Weicheng Zhu

Kangning Liu, Weicheng Zhu, Yiqiu Shen et al.

Learning representations for individual instances when only bag-level labels are available is a fundamental challenge in multiple instance learning (MIL). Recent works have shown promising results using contrastive self-supervised learning (CSSL), which learns to push apart representations corresponding to two different randomly-selected instances. Unfortunately, in real-world applications such as medical image classification, there is often class imbalance, so randomly-selected instances mostly belong to the same majority class, which precludes CSSL from learning inter-class differences. To address this issue, we propose a novel framework, Iterative Self-paced Supervised Contrastive Learning for MIL Representations (ItS2CLR), which improves the learned representation by exploiting instance-level pseudo labels derived from the bag-level labels. The framework employs a novel self-paced sampling strategy to ensure the accuracy of pseudo labels. We evaluate ItS2CLR on three medical datasets, showing that it improves the quality of instance-level pseudo labels and representations, and outperforms existing MIL methods in terms of both bag and instance level accuracy. Code is available at https://github.com/Kangningthu/ItS2CLR

Weicheng Zhu, Carlos Fernandez-Granda, Narges Razavian

Lung squamous cell carcinoma (LSCC) has a high recurrence and metastasis rate. Factors influencing recurrence and metastasis are currently unknown and there are no distinct histopathological or morphological features indicating the risks of recurrence and metastasis in LSCC. Our study focuses on the recurrence prediction of LSCC based on H&E-stained histopathological whole-slide images (WSI). Due to the small size of LSCC cohorts in terms of patients with available recurrence information, standard end-to-end learning with various convolutional neural networks for this task tends to overfit. Also, the predictions made by these models are hard to interpret. Histopathology WSIs are typically very large and are therefore processed as a set of smaller tiles. In this work, we propose a novel conditional self-supervised learning (SSL) method to learn representations of WSI at the tile level first, and leverage clustering algorithms to identify the tiles with similar histopathological representations. The resulting representations and clusters from self-supervision are used as features of a survival model for recurrence prediction at the patient level. Using two publicly available datasets from TCGA and CPTAC, we show that our LSCC recurrence prediction survival model outperforms both LSCC pathological stage-based approach and machine learning baselines such as multiple instance learning. The proposed method also enables us to explain the recurrence histopathological risk factors via the derived clusters. This can help pathologists derive new hypotheses regarding morphological features associated with LSCC recurrence.

Weicheng Zhu, Sheng Liu, Carlos Fernandez-Granda et al.

Self-supervised learning (SSL) has emerged as a powerful technique for learning rich representations from unlabeled data. The data representations are able to capture many underlying attributes of data, and be useful in downstream prediction tasks. In real-world settings, spurious correlations between some attributes (e.g. race, gender and age) and labels for downstream tasks often exist, e.g. cancer is usually more prevalent among elderly patients. In this paper, we investigate SSL in the presence of spurious correlations and show that the SSL training loss can be minimized by capturing only a subset of the conspicuous features relevant to those sensitive attributes, despite the presence of other important predictive features for the downstream tasks. To address this issue, we investigate the learning dynamics of SSL and observe that the learning is slower for samples that conflict with such correlations (e.g. elder patients without cancer). Motivated by these findings, we propose a learning-speed aware SSL (LA-SSL) approach, in which we sample each training data with a probability that is inversely related to its learning speed. We evaluate LA-SSL on three datasets that exhibit spurious correlations between different attributes, demonstrating that it improves the robustness of pretrained representations on downstream classification tasks.

Haresh Rengaraj Rajamohan, Xiang Gao, Weicheng Zhu et al.

While large-scale pretraining has revolutionized language modeling, its potential remains underexplored in healthcare with structured electronic health records (EHRs). We present RAVEN, a novel generative pretraining strategy for sequential EHR data based on Recurrence-Aware next-Visit EveNt prediction. Leveraging a dataset of over one million unique individuals, our model learns to autoregressively generate tokenized clinical events for the next visit conditioned on patient history. We introduce regularization on predicting repeated events and highlight a key pitfall in EHR-based foundation model evaluations: repeated event tokens can inflate performance metrics when new onsets are not distinguished from subsequent occurrences. Furthermore, we empirically investigate the scaling behaviors in a data-constrained, compute-saturated regime, showing that simply increasing model size is suboptimal without commensurate increases in data volume. We evaluate our model via zero-shot prediction for forecasting the incidence of a diverse set of diseases, where it rivals fully fine-tuned representation-based Transformer models and outperforms widely used simulation-based next-token approaches. Finally, without additional parameter updates, we show that RAVEN can generalize to an external patient cohort under lossy clinical code mappings and feature coverage gaps.

Zhihao Wen, Wenkang Wei, Yuan Fang et al.

Knowledge-based Visual Question Answering (KVQA) requires models to ground entities in images and reason over factual knowledge. Recent work has introduced its implicit-knowledge variant, IK-KVQA, where a multimodal large language model (MLLM) is the sole knowledge source and answers are produced without external retrieval. Existing IK-KVQA approaches, however, are typically trained with answer-only supervision: reasoning remains implicit, justifications are often weak or inconsistent, and generalization after standard supervised fine-tuning (SFT) can be brittle. We propose MODELNAME, a framework that equips IK-KVQA with dual-path structured reasoning traces (symbolic relation paths over text and vision together with path-grounded natural-language explanations) to provide a stronger inductive bias than generic answer-only supervision. These traces act as modality-aware scaffolds that guide the model toward relevant entities and attributes, offering more structure than generic chain-of-thought supervision while not constraining reasoning to any single fixed path. Using a single open-source MLLM, MODELNAME constructs and selects traces to build an offline trace-enriched dataset and then performs structure-aware self-distillation; no external retrievers, verifiers, or curated knowledge bases are used, and inference is a single autoregressive pass. Across benchmarks, MODELNAME consistently improves both answer accuracy and the transparency of intermediate reasoning, achieving up to 11.3% higher answer accuracy on OK-VQA over the strongest baseline.

Sheng Liu, Kangning Liu, Weicheng Zhu et al.

Deep learning in the presence of noisy annotations has been studied extensively in classification, but much less in segmentation tasks. In this work, we study the learning dynamics of deep segmentation networks trained on inaccurately-annotated data. We discover a phenomenon that has been previously reported in the context of classification: the networks tend to first fit the clean pixel-level labels during an "early-learning" phase, before eventually memorizing the false annotations. However, in contrast to classification, memorization in segmentation does not arise simultaneously for all semantic categories. Inspired by these findings, we propose a new method for segmentation from noisy annotations with two key elements. First, we detect the beginning of the memorization phase separately for each category during training. This allows us to adaptively correct the noisy annotations in order to exploit early learning. Second, we incorporate a regularization term that enforces consistency across scales to boost robustness against annotation noise. Our method outperforms standard approaches on a medical-imaging segmentation task where noises are synthesized to mimic human annotation errors. It also provides robustness to realistic noisy annotations present in weakly-supervised semantic segmentation, achieving state-of-the-art results on PASCAL VOC 2012. Code is available at https://github.com/Kangningthu/ADELE

Haoyang Fan, Fan Zhu, Changchun Liu et al.

In this manuscript, we introduce a real-time motion planning system based on the Baidu Apollo (open source) autonomous driving platform. The developed system aims to address the industrial level-4 motion planning problem while considering safety, comfort and scalability. The system covers multilane and single-lane autonomous driving in a hierarchical manner: (1) The top layer of the system is a multilane strategy that handles lane-change scenarios by comparing lane-level trajectories computed in parallel. (2) Inside the lane-level trajectory generator, it iteratively solves path and speed optimization based on a Frenet frame. (3) For path and speed optimization, a combination of dynamic programming and spline-based quadratic programming is proposed to construct a scalable and easy-to-tune framework to handle traffic rules, obstacle decisions and smoothness simultaneously. The planner is scalable to both highway and lower-speed city driving scenarios. We also demonstrate the algorithm through scenario illustrations and on-road test results. The system described in this manuscript has been deployed to dozens of Baidu Apollo autonomous driving vehicles since Apollo v1.5 was announced in September 2017. As of May 16th, 2018, the system has been tested under 3,380 hours and approximately 68,000 kilometers (42,253 miles) of closed-loop autonomous driving under various urban scenarios. The algorithm described in this manuscript is available at https://github.com/ApolloAuto/apollo/tree/master/modules/planning.

Weicheng Zhu, Haoxu Huang, Huanze Tang et al.

Head computed tomography (CT) imaging is a widely-used imaging modality with multitudes of medical indications, particularly in assessing pathology of the brain, skull, and cerebrovascular system. It is commonly the first-line imaging in neurologic emergencies given its rapidity of image acquisition, safety, cost, and ubiquity. Deep learning models may facilitate detection of a wide range of diseases. However, the scarcity of high-quality labels and annotations, particularly among less common conditions, significantly hinders the development of powerful models. To address this challenge, we introduce FM-CT: a Foundation Model for Head CT for generalizable disease detection, trained using self-supervised learning. Our approach pre-trains a deep learning model on a large, diverse dataset of 361,663 non-contrast 3D head CT scans without the need for manual annotations, enabling the model to learn robust, generalizable features. To investigate the potential of self-supervised learning in head CT, we employed both discrimination with self-distillation and masked image modeling, and we construct our model in 3D rather than at the slice level (2D) to exploit the structure of head CT scans more comprehensively and efficiently. The model's downstream classification performance is evaluated using internal and three external datasets, encompassing both in-distribution (ID) and out-of-distribution (OOD) data. Our results demonstrate that the self-supervised foundation model significantly improves performance on downstream diagnostic tasks compared to models trained from scratch and previous 3D CT foundation models on scarce annotated datasets. This work highlights the effectiveness of self-supervised learning in medical imaging and sets a new benchmark for head CT image analysis in 3D, enabling broader use of artificial intelligence for head CT-based diagnosis.

Zheyuan Zhang, Lin Ge, Hongjiang Li et al.

Large language models (LLMs) have demonstrated remarkable capabilities across diverse tasks, and LLM-based agents further extend these abilities to various practical workflows. While recent progress shows that multi-agent systems (MAS) can outperform single agents by coordinating specialized roles, designing effective MAS remains difficult due to prompt sensitivity and the compounded instability MAS creates. To cope with the challenge, recent efforts in automated prompt design have reduced manual effort. However, multi-agent prompt optimization remains largely unexplored. Challenges like exponentially expanding search space and ambiguous credit assignment together make systematic design intractable without principled methods. Therefore, we introduce M}ulti-Agent PRompt Optimization (MAPRO), a four-stage framework that first formulates MAS prompt optimization as a Maximum a Posteriori (MAP) inference problem and solves it using a language-guided variant of max-product belief propagation algorithm. To address credit assignment and updates the system iteratively, MAPRO employs a topology-aware refinement mechanism that integrates execution feedback and downstream blames to selectively update agent prompts. Through this process, MAPRO progressively converges to a coordinated set of agent-specific prompt policies. Across benchmarks in various tasks, MAPRO achieves state-of-the-art performance, consistently surpassing manually engineered baselines and recent automated alternatives. Beyond performance, our MAP-based formulation also delivers general guidelines for building more reliable and principled multi-agent systems in the future

Haresh Rengaraj Rajamohan, Xiang Gao, Weicheng Zhu et al.

Large-scale pretraining has transformed modeling of language and other data types, but its potential remains underexplored in healthcare with structured electronic health records (EHRs). We present a novel generative pretraining strategy for sequential EHR data using next-visit event prediction. Our model learns to autoregressively generate various tokenized clinical events for the next visit based on patient history and inherently handles the joint prediction of heterogeneous data types. Additionally, we introduce regularization on predicting repeated events and highlight a key pitfall in EHR-based foundation model evaluations: repeated event tokens can inflate performance metrics when new onsets are not distinguished from subsequent occurrences. Our model is evaluated via zero-shot prediction for forecasting dementia and knee osteoarthritis incidence within 2 and 5 years, and the model performance rivals a fully fine-tuned masked pretrained Transformer baseline, demonstrating that our approach captures complex clinical dependencies without requiring costly task-specific fine-tuning.

Qidong Yang, Weicheng Zhu, Joseph Keslin et al.

Probabilistic prediction of sequences from images and other high-dimensional data is a key challenge, particularly in risk-sensitive applications. In these settings, it is often desirable to quantify the uncertainty associated with the prediction (instead of just determining the most likely sequence, as in language modeling). In this paper, we propose a Monte Carlo framework to estimate probabilities and confidence intervals associated with the distribution of a discrete sequence. Our framework uses a Monte Carlo simulator, implemented as an autoregressively trained neural network, to sample sequences conditioned on an image input. We then use these samples to estimate the probabilities and confidence intervals. Experiments on synthetic and real data show that the framework produces accurate discriminative predictions, but can suffer from miscalibration. In order to address this shortcoming, we propose a time-dependent regularization method, which is shown to produce calibrated predictions.

Sheng Liu, Aakash Kaku, Weicheng Zhu et al.

Reliable probability estimation is of crucial importance in many real-world applications where there is inherent (aleatoric) uncertainty. Probability-estimation models are trained on observed outcomes (e.g. whether it has rained or not, or whether a patient has died or not), because the ground-truth probabilities of the events of interest are typically unknown. The problem is therefore analogous to binary classification, with the difference that the objective is to estimate probabilities rather than predicting the specific outcome. This work investigates probability estimation from high-dimensional data using deep neural networks. There exist several methods to improve the probabilities generated by these models but they mostly focus on model (epistemic) uncertainty. For problems with inherent uncertainty, it is challenging to evaluate performance without access to ground-truth probabilities. To address this, we build a synthetic dataset to study and compare different computable metrics. We evaluate existing methods on the synthetic data as well as on three real-world probability estimation tasks, all of which involve inherent uncertainty: precipitation forecasting from radar images, predicting cancer patient survival from histopathology images, and predicting car crashes from dashcam videos. We also give a theoretical analysis of a model for high-dimensional probability estimation which reproduces several of the phenomena evinced in our experiments. Finally, we propose a new method for probability estimation using neural networks, which modifies the training process to promote output probabilities that are consistent with empirical probabilities computed from the data. The method outperforms existing approaches on most metrics on the simulated as well as real-world data.

Weicheng Zhu, Narges Razavian

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

Yusheng Xie, Nan Du, Wei Fan et al.

Variational inference provides approximations to the computationally intractable posterior distribution in Bayesian networks. A prominent medical application of noisy-or Bayesian network is to infer potential diseases given observed symptoms. Previous studies focus on approximating a handful of complicated pathological cases using variational transformation. Our goal is to use variational transformation as part of a novel hybridized inference for serving reliable and real time diagnosis at web scale. We propose a hybridized inference that allows variational parameters to be estimated without disease posteriors or priors, making the inference faster and much of its computation recyclable. In addition, we propose a transformation ranking algorithm that is very stable to large variances in network prior probabilities, a common issue that arises in medical applications of Bayesian networks. In experiments, we perform comparative study on a large real life medical network and scalability study on a much larger (36,000x) synthesized network.