arXiv subjects

Chengsheng Mao

Publications and source records attributed to Chengsheng Mao.

At least 19 recordsLinked to original sources

arXiv2025

AMANDA: Agentic Medical Knowledge Augmentation for Data-Efficient Medical Visual Question Answering

Medical Multimodal Large Language Models (Med-MLLMs) have shown great promise in medical visual question answering (Med-VQA). However, when deployed in low-resource settings where abundant labeled data are unavailable, existing Med-MLLMs commonly fail due to their medical reasoning capability bottlenecks: (i) the intrinsic reasoning bottleneck that ignores the details from the medical image; (ii) the extrinsic reasoning bottleneck that fails to incorporate specialized medical knowledge. To address those limitations, we propose AMANDA, a training-free agentic framework that performs medical knowledge augmentation via LLM agents. Specifically, our intrinsic medical knowledge augmentation focuses on coarse-to-fine question decomposition for comprehensive diagnosis, while extrinsic medical knowledge augmentation grounds the reasoning process via biomedical knowledge graph retrieval. Extensive experiments across eight Med-VQA benchmarks demonstrate substantial improvements in both zero-shot and few-shot Med-VQA settings. The code is available at https://github.com/REAL-Lab-NU/AMANDA.

cs.CL↗

arXiv2024

Deep Reinforcement Learning for Efficient and Fair Allocation of Health Care Resources

Scarcity of health care resources could result in the unavoidable consequence of rationing. For example, ventilators are often limited in supply, especially during public health emergencies or in resource-constrained health care settings, such as amid the pandemic of COVID-19. Currently, there is no universally accepted standard for health care resource allocation protocols, resulting in different governments prioritizing patients based on various criteria and heuristic-based protocols. In this study, we investigate the use of reinforcement learning for critical care resource allocation policy optimization to fairly and effectively ration resources. We propose a transformer-based deep Q-network to integrate the disease progression of individual patients and the interaction effects among patients during the critical care resource allocation. We aim to improve both fairness of allocation and overall patient outcomes. Our experiments demonstrate that our method significantly reduces excess deaths and achieves a more equitable distribution under different levels of ventilator shortage, when compared to existing severity-based and comorbidity-based methods in use by different governments. Our source code is included in the supplement and will be released on Github upon publication.

cs.LG↗

arXiv2023

Exploring Large Language Models for Knowledge Graph Completion

Knowledge graphs play a vital role in numerous artificial intelligence tasks, yet they frequently face the issue of incompleteness. In this study, we explore utilizing Large Language Models (LLM) for knowledge graph completion. We consider triples in knowledge graphs as text sequences and introduce an innovative framework called Knowledge Graph LLM (KG-LLM) to model these triples. Our technique employs entity and relation descriptions of a triple as prompts and utilizes the response for predictions. Experiments on various benchmark knowledge graphs demonstrate that our method attains state-of-the-art performance in tasks such as triple classification and relation prediction. We also find that fine-tuning relatively smaller models (e.g., LLaMA-7B, ChatGLM-6B) outperforms recent ChatGPT and GPT-4.

cs.CL↗

arXiv2022

AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease

Objective: We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). Materials and Methods: We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000-2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting, and then pretrained a BERT model for AD (AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. The embeddings of all the sections of a patient's notes processed by AD-BERT were combined by MaxPooling to compute the probability of MCI-to-AD progression. For replication, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. Results: Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.8170 and F1 score of 0.4178 on NMEDW dataset and AUC of 0.8830 and F1 score of 0.6836 on WCM dataset. Conclusion: We developed a deep learning framework using BERT models which provide an effective solution for prediction of MCI-to-AD progression using clinical note analysis.

cs.CL↗

arXiv2022

AKI-BERT: a Pre-trained Clinical Language Model for Early Prediction of Acute Kidney Injury

Acute kidney injury (AKI) is a common clinical syndrome characterized by a sudden episode of kidney failure or kidney damage within a few hours or a few days. Accurate early prediction of AKI for patients in ICU who are more likely than others to have AKI can enable timely interventions, and reduce the complications of AKI. Much of the clinical information relevant to AKI is captured in clinical notes that are largely unstructured text and requires advanced natural language processing (NLP) for useful information extraction. On the other hand, pre-trained contextual language models such as Bidirectional Encoder Representations from Transformers (BERT) have improved performances for many NLP tasks in general domain recently. However, few have explored BERT on disease-specific medical domain tasks such as AKI early prediction. In this paper, we try to apply BERT to specific diseases and present an AKI domain-specific pre-trained language model based on BERT (AKI-BERT) that could be used to mine the clinical notes for early prediction of AKI. AKI-BERT is a BERT model pre-trained on the clinical notes of patients having risks for AKI. Our experiments on Medical Information Mart for Intensive Care III (MIMIC-III) dataset demonstrate that AKI-BERT can yield performance improvements for early AKI prediction, thus expanding the utility of the BERT model from general clinical domain to disease-specific domain.

cs.CL↗

arXiv2022

Distribution Preserving Graph Representation Learning

Graph neural network (GNN) is effective to model graphs for distributed representations of nodes and an entire graph. Recently, research on the expressive power of GNN attracted growing attention. A highly-expressive GNN has the ability to generate discriminative graph representations. However, in the end-to-end training process for a certain graph learning task, a highly-expressive GNN risks generating graph representations overfitting the training data for the target task, while losing information important for the model generalization. In this paper, we propose Distribution Preserving GNN (DP-GNN) - a GNN framework that can improve the generalizability of expressive GNN models by preserving several kinds of distribution information in graph representations and node representations. Besides the generalizability, by applying an expressive GNN backbone, DP-GNN can also have high expressive power. We evaluate the proposed DP-GNN framework on multiple benchmark datasets for graph classification tasks. The experimental results demonstrate that our model achieves state-of-the-art performances.

cs.LG↗

arXiv2022

ImageGCN: Multi-Relational Image Graph Convolutional Networks for Disease Identification with Chest X-rays

Image representation is a fundamental task in computer vision. However, most of the existing approaches for image representation ignore the relations between images and consider each input image independently. Intuitively, relations between images can help to understand the images and maintain model consistency over related images, leading to better explainability. In this paper, we consider modeling the image-level relations to generate more informative image representations, and propose ImageGCN, an end-to-end graph convolutional network framework for inductive multi-relational image modeling. We apply ImageGCN to chest X-ray images where rich relational information is available for disease identification. Unlike previous image representation models, ImageGCN learns the representation of an image using both its original pixel features and its relationship with other images. Besides learning informative representations for images, ImageGCN can also be used for object detection in a weakly supervised manner. The experimental results on 3 open-source x-ray datasets, ChestX-ray14, CheXpert and MIMIC-CXR demonstrate that ImageGCN can outperform respective baselines in both disease identification and localization tasks and can achieve comparable and often better results than the state-of-the-art methods.

cs.CV↗

arXiv2022

MedGCN: Medication recommendation and lab test imputation via graph convolutional networks

Laboratory testing and medication prescription are two of the most important routines in daily clinical practice. Developing an artificial intelligence system that can automatically make lab test imputations and medication recommendations can save costs on potentially redundant lab tests and inform physicians of a more effective prescription. We present an intelligent medical system (named MedGCN) that can automatically recommend the patients' medications based on their incomplete lab tests, and can even accurately estimate the lab values that have not been taken. In our system, we integrate the complex relations between multiple types of medical entities with their inherent features in a heterogeneous graph. Then we model the graph to learn a distributed representation for each entity in the graph based on graph convolutional networks (GCN). By the propagation of graph convolutional networks, the entity representations can incorporate multiple types of medical information that can benefit multiple medical tasks. Moreover, we introduce a cross regularization strategy to reduce overfitting for multi-task training by the interaction between the multiple tasks. In this study, we construct a graph to associate 4 types of medical entities, i.e., patients, encounters, lab tests, and medications, and applied a graph neural network to learn node embeddings for medication recommendation and lab test imputation. we validate our MedGCN model on two real-world datasets: NMEDW and MIMIC-III. The experimental results on both datasets demonstrate that our model can outperform the state-of-the-art in both tasks. We believe that our innovative system can provide a promising and reliable way to assist physicians to make medication prescriptions and to save costs on potentially redundant lab tests.

cs.LG↗

arXiv2021

Constrained tensor factorization for computational phenotyping and mortality prediction in patients with cancer

Background: The increasing adoption of electronic health records (EHR) across the US has created troves of computable data, to which machine learning methods have been applied to extract useful insights. EHR data, represented as a three-dimensional analogue of a matrix (tensor), is decomposed into two-dimensional factors that can be interpreted as computational phenotypes. Methods: We apply constrained tensor factorization to derive computational phenotypes and predict mortality in cohorts of patients with breast, prostate, colorectal, or lung cancer in the Northwestern Medicine Enterprise Data Warehouse from 2000 to 2015. In our experiments, we examined using a supervised term in the factorization algorithm, filtering tensor co-occurrences by medical indication, and incorporating additional social determinants of health (SDOH) covariates in the factorization process. We evaluated the resulting computational phenotypes qualitatively and by assessing their ability to predict five-year mortality using the area under the curve (AUC) statistic. Results: Filtering by medical indication led to more concise and interpretable phenotypes. Mortality prediction performance (AUC) varied under the different experimental conditions and by cancer type (breast: 0.623 - 0.694, prostate: 0.603 - 0.750, colorectal: 0.523 - 0.641, and lung: 0.517 - 0.623). Generally, prediction performance improved with the use of a supervised term and the incorporation of SDOH covariates. Conclusion: Constrained tensor factorization, applied to sparse EHR data of patients with cancer, can discover computational phenotypes predictive of five-year mortality. The incorporation of SDOH variables into the factorization algorithm is an easy-to-implement and effective way to improve prediction performance.

cs.LG↗

arXiv2021

Natural language processing to identify lupus nephritis phenotype in electronic health records

Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data. We developed four algorithms: a rule-based algorithm using only structured data (baseline algorithm) and three algorithms using different NLP models. The three NLP models are based on regularized logistic regression and use different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components respectively. The baseline algorithm and the best performed NLP algorithm were external validated on a dataset from Vanderbilt University Medical Center (VUMC). Our best performing NLP model incorporating features from both structured data, regular expression concepts, and mapped CUIs improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.62 vs 0.96) datasets compared to the baseline lupus nephritis algorithm.

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arXiv2020

PANTHER: Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

q-bio.QM↗

arXiv2020

Towards Expressive Graph Representation

Graph Neural Network (GNN) aggregates the neighborhood of each node into the node embedding and shows its powerful capability for graph representation learning. However, most existing GNN variants aggregate the neighborhood information in a fixed non-injective fashion, which may map different graphs or nodes to the same embedding, reducing the model expressiveness. We present a theoretical framework to design a continuous injective set function for neighborhood aggregation in GNN. Using the framework, we propose expressive GNN that aggregates the neighborhood of each node with a continuous injective set function, so that a GNN layer maps similar nodes with similar neighborhoods to similar embeddings, different nodes to different embeddings and the equivalent nodes or isomorphic graphs to the same embeddings. Moreover, the proposed expressive GNN can naturally learn expressive representations for graphs with continuous node attributes. We validate the proposed expressive GNN (ExpGNN) for graph classification on multiple benchmark datasets including simple graphs and attributed graphs. The experimental results demonstrate that our model achieves state-of-the-art performances on most of the benchmarks.

cs.LG↗

arXiv2019

KG-BERT: BERT for Knowledge Graph Completion

Knowledge graphs are important resources for many artificial intelligence tasks but often suffer from incompleteness. In this work, we propose to use pre-trained language models for knowledge graph completion. We treat triples in knowledge graphs as textual sequences and propose a novel framework named Knowledge Graph Bidirectional Encoder Representations from Transformer (KG-BERT) to model these triples. Our method takes entity and relation descriptions of a triple as input and computes scoring function of the triple with the KG-BERT language model. Experimental results on multiple benchmark knowledge graphs show that our method can achieve state-of-the-art performance in triple classification, link prediction and relation prediction tasks.

cs.CL↗

arXiv2018

Local Probabilistic Model for Bayesian Classification: a Generalized Local Classification Model

In Bayesian classification, it is important to establish a probabilistic model for each class for likelihood estimation. Most of the previous methods modeled the probability distribution in the whole sample space. However, real-world problems are usually too complex to model in the whole sample space; some fundamental assumptions are required to simplify the global model, for example, the class conditional independence assumption for naive Bayesian classification. In this paper, with the insight that the distribution in a local sample space should be simpler than that in the whole sample space, a local probabilistic model established for a local region is expected much simpler and can relax the fundamental assumptions that may not be true in the whole sample space. Based on these advantages we propose establishing local probabilistic models for Bayesian classification. In addition, a Bayesian classifier adopting a local probabilistic model can even be viewed as a generalized local classification model; by tuning the size of the local region and the corresponding local model assumption, a fitting model can be established for a particular classification problem. The experimental results on several real-world datasets demonstrate the effectiveness of local probabilistic models for Bayesian classification.

cs.LG↗

arXiv2018

Local Distribution in Neighborhood for Classification

The k-nearest-neighbor method performs classification tasks for a query sample based on the information contained in its neighborhood. Previous studies into the k-nearest-neighbor algorithm usually achieved the decision value for a class by combining the support of each sample in the neighborhood. They have generally considered the nearest neighbors separately, and potentially integral neighborhood information important for classification was lost, e.g. the distribution information. This article proposes a novel local learning method that organizes the information in the neighborhood through local distribution. In the proposed method, additional distribution information in the neighborhood is estimated and then organized; the classification decision is made based on maximum posterior probability which is estimated from the local distribution in the neighborhood. Additionally, based on the local distribution, we generate a generalized local classification form that can be effectively applied to various datasets through tuning the parameters. We use both synthetic and real datasets to evaluate the classification performance of the proposed method; the experimental results demonstrate the dimensional scalability, efficiency, effectiveness and robustness of the proposed method compared to some other state-of-the-art classifiers. The results indicate that the proposed method is effective and promising in a broad range of domains.

cs.LG↗

arXiv2018

Distribution Networks for Open Set Learning

In open set learning, a model must be able to generalize to novel classes when it encounters a sample that does not belong to any of the classes it has seen before. Open set learning poses a realistic learning scenario that is receiving growing attention. Existing studies on open set learning mainly focused on detecting novel classes, but few studies tried to model them for differentiating novel classes. In this paper, we recognize that novel classes should be different from each other, and propose distribution networks for open set learning that can model different novel classes based on probability distributions. We hypothesize that, through a certain mapping, samples from different classes with the same classification criterion should follow different probability distributions from the same distribution family. A deep neural network is learned to map the samples in the original feature space to a latent space where the distributions of known classes can be jointly learned with the network. We additionally propose a distribution parameter transfer and updating strategy for novel class modeling when a novel class is detected in the latent space. By novel class modeling, the detected novel classes can serve as known classes to the subsequent classification. Our experimental results on image datasets MNIST and CIFAR10 show that the distribution networks can detect novel classes accurately, and model them well for the subsequent classification tasks.

cs.LG↗

arXiv2018

Graph Convolutional Networks for Text Classification

Text classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.

cs.CL↗

arXiv2018

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes

Acute kidney injury (AKI) in critically ill patients is associated with significant morbidity and mortality. Development of novel methods to identify patients with AKI earlier will allow for testing of novel strategies to prevent or reduce the complications of AKI. We developed data-driven prediction models to estimate the risk of new AKI onset. We generated models from clinical notes within the first 24 hours following intensive care unit (ICU) admission extracted from Medical Information Mart for Intensive Care III (MIMIC-III). From the clinical notes, we generated clinically meaningful word and concept representations and embeddings, respectively. Five supervised learning classifiers and knowledge-guided deep learning architecture were used to construct prediction models. The best configuration yielded a competitive AUC of 0.779. Our work suggests that natural language processing of clinical notes can be applied to assist clinicians in identifying the risk of incident AKI onset in critically ill patients upon admission to the ICU.

cs.LG↗