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Yue Ning

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6 papers

1 author row

JBHI Journal 2026 Journal Article

Bridging Stepwise Lab-Informed Pretraining and Knowledge-Guided Learning for Diagnostic Reasoning

Pengfei Hu
Chang Lu
Fei Wang
Yue Ning

Despite the growing use of Electronic Health Records (EHR) for AI-assisted diagnosis prediction, most data-driven models struggle to incorporate clinically meaningful medical knowledge. They often rely on limited ontologies, lacking structured reasoning capabilities and comprehensive coverage. This raises an important research question: Will medical knowledge improve predictive models to support stepwise clinical reasoning as performed by human doctors? To address this problem, we propose DuaLK, a dual-expertise framework that combines two complementary sources of information. For external knowledge, we construct a Diagnosis Knowledge Graph (KG) that encodes both hierarchical and semantic relations enriched by large language models (LLM). To align with patient data, we further introduce a lab-informed proxy task that guides the model to follow a clinically consistent, stepwise reasoning process based on lab test signals. Experimental results on two public EHR datasets demonstrate that DuaLK consistently outperforms existing baselines across four clinical prediction tasks. These findings highlight the potential of combining structured medical knowledge with individual-level clinical signals to achieve more accurate and interpretable diagnostic predictions. The source code is publicly available on https://github.com/humphreyhuu/DuaLK.

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NeurIPS Conference 2024 Conference Paper

A Topology-aware Graph Coarsening Framework for Continual Graph Learning

Xiaoxue Han
Zhuo Feng
Yue Ning

Graph Neural Networks (GNNs) experience "catastrophic forgetting" in continual learning setups, where they tend to lose previously acquired knowledge and perform poorly on old tasks. Rehearsal-based methods, which consolidate old knowledge with a replay memory buffer, are a de facto solution due to their straightforward workflow. However, these methods often fail to adequately capture topological information, leading to incorrect input-label mappings in replay samples. To address this, we propose TACO, a topology-aware graph coarsening and continual learning framework that stores information from previous tasks as a reduced graph. Throughout each learning period, this reduced graph expands by integrating with a new graph and aligning shared nodes, followed by a "zoom-out" reduction process to maintain a stable size. We have developed a graph coarsening algorithm based on node representation proximities to efficiently reduce a graph while preserving essential topological information. We empirically demonstrate that the learning process on the reduced graph can closely approximate that on the original graph. We compare TACO with a wide range of state-of-the-art baselines, proving its superiority and the necessity of preserving high-quality topological information for effective replaying.

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NeurIPS Conference 2023 Conference Paper

Towards Semi-Structured Automatic ICD Coding via Tree-based Contrastive Learning

Chang Lu
Chandan Reddy
Ping Wang
Yue Ning

Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural language processing (NLP) techniques, there are still challenges including limited availability of data due to privacy constraints and the high variability of clinical notes caused by different writing habits of medical professionals and various pathological features of patients. In this work, we investigate the semi-structured nature of clinical notes and propose an automatic algorithm to segment them into sections. To address the variability issues in existing ICD coding models with limited data, we introduce a contrastive pre-training approach on sections using a soft multi-label similarity metric based on tree edit distance. Additionally, we design a masked section training strategy to enable ICD coding models to locate sections related to ICD codes. Extensive experimental results demonstrate that our proposed training strategies effectively enhance the performance of existing ICD coding methods.

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AAAI Conference 2022 Conference Paper

Context-Aware Health Event Prediction via Transition Functions on Dynamic Disease Graphs

Chang Lu
Tian Han
Yue Ning

With the wide application of electronic health records (EHR) in healthcare facilities, health event prediction with deep learning has gained more and more attention. A common feature of EHR data used for deep-learning-based predictions is historical diagnoses. Existing work mainly regards a diagnosis as an independent disease and does not consider clinical relations among diseases in a visit. Many machine learning approaches assume disease representations are static in different visits of a patient. However, in real practice, multiple diseases that are frequently diagnosed at the same time reflect hidden patterns that are conducive to prognosis. Moreover, the development of a disease is not static since some diseases can emerge or disappear and show various symptoms in different visits of a patient. To effectively utilize this combinational disease information and explore the dynamics of diseases, we propose a novel context-aware learning framework using transition functions on dynamic disease graphs. Specifically, we construct a global disease co-occurrence graph with multiple node properties for disease combinations. We design dynamic subgraphs for each patient’s visit to leverage global and local contexts. We further define three diagnosis roles in each visit based on the variation of node properties to model disease transition processes. Experimental results on two real-world EHR datasets show that the proposed model outperforms state of the art in predicting health events.

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IJCAI Conference 2021 Conference Paper

Collaborative Graph Learning with Auxiliary Text for Temporal Event Prediction in Healthcare

Chang Lu
Chandan K Reddy
Prithwish Chakraborty
Samantha Kleinberg
Yue Ning

Accurate and explainable health event predictions are becoming crucial for healthcare providers to develop care plans for patients. The availability of electronic health records (EHR) has enabled machine learning advances in providing these predictions. However, many deep-learning-based methods are not satisfactory in solving several key challenges: 1) effectively utilizing disease domain knowledge; 2) collaboratively learning representations of patients and diseases; and 3) incorporating unstructured features. To address these issues, we propose a collaborative graph learning model to explore patient-disease interactions and medical domain knowledge. Our solution is able to capture structural features of both patients and diseases. The proposed model also utilizes unstructured text data by employing an attention manipulating strategy and then integrates attentive text features into a sequential learning process. We conduct extensive experiments on two important healthcare problems to show the competitive prediction performance of the proposed method compared with various state-of-the-art models. We also confirm the effectiveness of learned representations and model interpretability by a set of ablation and case studies.

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AAAI Conference 2016 Conference Paper

Topical Analysis of Interactions Between News and Social Media

Ting Hua
Yue Ning
Feng Chen
Chang-Tien Lu
Naren Ramakrishnan

The analysis of interactions between social media and traditional news streams is becoming increasingly relevant for a variety of applications, including: understanding the underlying factors that drive the evolution of data sources, tracking the triggers behind events, and discovering emerging trends. Researchers have explored such interactions by examining volume changes or information diffusions, however, most of them ignore the semantical and topical relationships between news and social media data. Our work is the ﬁrst attempt to study how news inﬂuences social media, or inversely, based on topical knowledge. We propose a hierarchical Bayesian model that jointly models the news and social media topics and their interactions. We show that our proposed model can capture distinct topics for individual datasets as well as discover the topic inﬂuences among multiple datasets. By applying our model to large sets of news and tweets, we demonstrate its signiﬁcant improvement over baseline methods and explore its power in the discovery of interesting patterns for real world cases.

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