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Pengcheng Jiang

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5 papers

2 author rows

AAAI Conference 2025 Conference Paper

Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations

Pengcheng Jiang
Cao Xiao
Tianfan Fu
Parminder Bhatia
Taha Kass-Hout
Jimeng Sun
Jiawei Han

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called Gode, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. Gode integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, Gode effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, Gode surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.

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ICLR Conference 2025 Conference Paper

Reasoning-Enhanced Healthcare Predictions with Knowledge Graph Community Retrieval

Pengcheng Jiang
Cao Xiao
Minhao Jiang
Parminder Bhatia
Taha A. Kass-Hout
Jimeng Sun 0001
Jiawei Han 0001

Large language models (LLMs) have demonstrated significant potential in clinical decision support. Yet LLMs still suffer from hallucinations and lack fine-grained contextual medical knowledge, limiting their high-stake healthcare applications such as clinical diagnosis. Traditional retrieval-augmented generation (RAG) methods attempt to address these limitations but frequently retrieve sparse or irrelevant information, undermining prediction accuracy. We introduce KARE, a novel framework that integrates knowledge graph (KG) community-level retrieval with LLM reasoning to enhance healthcare predictions. KARE constructs a comprehensive multi-source KG by integrating biomedical databases, clinical literature, and LLM-generated insights, and organizes it using hierarchical graph community detection and summarization for precise and contextually relevant information retrieval. Our key innovations include: (1) a dense medical knowledge structuring approach enabling accurate retrieval of relevant information; (2) a dynamic knowledge retrieval mechanism that enriches patient contexts with focused, multi-faceted medical insights; and (3) a reasoning-enhanced prediction framework that leverages these enriched contexts to produce both accurate and interpretable clinical predictions. Extensive experiments demonstrate that KARE outperforms leading models by up to 10.8-15.0\% on MIMIC-III and 12.6-12.7\% on MIMIC-IV for mortality and readmission predictions. In addition to its impressive prediction accuracy, our framework leverages the reasoning capabilities of LLMs, enhancing the trustworthiness of clinical predictions.

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ICLR Conference 2024 Conference Paper

GraphCare: Enhancing Healthcare Predictions with Personalized Knowledge Graphs

Pengcheng Jiang
Cao Xiao
Adam Cross
Jimeng Sun 0001

Clinical predictive models often rely on patients’ electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6% and 6.6% for mortality and readmission, and F1-score by 7.9% and 10.8% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

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NeurIPS Conference 2024 Conference Paper

KG-FIT: Knowledge Graph Fine-Tuning Upon Open-World Knowledge

Pengcheng Jiang
Lang Cao
Cao Xiao
Parminder Bhatia
Jimeng Sun
Jiawei Han

Knowledge Graph Embedding (KGE) techniques are crucial in learning compact representations of entities and relations within a knowledge graph, facilitating efficient reasoning and knowledge discovery. While existing methods typically focus either on training KGE models solely based on graph structure or fine-tuning pre-trained language models with classification data in KG, KG-FIT leverages LLM-guided refinement to construct a semantically coherent hierarchical structure of entity clusters. By incorporating this hierarchical knowledge along with textual information during the fine-tuning process, KG-FIT effectively captures both global semantics from the LLM and local semantics from the KG. Extensive experiments on the benchmark datasets FB15K-237, YAGO3-10, and PrimeKG demonstrate the superiority of KG-FIT over state-of-the-art pre-trained language model-based methods, achieving improvements of 14. 4\%, 13. 5\%, and 11. 9\% in the Hits@10 metric for the link prediction task, respectively. Furthermore, KG-FIT yields substantial performance gains of 12. 6\%, 6. 7\%, and 17. 7\% compared to the structure-based base models upon which it is built. These results highlight the effectiveness of KG-FIT in incorporating open-world knowledge from LLMs to significantly enhance the expressiveness and informativeness of KG embeddings.

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EAAI Journal 2023 Journal Article

Continuously evolving dropout with multi-objective evolutionary optimisation

Pengcheng Jiang
Yu Xue
Ferrante Neri

Dropout is an effective method of mitigating over-fitting while training deep neural networks (DNNs). This method consists of switching off (dropping) some of the neurons of the DNN and training it by keeping the remaining neurons active. This approach makes the DNN general and resilient to changes in its inputs. However, the probability of a neuron belonging to a layer to be dropped, the ’dropout rate’, is a hard-to-tune parameter that affects the performance of the trained model. Moreover, there is no reason, besides being more practical during parameter tuning, why the dropout rate should be the same for all neurons across a layer. This paper proposes a novel method to guide the dropout rate based on an evolutionary algorithm. In contrast to previous studies, we associate a dropout with each individual neuron of the network, thus allowing more flexibility in the training phase. The vector encoding the dropouts for the entire network is interpreted as the candidate solution of a bi-objective optimisation problem, where the first objective is the error reduction due to a set of dropout rates for a given data batch, while the second objective is the distance of the used dropout rates from a pre-arranged constant. The second objective is used to control the dropout rates and prevent them from becoming too small, hence ineffective; or too large, thereby dropping a too-large portion of the network. Experimental results show that the proposed method, namely GADropout, produces DNNs that consistently outperform DNNs designed by other dropout methods, some of them being modern advanced dropout methods representing the state-of-the-art. GADroput has been tested on multiple datasets and network architectures.

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