Hanyuan Zhang

Jianyou Wang, Youze Zheng, Longtian Bao et al.

Scientists have long sought to accurately predict outcomes of real-world events before they happen. Can AI systems do so more reliably? We study this question through clinical trial outcome prediction, a high-stakes open challenge even for domain experts. We introduce CT Open, an open-access, live platform that will run four challenge every year. Anyone can submit predictions for each challenge. CT Open evaluates those submissions on trials whose outcomes were not yet public at the time of submission but were made public afterwards. Determining if a trial's outcome is public on the internet before a certain date is surprisingly difficult. Outcomes posted on official registries may lag behind by years, while the first mention may appear in obscure articles. To address this, we propose a novel, fully automated decontamination pipeline that uses iterative LLM-powered web search to identify the earliest mention of trial outcomes. We validate the pipeline's quality and accuracy by human expert's annotations. Since CT Open's pipeline ensures that every evaluated trial had no publicly reported outcome when the prediction was made, it allows participants to use any methodology and any data source. In this paper, we release a training set and two time-stamped test benchmarks, Winter 2025 and Summer 2025. We believe CT Open can serve as a central hub for advancing AI research on forecasting real-world outcomes before they occur, while also informing biomedical research and improving clinical trial design. CT Open Platform is hosted at $\href{https://ct-open.net/}{https://ct-open.net/}$

Lucas He, Krinos Li, Hanyuan Zhang et al.

Cerebral small vessel disease (CSVD) markers, specifically enlarged perivascular spaces (EPVS) and lacunae, present a unique challenge in medical image analysis due to their radiological mimicry. Standard segmentation networks struggle with feature interference and extreme class imbalance when handling these divergent targets simultaneously. To address these issues, we propose a morphology-decoupled framework where Zero-Initialized Gated Cross-Task Attention exploits dense EPVS context to guide sparse lacune detection. Furthermore, biological and topological consistency are enforced via a mixed-supervision strategy integrating Mutual Exclusion and Centerline Dice losses. Finally, we introduce an Anatomically-Informed Inference Calibration mechanism to dynamically suppress false positives based on tissue semantics. Extensive 5-folds cross-validation on the VALDO 2021 dataset (N=40) demonstrates state-of-the-art performance, notably surpassing task winners in lacunae detection precision (71.1%, p=0.01) and F1-score (62.6%, p=0.03). Furthermore, evaluation on the external EPAD cohort (N=1762) confirms the model's robustness for large-scale population studies. Code will be released upon acceptance.

Yuqi Chen, Hanyuan Zhang, Weiwei Sun et al.

GPS trajectories are the essential foundations for many trajectory-based applications, such as travel time estimation, traffic prediction and trajectory similarity measurement. Most applications require a large amount of high sample rate trajectories to achieve a good performance. However, many real-life trajectories are collected with low sample rate due to energy concern or other constraints.We study the task of trajectory recovery in this paper as a means for increasing the sample rate of low sample trajectories. Currently, most existing works on trajectory recovery follow a sequence-to-sequence diagram, with an encoder to encode a trajectory and a decoder to recover real GPS points in the trajectory. However, these works ignore the topology of road network and only use grid information or raw GPS points as input. Therefore, the encoder model is not able to capture rich spatial information of the GPS points along the trajectory, making the prediction less accurate and lack spatial consistency. In this paper, we propose a road network enhanced transformer-based framework, namely RNTrajRec, for trajectory recovery. RNTrajRec first uses a graph model, namely GridGNN, to learn the embedding features of each road segment. It next develops a spatial-temporal transformer model, namely GPSFormer, to learn rich spatial and temporal features along with a Sub-Graph Generation module to capture the spatial features for each GPS point in the trajectory. It finally forwards the outputs of encoder model into a multi-task decoder model to recover the missing GPS points. Extensive experiments based on three large-scale real-life trajectory datasets confirm the effectiveness of our approach.

Hanyuan Zhang, Lucas He, Zijie Cheng et al.

Registration between preoperative CT and intraoperative laparoscopic video plays a crucial role in augmented reality (AR) guidance for minimally invasive surgery. Learning-based methods have recently achieved registration errors comparable to optimization-based approaches while offering faster inference. However, many supervised methods produce coarse alignments that rely on additional optimization-based refinement, thereby increasing inference time. We present a discrete-action reinforcement learning (RL) framework that formulates CT-to-video registration as a sequential decision-making process. A shared feature encoder, warm-started from a supervised pose estimation network to provide stable geometric features and faster convergence, extracts representations from CT renderings and laparoscopic frames, while an RL policy head learns to choose rigid transformations along six degrees of freedom and to decide when to stop the iteration. Experiments on a public laparoscopic dataset demonstrated that our method achieved an average target registration error (TRE) of 15.70 mm, comparable to supervised approaches with optimization, while achieving faster convergence. The proposed RL-based formulation enables automated, efficient iterative registration without manually tuned step sizes or stopping criteria. This discrete framework provides a practical foundation for future continuous-action and deformable registration models in surgical AR applications.

Hanyuan Zhang, Lucas He, Runlong He et al.

Augmented reality can improve tumor localization in laparoscopic liver surgery. Existing registration pipelines typically depend on organ contours; deformable (non-rigid) alignment is often handled with finite-element (FE) models coupled to dimensionality-reduction or machine-learning components. We integrate laparoscopic depth maps with a foundation pose estimator for camera-liver pose estimation and replace FE-based deformation with non-rigid iterative closest point (NICP) to lower engineering/modeling complexity and expertise requirements. On real patient data, the depth-augmented foundation pose approach achieved 9.91 mm mean registration error in 3 cases. Combined rigid-NICP registration outperformed rigid-only registration, demonstrating NICP as an efficient substitute for finite-element deformable models. This pipeline achieves clinically relevant accuracy while offering a lightweight, engineering-friendly alternative to FE-based deformation.

Yun-Chen Lin, Jiayuan Huang, Hanyuan Zhang et al.

Accurate detection and delineation of anatomical structures in medical imaging are critical for computer-assisted interventions, particularly in laparoscopic liver surgery where 2D video streams limit depth perception and complicate landmark localization. While recent works have leveraged monocular depth cues for enhanced landmark detection, challenges remain in fusing RGB and depth features and in efficiently adapting large-scale vision models to surgical domains. We propose a depth-guided liver landmark segmentation framework integrating semantic and geometric cues via vision foundation encoders. We employ Segment Anything Model V2 (SAM2) encoder to extract RGB features and Depth Anything V2 (DA2) encoder to extract depth-aware features. To efficiently adapt SAM2, we introduce SRFT-GaLore, a novel low-rank gradient projection method that replaces the computationally expensive SVD with a Subsampled Randomized Fourier Transform (SRFT). This enables efficient fine-tuning of high-dimensional attention layers without sacrificing representational power. A cross-attention fusion module further integrates RGB and depth cues. To assess cross-dataset generalization, we also construct a new Laparoscopic Liver Surgical Dataset (LLSD) as an external validation benchmark. On the public L3D dataset, our method achieves a 4.85% improvement in Dice Similarity Coefficient and a 11.78-point reduction in Average Symmetric Surface Distance compared to the D2GPLand. To further assess generalization capability, we evaluate our model on LLSD dataset. Our model maintains competitive performance and significantly outperforms SAM-based baselines, demonstrating strong cross-dataset robustness and adaptability to unseen surgical environments. These results demonstrate that our SRFT-GaLore-enhanced dual-encoder framework enables scalable and precise segmentation under real-time, depth-constrained surgical settings.

Youze Zheng, Jianyou Wang, Yuhan Chen et al.

Predicting the outcomes of prospective clinical trials remains a major challenge for large language models. Prior work has shown that both traditional correlational predictors, such as random forests and logistic regression, and strong commercial LLMs achieve limited performance on this task. In this paper, we propose DeepImagine, a framework for teaching LLMs biomedical reasoning through successive counterfactual imagining. The central idea is to approximate hidden causal mechanisms of clinical trials by training models to infer how observed trial results would change under controlled perturbations of experimental conditions, such as dosage, outcome measures, study arms, geography, and other trial attributes. To support this objective, we construct both natural and approximate counterfactual pairs from real clinical trials with reported outcomes. For settings where strict counterfactual supervision is available, such as paired outcome measures or dose-ranging study arms within the same trial, we train models with supervised fine-tuning. For broader settings where only approximate counterfactual pairs can be retrieved, we optimize models with reinforcement learning using verifiable rewards based on downstream benchmark correctness. We further augment training with synthetic reasoning traces that provide causally plausible explanations for local counterfactual transitions. Using this pipeline, we train language models under 10B parameters, including Qwen3.5-9B, and evaluate them on clinical trial outcome prediction. We aim to show that DeepImagine consistently improves over untuned language models and traditional correlational baselines. Finally, we aim to show that the learned reasoning trajectories provide interpretable signals about how models represent trial-level mechanisms, suggesting a practical path toward more mechanistic and scientifically useful biomedical language models.

Weixi Yi, Yipei Wang, Wen Yan et al.

Multiparametric MRI is increasingly recommended as a first-line noninvasive approach to detect and localize prostate cancer, requiring at minimum diffusion-weighted (DWI) and T2-weighted (T2w) MR sequences. Early machine learning attempts using only T2w images have shown promising diagnostic performance in segmenting radiologist-annotated lesions. Such uni-modal T2-only approaches deliver substantial clinical benefits by reducing costs and expertise required to acquire other sequences. This work investigates an arguably more challenging application using only T2w at inference, but to localize individual cancers based on independent histopathology labels. We formulate DWI images as a latent modality (readily available during training) to classify cancer presence at local Barzell zones, given only T2w images as input. In the resulting expectation-maximization algorithm, a latent modality generator (implemented using a flow matching-based generative model) approximates the latent DWI image posterior distribution in the E-steps, while in M-steps a cancer localizer is simultaneously optimized with the generative model to maximize the expected likelihood of cancer presence. The proposed approach provides a novel theoretical framework for learning from a privileged DWI modality, yielding superior cancer localization performance compared to approaches that lack training DWI images or existing frameworks for privileged learning and incomplete modalities. The proposed T2-only methods perform competitively or better than baseline methods using multiple input sequences (e.g., improving the patient-level F1 score by 14.4\% and zone-level QWK by 5.3\% over the T2w+DWI baseline). We present quantitative evaluations using internal and external datasets from 4,133 prostate cancer patients with histopathology-verified labels.

Wen Sheng, Zhong Zheng, Jiajun Liu et al.

Background: Liver tumors are abnormal growths in the liver that can be either benign or malignant, with liver cancer being a significant health concern worldwide. However, there is no dataset for plain scan segmentation of liver tumors, nor any related algorithms. To fill this gap, we propose Plain Scan Liver Tumors(PSLT) and YNetr. Methods: A collection of 40 liver tumor plain scan segmentation datasets was assembled and annotated. Concurrently, we utilized Dice coefficient as the metric for assessing the segmentation outcomes produced by YNetr, having advantage of capturing different frequency information. Results: The YNetr model achieved a Dice coefficient of 62.63% on the PSLT dataset, surpassing the other publicly available model by an accuracy margin of 1.22%. Comparative evaluations were conducted against a range of models including UNet 3+, XNet, UNetr, Swin UNetr, Trans-BTS, COTr, nnUNetv2 (2D), nnUNetv2 (3D fullres), MedNext (2D) and MedNext(3D fullres). Conclusions: We not only proposed a dataset named PSLT(Plain Scan Liver Tumors), but also explored a structure called YNetr that utilizes wavelet transform to extract different frequency information, which having the SOTA in PSLT by experiments.

Hao Wu, Hanyuan Zhang, Xinyu Zhang et al.

Automatic map extraction is of great importance to urban computing and location-based services. Aerial image and GPS trajectory data refer to two different data sources that could be leveraged to generate the map, although they carry different types of information. Most previous works on data fusion between aerial images and data from auxiliary sensors do not fully utilize the information of both modalities and hence suffer from the issue of information loss. We propose a deep convolutional neural network called DeepDualMapper which fuses the aerial image and trajectory data in a more seamless manner to extract the digital map. We design a gated fusion module to explicitly control the information flows from both modalities in a complementary-aware manner. Moreover, we propose a novel densely supervised refinement decoder to generate the prediction in a coarse-to-fine way. Our comprehensive experiments demonstrate that DeepDualMapper can fuse the information of images and trajectories much more effectively than existing approaches, and is able to generate maps with higher accuracy.

Hanyuan Zhang, Hao Wu, Weiwei Sun et al.

Estimating the travel time of a path is of great importance to smart urban mobility. Existing approaches are either based on estimating the time cost of each road segment which are not able to capture many cross-segment complex factors, or designed heuristically in a non-learning-based way which fail to utilize the existing abundant temporal labels of the data, i.e., the time stamp of each trajectory point. In this paper, we leverage on new development of deep neural networks and propose a novel auxiliary supervision model, namely DeepTravel, that can automatically and effectively extract different features, as well as make full use of the temporal labels of the trajectory data. We have conducted comprehensive experiments on real datasets to demonstrate the out-performance of DeepTravel over existing approaches.