). Errors were identified by comparing extracted responses to source publications. AI was highly consistent with humans for concrete, explicitly stated questions (e.g., title, aims) and lower for questions requiring subjective interpretation or absent in text (e.g., Kirkpatrick's outcomes, study rationale). Human-human consistency was not higher than AI-human and showed the same question-dependent variability. Discordant AI-human responses (769/3179 = 24.2%) were mostly due to interpretive differences (18.3%); AI inaccuracies were rare (1.51%), while humans were nearly three times more likely to state inaccuracies (4.37%). Findings suggest AI variability depends more on interpretability than hallucination. Repeating AI extraction can identify interpretive complexity or ambiguity, refining processes before human review. AI can be a transparent, trustworthy partner in knowledge synthesis, though caution is needed to preserve critical human insights.

Biwen Meng, Xi Long, Wanrong Yang et al.

Deep learning has made significant progress in addressing challenges in various fields including computational pathology (CPath). However, due to the complexity of the domain shift problem, the performance of existing models will degrade, especially when it comes to multi-domain or cross-domain tasks. In this paper, we propose a Test-time style transfer (T3s) that uses a bidirectional mapping mechanism to project the features of the source and target domains into a unified feature space, enhancing the generalization ability of the model. To further increase the style expression space, we introduce a Cross-domain style diversification module (CSDM) to ensure the orthogonality between style bases. In addition, data augmentation and low-rank adaptation techniques are used to improve feature alignment and sensitivity, enabling the model to adapt to multi-domain inputs effectively. Our method has demonstrated effectiveness on three unseen datasets.

Biwen Meng, Xi Long, Jingxin Liu

Atypical mitotic figures (AMFs) are clinically relevant indicators of abnormal cell division, yet their reliable detection remains challenging due to morphological ambiguity and scanner variability. In this work, we investigated three variants of adapting the pathology foundation model UNI2 for the MIDOG2025 Track 2 challenge: (1) LoRA + UNI2, (2) VPT + UNI2 + Vahadane Normalizer, and (3) VPT + UNI2 + GRL + Stain TTA. We observed that the integration of Visual Prompt Tuning (VPT) with stain normalization techniques contributed to improved generalization. The best robustness was achieved by further incorporating test-time augmentation (TTA) with Vahadane and Macenko stain normalization. Our final submission achieved a balanced accuracy of 0.8837 and an ROC-AUC of 0.9513 on the preliminary leaderboard, ranking within the top 10 teams. These results suggest that prompt-based adaptation combined with stain-normalization TTA offers a promising strategy for atypical mitosis classification under diverse imaging conditions.

Feng Ren, Xiao Ding, Min Zheng et al.

The AlphaFold computer program predicted protein structures for the whole human genome, which has been considered as a remarkable breakthrough both in artificial intelligence (AI) application and structural biology. Despite the varying confidence level, these predicted structures still could significantly contribute to structure-based drug design of novel targets, especially the ones with no or limited structural information. In this work, we successfully applied AlphaFold in our end-to-end AI-powered drug discovery engines constituted of a biocomputational platform PandaOmics and a generative chemistry platform Chemistry42, to identify a first-in-class hit molecule of a novel target without an experimental structure starting from target selection towards hit identification in a cost- and time-efficient manner. PandaOmics provided the targets of interest and Chemistry42 generated the molecules based on the AlphaFold predicted structure, and the selected molecules were synthesized and tested in biological assays. Through this approach, we identified a small molecule hit compound for CDK20 with a Kd value of 8.9 +/- 1.6 uM (n = 4) within 30 days from target selection and after only synthesizing 7 compounds. Based on the available data, the second round of AI-powered compound generation was conducted and through which, a more potent hit molecule, ISM042-2 048, was discovered with a Kd value of 210.0 +/- 42.4 nM (n = 2), within 30 days and after synthesizing 6 compounds from the discovery of the first hit ISM042-2-001. To the best of our knowledge, this is the first reported small molecule targeting CDK20 and more importantly, this work is the first demonstration of AlphaFold application in the hit identification process in early drug discovery.

Xi Long, Ying Cheng, Xiao Mu et al.

We present a summary of the domain adaptive cascade R-CNN method for mitosis detection of digital histopathology images. By comprehensive data augmentation and adapting existing popular detection architecture, our proposed method has achieved an F1 score of 0.7500 on the preliminary test set in MItosis DOmain Generalization (MIDOG) Challenge at MICCAI 2021.

Yingxiao Wu, Yan Zhuang, Xi Long et al.

Gender contains a wide range of information regarding to the characteristics difference between male and female. Successful gender recognition is essential and critical for many applications in the commercial domains such as applications of human-computer interaction and computer-aided physiological or psychological analysis. Some have proposed various approaches for automatic gender classification using the features derived from human bodies and/or behaviors. First, this paper introduces the challenge and application for gender classification research. Then, the development and framework of gender classification are described. Besides, we compare these state-of-the-art approaches, including vision-based methods, biological information-based method, and social network information-based method, to provide a comprehensive review in the area of gender classification. In mean time, we highlight the strength and discuss the limitation of each method. Finally, this review also discusses several promising applications for the future work.