Jianan Chen

Jianan Chen, Lu Zhang, Qiong Wang et al.

Cross-modal retrieval has drawn much attention in both computer vision and natural language processing domains. With the development of convolutional and recurrent neural networks, the bottleneck of retrieval across image-text modalities is no longer the extraction of image and text features but an efficient loss function learning in embedding space. Many loss functions try to closer pairwise features from heterogeneous modalities. This paper proposes a method for learning joint embedding of images and texts using an intra-modal constraint loss function to reduce the violation of negative pairs from the same homogeneous modality. Experimental results show that our approach outperforms state-of-the-art bi-directional image-text retrieval methods on Flickr30K and Microsoft COCO datasets. Our code is publicly available: https://github.com/CanonChen/IMC.

Jianan Chen, Anne L. Martel · utoronto

Cancer stage is a large determinant of patient prognosis and management in many cancer types, and is often assessed using medical imaging modalities, such as CT and MRI. These medical images contain rich information that can be explored to stratify patients within each stage group to further improve prognostic algorithms. Although the majority of cancer deaths result from metastatic and multifocal disease, building imaging biomarkers for patients with multiple tumors has been a challenging task due to the lack of annotated datasets and standard study framework. In this paper, we process two public datasets to set up a benchmark cohort of 341 patient in total for studying outcome prediction of multifocal metastatic cancer. We identify the lack of expressiveness in common multiple instance classification networks and propose two injective multiple instance pooling functions that are better suited to outcome prediction. Our results show that multiple instance learning with injective pooling functions can achieve state-of-the-art performance in the non-small-cell lung cancer CT and head and neck CT outcome prediction benchmarking tasks. We will release the processed multifocal datasets, our code and the intermediate files i.e. extracted radiomic features to support further transparent and reproducible research.

Jianan Chen, Vishwesh Ramanathan, Tony Xu et al.

Machine learning models experience deteriorated performance when trained in the presence of noisy labels. This is particularly problematic for medical tasks, such as survival prediction, which typically face high label noise complexity with few clear-cut solutions. Inspired by the large fluctuations across folds in the cross-validation performance of survival analyses, we design Monte-Carlo experiments to show that such fluctuation could be caused by label noise. We propose two novel and straightforward label noise detection algorithms that effectively identify noisy examples by pinpointing the samples that more frequently contribute to inferior cross-validation results. We first introduce Repeated Cross-Validation (ReCoV), a parameter-free label noise detection algorithm that is robust to model choice. We further develop fastReCoV, a less robust but more tractable and efficient variant of ReCoV suitable for deep learning applications. Through extensive experiments, we show that ReCoV and fastReCoV achieve state-of-the-art label noise detection performance in a wide range of modalities, models and tasks, including survival analysis, which has yet to be addressed in the literature. Our code and data are publicly available at https://github.com/GJiananChen/ReCoV.

Muhammad Alberb, Jianan Chen, Hossam El-rewaidy et al.

While colorectal liver metastasis (CRLM) is potentially curable via hepatectomy, patient outcomes remain highly heterogeneous. Postoperative survival prediction is necessary to avoid non-beneficial surgeries and guide personalized therapy. In this study, we present an automated AI-based framework for postoperative CRLM survival prediction using pre- and post-contrast MRI. We performed a retrospective study of 227 CRLM patients who had gadoxetate-enhanced MRI prior to curative-intent hepatectomy between 2013 and 2020. We developed a survival prediction framework comprising an anatomy-aware segmentation pipeline followed by a radiomics pipeline. The segmentation pipeline learns liver, CRLMs, and spleen segmentation from partially-annotated data, leveraging promptable foundation models to generate pseudo-labels. To support this pipeline, we propose SAMONAI, a prompt propagation algorithm that extends Segment Anything Model to 3D point-based segmentation. Predicted pre- and post-contrast segmentations are then fed into our radiomics pipeline, which extracts per-tumor features and predicts survival using SurvAMINN, an autoencoder-based multiple instance neural network for time-to-event survival prediction. SurvAMINN jointly learns dimensionality reduction and survival prediction from right-censored data, emphasizing high-risk metastases. We compared our framework against established methods and biomarkers using univariate and multivariate Cox regression. Our segmentation pipeline achieves median Dice scores of 0.96 (liver) and 0.93 (spleen), driving a CRLM segmentation Dice score of 0.78 and a detection F1-score of 0.79. Accurate segmentation enables our radiomics pipeline to achieve a survival prediction C-index of 0.69. Our results show the potential of integrating segmentation algorithms with radiomics-based survival analysis to deliver accurate and automated CRLM outcome prediction.

Jianan Chen, Qin Hu, Fangtian Zhong et al.

In Federated Learning (FL), multiple clients collaboratively train a model without sharing raw data. This paradigm can be further enhanced by Differential Privacy (DP) to protect local data from information inference attacks and is thus termed DPFL. An emerging privacy requirement, ``the right to be forgotten'' for clients, poses new challenges to DPFL but remains largely unexplored. Despite numerous studies on federated unlearning (FU), they are inapplicable to DPFL because the noise introduced by the DP mechanism compromises their effectiveness and efficiency. In this paper, we propose Federated Unlearning with Indistinguishability (FUI) to unlearn the local data of a target client in DPFL for the first time. FUI consists of two main steps: local model retraction and global noise calibration, resulting in an unlearning model that is statistically indistinguishable from the retrained model. Specifically, we demonstrate that the noise added in DPFL can endow the unlearning model with a certain level of indistinguishability after local model retraction, and then fortify the degree of unlearning through global noise calibration. Additionally, for the efficient and consistent implementation of the proposed FUI, we formulate a two-stage Stackelberg game to derive optimal unlearning strategies for both the server and the target client. Privacy and convergence analyses confirm theoretical guarantees, while experimental results based on four real-world datasets illustrate that our proposed FUI achieves superior model performance and higher efficiency compared to mainstream FU schemes. Simulation results further verify the optimality of the derived unlearning strategies.

Shi Pan, Jianan Chen, Maria Secrier

Gene expression profiling provides critical insights into cellular heterogeneity, biological processes and disease mechanisms. There has been an increasing interest in computational approaches that can predict gene expression directly from digitalized histopathology images. While image foundation models have shown promise in a variety of pathology downstream analysis, their performances on gene-expression prediction are still limited. Explicitly incorporating information from the transcriptomic models can help image models to address domain shift, yet the fine-tuning and alignment of foundation models can be expensive. In the work, we propose Parameter Efficient Knowledge trAnsfer (PEKA), a novel framework that leverages Block-Affine Adaptation and integrates knowledge distillation and structure alignment losses for cross-modal knowledge transfer. We evaluated PEKA for gene expression prediction using multiple spatial transcriptomics datasets (comprising 206,123 image tiles with matched gene expression profiles) that encompassed various types of tissue. PEKA achieved at least 5\% performance improvement over baseline foundation models while also outperforming alternative parameter-efficient fine-tuning strategies. We will release the code, datasets and aligned models after peer-review to facilitate broader adoption and further development for parameter efficient model alignment.

Chenyu Tang, Ruizhi Zhang, Shuo Gao et al.

At-home rehabilitation for post-stroke patients presents significant challenges, as continuous, personalized care is often limited outside clinical settings. Moreover, the lack of integrated solutions capable of simultaneously monitoring motor recovery and providing intelligent assistance in home environments hampers rehabilitation outcomes. Here, we present a multimodal smart home platform designed for continuous, at-home rehabilitation of post-stroke patients, integrating wearable sensing, ambient monitoring, and adaptive automation. A plantar pressure insole equipped with a machine learning pipeline classifies users into motor recovery stages with up to 94\% accuracy, enabling quantitative tracking of walking patterns during daily activities. An optional head-mounted eye-tracking module, together with ambient sensors such as cameras and microphones, supports seamless hands-free control of household devices with a 100\% success rate and sub-second response time. These data streams are fused locally via a hierarchical Internet of Things (IoT) architecture, ensuring low latency and data privacy. An embedded large language model (LLM) agent, Auto-Care, continuously interprets multimodal data to provide real-time interventions -- issuing personalized reminders, adjusting environmental conditions, and notifying caregivers. Implemented in a post-stroke context, this integrated smart home platform increased mean user satisfaction from 3.9 $\pm$ 0.8 in conventional home environments to 8.4 $\pm$ 0.6 with the full system ($n=20$). Beyond stroke, the system offers a scalable, patient-centered framework with potential for long-term use in broader neurorehabilitation and aging-in-place applications.

Jianan Chen, Helen M. C. Cheung, Laurent Milot et al.

Colorectal cancer is one of the most common and lethal cancers and colorectal cancer liver metastases (CRLM) is the major cause of death in patients with colorectal cancer. Multifocality occurs frequently in CRLM, but is relatively unexplored in CRLM outcome prediction. Most existing clinical and imaging biomarkers do not take the imaging features of all multifocal lesions into account. In this paper, we present an end-to-end autoencoder-based multiple instance neural network (AMINN) for the prediction of survival outcomes in multifocal CRLM patients using radiomic features extracted from contrast-enhanced MRIs. Specifically, we jointly train an autoencoder to reconstruct input features and a multiple instance network to make predictions by aggregating information from all tumour lesions of a patient. Also, we incorporate a two-step normalization technique to improve the training of deep neural networks, built on the observation that the distributions of radiomic features are almost always severely skewed. Experimental results empirically validated our hypothesis that incorporating imaging features of all lesions improves outcome prediction for multifocal cancer. The proposed AMINN framework achieved an area under the ROC curve (AUC) of 0.70, which is 11.4% higher than the best baseline method. A risk score based on the outputs of AMINN achieved superior prediction in our multifocal CRLM cohort. The effectiveness of incorporating all lesions and applying two-step normalization is demonstrated by a series of ablation studies. A Keras implementation of AMINN is released.

Fei Tang, Wanling Gao, Jianfeng Zhan et al.

Earlier-stage evaluations of a new AI architecture/system need affordable benchmarks. Only using a few AI component benchmarks like MLPerfalone in the other stages may lead to misleading conclusions. Moreover, the learning dynamics are not well understood, and the benchmarks' shelf-life is short. This paper proposes a balanced benchmarking methodology. We use real-world benchmarks to cover the factors space that impacts the learning dynamics to the most considerable extent. After performing an exhaustive survey on Internet service AI domains, we identify and implement nineteen representative AI tasks with state-of-the-art models. For repeatable performance ranking (RPR subset) and workload characterization (WC subset), we keep two subsets to a minimum for affordability. We contribute by far the most comprehensive AI training benchmark suite. The evaluations show: (1) AIBench Training (v1.1) outperforms MLPerfTraining (v0.7) in terms of diversity and representativeness of model complexity, computational cost, convergent rate, computation, and memory access patterns, and hotspot functions; (2) Against the AIBench full benchmarks, its RPR subset shortens the benchmarking cost by 64%, while maintaining the primary workload characteristics; (3) The performance ranking shows the single-purpose AI accelerator like TPU with the optimized TensorFlowframework performs better than that of GPUs while losing the latter's general support for various AI models. The specification, source code, and performance numbers are available from the AIBench homepage https://www.benchcouncil.org/aibench-training/index.html.

Jianan Chen, Laurent Milot, Helen M. C. Cheung et al.

Quantitative medical image computing (radiomics) has been widely applied to build prediction models from medical images. However, overfitting is a significant issue in conventional radiomics, where a large number of radiomic features are directly used to train and test models that predict genotypes or clinical outcomes. In order to tackle this problem, we propose an unsupervised learning pipeline composed of an autoencoder for representation learning of radiomic features and a Gaussian mixture model based on minimum message length criterion for clustering. By incorporating probabilistic modeling, disease heterogeneity has been taken into account. The performance of the proposed pipeline was evaluated on an institutional MRI cohort of 108 patients with colorectal cancer liver metastases. Our approach is capable of automatically selecting the optimal number of clusters and assigns patients into clusters (imaging subtypes) with significantly different survival rates. Our method outperforms other unsupervised clustering methods that have been used for radiomics analysis and has comparable performance to a state-of-the-art imaging biomarker.

Ozan Ciga, Jianan Chen, Anne Martel

Despite their success in many computer vision tasks, convolutional networks tend to require large amounts of labeled data to achieve generalization. Furthermore, the performance is not guaranteed on a sample from an unseen domain at test time, if the network was not exposed to similar samples from that domain at training time. This hinders the adoption of these techniques in clinical setting where the imaging data is scarce, and where the intra- and inter-domain variance of the data can be substantial. We propose a domain adaptation technique that is especially suitable for deep networks to alleviate this requirement of labeled data. Our method utilizes gradient reversal layers and Squeezeand-Excite modules to stabilize the training in deep networks. The proposed method was applied to publicly available histopathology and chest X-ray databases and achieved superior performance to existing state-of-the-art networks with and without domain adaptation. Depending on the application, our method can improve multi-class classification accuracy by 5-20% compared to DANN introduced in (Ganin, 2014).