Ying Ding

Ajay Jaiswal, Haoyu Ma, Tianlong Chen et al. · meta-ai

Pruning large neural networks to create high-quality, independently trainable sparse masks, which can maintain similar performance to their dense counterparts, is very desirable due to the reduced space and time complexity. As research effort is focused on increasingly sophisticated pruning methods that leads to sparse subnetworks trainable from the scratch, we argue for an orthogonal, under-explored theme: improving training techniques for pruned sub-networks, i.e. sparse training. Apart from the popular belief that only the quality of sparse masks matters for sparse training, in this paper we demonstrate an alternative opportunity: one can carefully customize the sparse training techniques to deviate from the default dense network training protocols, consisting of introducing ``ghost" neurons and skip connections at the early stage of training, and strategically modifying the initialization as well as labels. Our new sparse training recipe is generally applicable to improving training from scratch with various sparse masks. By adopting our newly curated techniques, we demonstrate significant performance gains across various popular datasets (CIFAR-10, CIFAR-100, TinyImageNet), architectures (ResNet-18/32/104, Vgg16, MobileNet), and sparse mask options (lottery ticket, SNIP/GRASP, SynFlow, or even randomly pruning), compared to the default training protocols, especially at high sparsity levels. Code is at https://github.com/VITA-Group/ToST

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Large pre-trained transformers have been receiving explosive attention in the past few years, due to their wide adaptability for numerous downstream applications via fine-tuning, but their exponentially increasing parameter counts are becoming a primary hurdle to even just fine-tune them without industry-standard hardware. Recently, Lottery Ticket Hypothesis (LTH) and its variants, have been exploited to prune these large pre-trained models generating subnetworks that can achieve similar performance as their dense counterparts, but LTH pragmatism is enormously inhibited by repetitive full training and pruning routine of iterative magnitude pruning (IMP) which worsens with increasing model size. Motivated by the recent observations of model soups, which suggest that fine-tuned weights of multiple models can be merged to a better minima, we propose Instant Soup Pruning (ISP) to generate lottery ticket quality subnetworks, using a fraction of the original IMP cost by replacing the expensive intermediate pruning stages of IMP with computationally efficient weak mask generation and aggregation routine. More specifically, during the mask generation stage, ISP takes a small handful of iterations using varying training protocols and data subsets to generate many weak and noisy subnetworks, and superpose them to average out the noise creating a high-quality denoised subnetwork. Our extensive experiments and ablation on two popular large-scale pre-trained models: CLIP (unexplored in pruning till date) and BERT across multiple benchmark vision and language datasets validate the effectiveness of ISP compared to several state-of-the-art pruning methods. Codes are available at: \url{https://github.com/VITA-Group/instant_soup}

Ajay Jaiswal, Peihao Wang, Tianlong Chen et al.

Despite the enormous success of Graph Convolutional Networks (GCNs) in modeling graph-structured data, most of the current GCNs are shallow due to the notoriously challenging problems of over-smoothening and information squashing along with conventional difficulty caused by vanishing gradients and over-fitting. Previous works have been primarily focused on the study of over-smoothening and over-squashing phenomena in training deep GCNs. Surprisingly, in comparison with CNNs/RNNs, very limited attention has been given to understanding how healthy gradient flow can benefit the trainability of deep GCNs. In this paper, firstly, we provide a new perspective of gradient flow to understand the substandard performance of deep GCNs and hypothesize that by facilitating healthy gradient flow, we can significantly improve their trainability, as well as achieve state-of-the-art (SOTA) level performance from vanilla-GCNs. Next, we argue that blindly adopting the Glorot initialization for GCNs is not optimal, and derive a topology-aware isometric initialization scheme for vanilla-GCNs based on the principles of isometry. Additionally, contrary to ad-hoc addition of skip-connections, we propose to use gradient-guided dynamic rewiring of vanilla-GCNs} with skip connections. Our dynamic rewiring method uses the gradient flow within each layer during training to introduce on-demand skip-connections adaptively. We provide extensive empirical evidence across multiple datasets that our methods improve gradient flow in deep vanilla-GCNs and significantly boost their performance to comfortably compete and outperform many fancy state-of-the-art methods. Codes are available at: https://github.com/VITA-Group/GradientGCN.

Song Wang, Mingquan Lin, Ying Ding et al.

Analyzing radiology reports is a time-consuming and error-prone task, which raises the need for an efficient automated radiology report analysis system to alleviate the workloads of radiologists and encourage precise diagnosis. In this work, we present RadText, an open-source radiology text analysis system developed by Python. RadText offers an easy-to-use text analysis pipeline, including de-identification, section segmentation, sentence split and word tokenization, named entity recognition, parsing, and negation detection. RadText features a flexible modular design, provides a hybrid text processing schema, and supports raw text processing and local processing, which enables better usability and improved data privacy. RadText adopts BioC as the unified interface, and also standardizes the input / output into a structured representation compatible with Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). This allows for a more systematic approach to observational research across multiple, disparate data sources. We evaluated RadText on the MIMIC-CXR dataset, with five new disease labels we annotated for this work. RadText demonstrates highly accurate classification performances, with an average precision of, a recall of 0.94, and an F-1 score of 0.92. We have made our code, documentation, examples, and the test set available at https://github.com/bionlplab/radtext .

Ajay Jaiswal, Shiwei Liu, Tianlong Chen et al.

Graphs are omnipresent and GNNs are a powerful family of neural networks for learning over graphs. Despite their popularity, scaling GNNs either by deepening or widening suffers from prevalent issues of unhealthy gradients, over-smoothening, information squashing, which often lead to sub-standard performance. In this work, we are interested in exploring a principled way to scale GNNs capacity without deepening or widening, which can improve its performance across multiple small and large graphs. Motivated by the recent intriguing phenomenon of model soups, which suggest that fine-tuned weights of multiple large-language pre-trained models can be merged to a better minima, we argue to exploit the fundamentals of model soups to mitigate the aforementioned issues of memory bottleneck and trainability during GNNs scaling. More specifically, we propose not to deepen or widen current GNNs, but instead present a data-centric perspective of model soups tailored for GNNs, i.e., to build powerful GNNs. By dividing giant graph data, we build multiple independently and parallelly trained weaker GNNs (soup ingredient) without any intermediate communication, and combine their strength using a greedy interpolation soup procedure to achieve state-of-the-art performance. Compared to concurrent distributed GNN training works such as Jiong et. al. 2023, we train each soup ingredient by sampling different subgraphs per epoch and their respective sub-models are merged only after being fully trained (rather than intermediately so). Moreover, we provide a wide variety of model soup preparation techniques by leveraging state-of-the-art graph sampling and graph partitioning approaches that can handle large graphs. Codes are available at: \url{https://github.com/VITA-Group/graph_ladling}.

Ajay Jaiswal, Tianlong Chen, Justin F. Rousseau et al.

Deep neural networks (DNNs) have rapidly become a \textit{de facto} choice for medical image understanding tasks. However, DNNs are notoriously fragile to the class imbalance in image classification. We further point out that such imbalance fragility can be amplified when it comes to more sophisticated tasks such as pathology localization, as imbalances in such problems can have highly complex and often implicit forms of presence. For example, different pathology can have different sizes or colors (w.r.t.the background), different underlying demographic distributions, and in general different difficulty levels to recognize, even in a meticulously curated balanced distribution of training data. In this paper, we propose to use pruning to automatically and adaptively identify \textit{hard-to-learn} (HTL) training samples, and improve pathology localization by attending them explicitly, during training in \textit{supervised, semi-supervised, and weakly-supervised} settings. Our main inspiration is drawn from the recent finding that deep classification models have difficult-to-memorize samples and those may be effectively exposed through network pruning \cite{hooker2019compressed} - and we extend such observation beyond classification for the first time. We also present an interesting demographic analysis which illustrates HTLs ability to capture complex demographic imbalances. Our extensive experiments on the Skin Lesion Localization task in multiple training settings by paying additional attention to HTLs show significant improvement of localization performance by $\sim$2-3\%.

Li Shi, Redoan Rahman, Esther Melamed et al.

This paper applies eXplainable Artificial Intelligence (XAI) methods to investigate the socioeconomic disparities in COVID patient mortality. An Extreme Gradient Boosting (XGBoost) prediction model is built based on a de-identified Austin area hospital dataset to predict the mortality of COVID-19 patients. We apply two XAI methods, Shapley Additive exPlanations (SHAP) and Locally Interpretable Model Agnostic Explanations (LIME), to compare the global and local interpretation of feature importance. This paper demonstrates the advantages of using XAI which shows the feature importance and decisive capability. Furthermore, we use the XAI methods to cross-validate their interpretations for individual patients. The XAI models reveal that Medicare financial class, older age, and gender have high impact on the mortality prediction. We find that LIME local interpretation does not show significant differences in feature importance comparing to SHAP, which suggests pattern confirmation. This paper demonstrates the importance of XAI methods in cross-validation of feature attributions.

Tianhao Li, Sandesh Shetty, Advaith Kamath et al.

Large pre-trained language models (LLMs) have been shown to have significant potential in few-shot learning across various fields, even with minimal training data. However, their ability to generalize to unseen tasks in more complex fields, such as biology, has yet to be fully evaluated. LLMs can offer a promising alternative approach for biological inference, particularly in cases where structured data and sample size are limited, by extracting prior knowledge from text corpora. Our proposed few-shot learning approach uses LLMs to predict the synergy of drug pairs in rare tissues that lack structured data and features. Our experiments, which involved seven rare tissues from different cancer types, demonstrated that the LLM-based prediction model achieved significant accuracy with very few or zero samples. Our proposed model, the CancerGPT (with $\sim$ 124M parameters), was even comparable to the larger fine-tuned GPT-3 model (with $\sim$ 175B parameters). Our research is the first to tackle drug pair synergy prediction in rare tissues with limited data. We are also the first to utilize an LLM-based prediction model for biological reaction prediction tasks.

Mingquan Lin, Song Wang, Ying Ding et al.

Background: The predictive Intensive Care Unit (ICU) scoring system plays an important role in ICU management because it predicts important outcomes, especially mortality. Many scoring systems have been developed and used in the ICU. These scoring systems are primarily based on the structured clinical data in the electronic health record (EHR), which may suffer the loss of important clinical information in the narratives and images. Methods: In this work, we build a deep learning based survival prediction model with multi-modality data to predict ICU mortality. Four sets of features are investigated: (1) physiological measurements of Simplified Acute Physiology Score (SAPS) II, (2) common thorax diseases pre-defined by radiologists, (3) BERT-based text representations, and (4) chest X-ray image features. We use the Medical Information Mart for Intensive Care IV (MIMIC-IV) dataset to evaluate the proposed model. Results: Our model achieves the average C-index of 0.7829 (95% confidence interval, 0.7620-0.8038), which substantially exceeds that of the baseline with SAPS-II features (0.7470 (0.7263-0.7676)). Ablation studies further demonstrate the contributions of pre-defined labels (2.00%), text features (2.44%), and image features (2.82%).

Ajay Jaiswal, Nurendra Choudhary, Ravinarayana Adkathimar et al.

Graph Neural Networks (GNNs) have attracted immense attention in the past decade due to their numerous real-world applications built around graph-structured data. On the other hand, Large Language Models (LLMs) with extensive pretrained knowledge and powerful semantic comprehension abilities have recently shown a remarkable ability to benefit applications using vision and text data. In this paper, we investigate how LLMs can be leveraged in a computationally efficient fashion to benefit rich graph-structured data, a modality relatively unexplored in LLM literature. Prior works in this area exploit LLMs to augment every node features in an ad-hoc fashion (not scalable for large graphs), use natural language to describe the complex structural information of graphs, or perform computationally expensive finetuning of LLMs in conjunction with GNNs. We propose E-LLaGNN (Efficient LLMs augmented GNNs), a framework with an on-demand LLM service that enriches message passing procedure of graph learning by enhancing a limited fraction of nodes from the graph. More specifically, E-LLaGNN relies on sampling high-quality neighborhoods using LLMs, followed by on-demand neighborhood feature enhancement using diverse prompts from our prompt catalog, and finally information aggregation using message passing from conventional GNN architectures. We explore several heuristics-based active node selection strategies to limit the computational and memory footprint of LLMs when handling millions of nodes. Through extensive experiments & ablation on popular graph benchmarks of varying scales (Cora, PubMed, ArXiv, & Products), we illustrate the effectiveness of our E-LLaGNN framework and reveal many interesting capabilities such as improved gradient flow in deep GNNs, LLM-free inference ability etc.

Redoan Rahman, Jooyeong Kang, Justin F Rousseau et al.

This paper applies multiple machine learning (ML) algorithms to a dataset of de-identified COVID-19 patients provided by the COVID-19 Research Database. The dataset consists of 20,878 COVID-positive patients, among which 9,177 patients died in the year 2020. This paper aims to understand and interpret the association of socio-economic characteristics of patients with their mortality instead of maximizing prediction accuracy. According to our analysis, a patients households annual and disposable income, age, education, and employment status significantly impacts a machine learning models prediction. We also observe several individual patient data, which gives us insight into how the feature values impact the prediction for that data point. This paper analyzes the global and local interpretation of machine learning models on socio-economic data of COVID patients.

Tianqi Shang, Weiqing He, Tianlong Chen et al.

Social determinants of health (SDoH) play a crucial role in patient health outcomes, yet their integration into biomedical knowledge graphs remains underexplored. This study addresses this gap by constructing an SDoH-enriched knowledge graph using the MIMIC-III dataset and PrimeKG. We introduce a novel fairness formulation for graph embeddings, focusing on invariance with respect to sensitive SDoH information. Via employing a heterogeneous-GCN model for drug-disease link prediction, we detect biases related to various SDoH factors. To mitigate these biases, we propose a post-processing method that strategically reweights edges connected to SDoHs, balancing their influence on graph representations. This approach represents one of the first comprehensive investigations into fairness issues within biomedical knowledge graphs incorporating SDoH. Our work not only highlights the importance of considering SDoH in medical informatics but also provides a concrete method for reducing SDoH-related biases in link prediction tasks, paving the way for more equitable healthcare recommendations. Our code is available at \url{https://github.com/hwq0726/SDoH-KG}.

Chi-Yang Hsu, Kyle Cox, Jiawei Xu et al.

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine.

Shrey Pandit, Jiawei Xu, Junyuan Hong et al.

Advancements in Large Language Models (LLMs) and their increasing use in medical question-answering necessitate rigorous evaluation of their reliability. A critical challenge lies in hallucination, where models generate plausible yet factually incorrect outputs. In the medical domain, this poses serious risks to patient safety and clinical decision-making. To address this, we introduce MedHallu, the first benchmark specifically designed for medical hallucination detection. MedHallu comprises 10,000 high-quality question-answer pairs derived from PubMedQA, with hallucinated answers systematically generated through a controlled pipeline. Our experiments show that state-of-the-art LLMs, including GPT-4o, Llama-3.1, and the medically fine-tuned UltraMedical, struggle with this binary hallucination detection task, with the best model achieving an F1 score as low as 0.625 for detecting "hard" category hallucinations. Using bidirectional entailment clustering, we show that harder-to-detect hallucinations are semantically closer to ground truth. Through experiments, we also show incorporating domain-specific knowledge and introducing a "not sure" category as one of the answer categories improves the precision and F1 scores by up to 38% relative to baselines.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Congenital heart disease (CHD) presents complex, lifelong challenges often underrepresented in traditional clinical metrics. While unstructured narratives offer rich insights into patient and caregiver experiences, manual thematic analysis (TA) remains labor-intensive and unscalable. We propose a fully automated large language model (LLM) pipeline that performs end-to-end TA on clinical narratives, which eliminates the need for manual coding or full transcript review. Our system employs a novel multi-agent framework, where specialized LLM agents assume roles to enhance theme quality and alignment with human analysis. To further improve thematic relevance, we optionally integrate reinforcement learning from human feedback (RLHF). This supports scalable, patient-centered analysis of large qualitative datasets and allows LLMs to be fine-tuned for specific clinical contexts.

Francis Tang, Ying Ding

Time series data plays a critical role across diverse domains such as healthcare, energy, and finance, where tasks like classification, anomaly detection, and forecasting are essential for informed decision-making. Recently, large language models (LLMs) have gained prominence for their ability to handle complex data and extract meaningful insights. This study investigates whether LLMs are effective for time series data analysis by comparing their performance with non-LLM-based approaches across three tasks: classification, anomaly detection, and forecasting. Through a series of experiments using GPT4TS and autoregressive models, we evaluate their performance on benchmark datasets and assess their accuracy, precision, and ability to generalize. Our findings indicate that while LLM-based methods excel in specific tasks like anomaly detection, their benefits are less pronounced in others, such as forecasting, where simpler models sometimes perform comparably or better. This research highlights the role of LLMs in time series analysis and lays the groundwork for future studies to systematically explore their applications and limitations in handling temporal data.

Huimin Xu, Seungjun Yi, Terence Lim et al.

Thematic analysis (TA) is a widely used qualitative approach for uncovering latent meanings in unstructured text data. TA provides valuable insights in healthcare but is resource-intensive. Large Language Models (LLMs) have been introduced to perform TA, yet their applications in healthcare remain unexplored. Here, we propose TAMA: A Human-AI Collaborative Thematic Analysis framework using Multi-Agent LLMs for clinical interviews. We leverage the scalability and coherence of multi-agent systems through structured conversations between agents and coordinate the expertise of cardiac experts in TA. Using interview transcripts from parents of children with Anomalous Aortic Origin of a Coronary Artery (AAOCA), a rare congenital heart disease, we demonstrate that TAMA outperforms existing LLM-assisted TA approaches, achieving higher thematic hit rate, coverage, and distinctiveness. TAMA demonstrates strong potential for automated TA in clinical settings by leveraging multi-agent LLM systems with human-in-the-loop integration by enhancing quality while significantly reducing manual workload.

Seungjun Yi, Joakim Nguyen, Terence Lim et al.

This position paper examines how large language models (LLMs) can support thematic analysis of unstructured clinical transcripts, a widely used but resource-intensive method for uncovering patterns in patient and provider narratives. We conducted a systematic review of recent studies applying LLMs to thematic analysis, complemented by an interview with a practicing clinician. Our findings reveal that current approaches remain fragmented across multiple dimensions including types of thematic analysis, datasets, prompting strategies and models used, most notably in evaluation. Existing evaluation methods vary widely (from qualitative expert review to automatic similarity metrics), hindering progress and preventing meaningful benchmarking across studies. We argue that establishing standardized evaluation practices is critical for advancing the field. To this end, we propose an evaluation framework centered on three dimensions: validity, reliability, and interpretability.

Deepthi Potluri, Aby Mammen Mathew, Jeffrey B DeWitt et al.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Seungjun Yi, Joakim Nguyen, Huimin Xu et al.

Thematic Analysis (TA) is a widely used qualitative method that provides a structured yet flexible framework for identifying and reporting patterns in clinical interview transcripts. However, manual thematic analysis is time-consuming and limits scalability. Recent advances in LLMs offer a pathway to automate thematic analysis, but alignment with human results remains limited. To address these limitations, we propose SFT-TA, an automated thematic analysis framework that embeds supervised fine-tuned (SFT) agents within a multi-agent system. Our framework outperforms existing frameworks and the gpt-4o baseline in alignment with human reference themes. We observed that SFT agents alone may underperform, but achieve better results than the baseline when embedded within a multi-agent system. Our results highlight that embedding SFT agents in specific roles within a multi-agent system is a promising pathway to improve alignment with desired outputs for thematic analysis.

Junyi Chen, Mengjia Wu, Qian Liu et al.

The degraded performance and group unfairness caused by confounding sensitive attributes in rumor detection remains relatively unexplored. To address this, we propose a two-step framework. Initially, it identifies confounding sensitive attributes that limit rumor detection performance and cause unfairness across groups. Subsequently, we aim to learn equally informative representations through invariant learning. Our method considers diverse sets of groups without sensitive attribute annotations. Experiments show our method easily integrates with existing rumor detectors, significantly improving both their detection performance and fairness.

Liyan Tang, Yifan Peng, Yanshan Wang et al.

A human decision-maker benefits the most from an AI assistant that corrects for their biases. For problems such as generating interpretation of a radiology report given findings, a system predicting only highly likely outcomes may be less useful, where such outcomes are already obvious to the user. To alleviate biases in human decision-making, it is worth considering a broad differential diagnosis, going beyond the most likely options. We introduce a new task, "less likely brainstorming," that asks a model to generate outputs that humans think are relevant but less likely to happen. We explore the task in two settings: a brain MRI interpretation generation setting and an everyday commonsense reasoning setting. We found that a baseline approach of training with less likely hypotheses as targets generates outputs that humans evaluate as either likely or irrelevant nearly half of the time; standard MLE training is not effective. To tackle this problem, we propose a controlled text generation method that uses a novel contrastive learning strategy to encourage models to differentiate between generating likely and less likely outputs according to humans. We compare our method with several state-of-the-art controlled text generation models via automatic and human evaluations and show that our models' capability of generating less likely outputs is improved.

Xiangjie Kong, Jun Zhang, Da Zhang et al.

This paper elaborates how to identify and evaluate causal factors to improve scientific impact. Currently, analyzing scientific impact can be beneficial to various academic activities including funding application, mentor recommendation, and discovering potential cooperators etc. It is universally acknowledged that high-impact scholars often have more opportunities to receive awards as an encouragement for their hard working. Therefore, scholars spend great efforts in making scientific achievements and improving scientific impact during their academic life. However, what are the determinate factors that control scholars' academic success? The answer to this question can help scholars conduct their research more efficiently. Under this consideration, our paper presents and analyzes the causal factors that are crucial for scholars' academic success. We first propose five major factors including article-centered factors, author-centered factors, venue-centered factors, institution-centered factors, and temporal factors. Then, we apply recent advanced machine learning algorithms and jackknife method to assess the importance of each causal factor. Our empirical results show that author-centered and article-centered factors have the highest relevancy to scholars' future success in the computer science area. Additionally, we discover an interesting phenomenon that the h-index of scholars within the same institution or university are actually very close to each other.

Ajay Jaiswal, Liyan Tang, Meheli Ghosh et al.

Radiology reports are unstructured and contain the imaging findings and corresponding diagnoses transcribed by radiologists which include clinical facts and negated and/or uncertain statements. Extracting pathologic findings and diagnoses from radiology reports is important for quality control, population health, and monitoring of disease progress. Existing works, primarily rely either on rule-based systems or transformer-based pre-trained model fine-tuning, but could not take the factual and uncertain information into consideration, and therefore generate false-positive outputs. In this work, we introduce three sedulous augmentation techniques which retain factual and critical information while generating augmentations for contrastive learning. We introduce RadBERT-CL, which fuses these information into BlueBert via a self-supervised contrastive loss. Our experiments on MIMIC-CXR show superior performance of RadBERT-CL on fine-tuning for multi-class, multi-label report classification. We illustrate that when few labeled data are available, RadBERT-CL outperforms conventional SOTA transformers (BERT/BlueBert) by significantly larger margins (6-11%). We also show that the representations learned by RadBERT-CL can capture critical medical information in the latent space.

Ajay Jaiswal, Tianhao Li, Cyprian Zander et al.

Computer-aided diagnosis plays a salient role in more accessible and accurate cardiopulmonary diseases classification and localization on chest radiography. Millions of people get affected and die due to these diseases without an accurate and timely diagnosis. Recently proposed contrastive learning heavily relies on data augmentation, especially positive data augmentation. However, generating clinically-accurate data augmentations for medical images is extremely difficult because the common data augmentation methods in computer vision, such as sharp, blur, and crop operations, can severely alter the clinical settings of medical images. In this paper, we proposed a novel and simple data augmentation method based on patient metadata and supervised knowledge to create clinically accurate positive and negative augmentations for chest X-rays. We introduce an end-to-end framework, SCALP, which extends the self-supervised contrastive approach to a supervised setting. Specifically, SCALP pulls together chest X-rays from the same patient (positive keys) and pushes apart chest X-rays from different patients (negative keys). In addition, it uses ResNet-50 along with the triplet-attention mechanism to identify cardiopulmonary diseases, and Grad-CAM++ to highlight the abnormal regions. Our extensive experiments demonstrate that SCALP outperforms existing baselines with significant margins in both classification and localization tasks. Specifically, the average classification AUCs improve from 82.8% (SOTA using DenseNet-121) to 83.9% (SCALP using ResNet-50), while the localization results improve on average by 3.7% over different IoU thresholds.

Tingyi Wanyan, Jing Zhang, Ying Ding et al.

Electronic Health Record (EHR) data has been of tremendous utility in Artificial Intelligence (AI) for healthcare such as predicting future clinical events. These tasks, however, often come with many challenges when using classical machine learning models due to a myriad of factors including class imbalance and data heterogeneity (i.e., the complex intra-class variances). To address some of these research gaps, this paper leverages the exciting contrastive learning framework and proposes a novel contrastive regularized clinical classification model. The contrastive loss is found to substantially augment EHR-based prediction: it effectively characterizes the similar/dissimilar patterns (by its "push-and-pull" form), meanwhile mitigating the highly skewed class distribution by learning more balanced feature spaces (as also echoed by recent findings). In particular, when naively exporting the contrastive learning to the EHR data, one hurdle is in generating positive samples, since EHR data is not as amendable to data augmentation as image data. To this end, we have introduced two unique positive sampling strategies specifically tailored for EHR data: a feature-based positive sampling that exploits the feature space neighborhood structure to reinforce the feature learning; and an attribute-based positive sampling that incorporates pre-generated patient similarity metrics to define the sample proximity. Both sampling approaches are designed with an awareness of unique high intra-class variance in EHR data. Our overall framework yields highly competitive experimental results in predicting the mortality risk on real-world COVID-19 EHR data with a total of 5,712 patients admitted to a large, urban health system. Specifically, our method reaches a high AUROC prediction score of 0.959, which outperforms other baselines and alternatives: cross-entropy(0.873) and focal loss(0.931).

Yan Han, Chongyan Chen, Ahmed H Tewfik et al.

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. With the rise of deep learning, the explainability of deep neural networks on chest X-ray diagnosis remains opaque. In this study, we proposed a novel framework that leverages radiomics features and contrastive learning to detect pneumonia in chest X-ray. Experiments on the RSNA Pneumonia Detection Challenge dataset show that our model achieves superior results to several state-of-the-art models (> 10% in F1-score) and increases the model's interpretability.

Tingyi Wanyan, Hossein Honarvar, Suraj K. Jaladanki et al.

Machine Learning (ML) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing ML models for the coronavirus-disease 2019 (COVID-19) pandemic where data is highly imbalanced, particularly within electronic health records (EHR) research. Conventional approaches in ML use cross-entropy loss (CEL) that often suffers from poor margin classification. For the first time, we show that contrastive loss (CL) improves the performance of CEL especially for imbalanced EHR data and the related COVID-19 analyses. This study has been approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai. We use EHR data from five hospitals within the Mount Sinai Health System (MSHS) to predict mortality, intubation, and intensive care unit (ICU) transfer in hospitalized COVID-19 patients over 24 and 48 hour time windows. We train two sequential architectures (RNN and RETAIN) using two loss functions (CEL and CL). Models are tested on full sample data set which contain all available data and restricted data set to emulate higher class imbalance.CL models consistently outperform CEL models with the restricted data set on these tasks with differences ranging from 0.04 to 0.15 for AUPRC and 0.05 to 0.1 for AUROC. For the restricted sample, only the CL model maintains proper clustering and is able to identify important features, such as pulse oximetry. CL outperforms CEL in instances of severe class imbalance, on three EHR outcomes with respect to three performance metrics: predictive power, clustering, and feature importance. We believe that the developed CL framework can be expanded and used for EHR ML work in general.

Tingyi Wanyan, Hossein Honarvar, Ariful Azad et al.

Computational prediction of in-hospital mortality in the setting of an intensive care unit can help clinical practitioners to guide care and make early decisions for interventions. As clinical data are complex and varied in their structure and components, continued innovation of modeling strategies is required to identify architectures that can best model outcomes. In this work, we train a Heterogeneous Graph Model (HGM) on Electronic Health Record data and use the resulting embedding vector as additional information added to a Convolutional Neural Network (CNN) model for predicting in-hospital mortality. We show that the additional information provided by including time as a vector in the embedding captures the relationships between medical concepts, lab tests, and diagnoses, which enhances predictive performance. We find that adding HGM to a CNN model increases the mortality prediction accuracy up to 4\%. This framework serves as a foundation for future experiments involving different EHR data types on important healthcare prediction tasks.

Xuli Tang, Xin Li, Ying Ding et al.

This paper analyzes team collaboration in the field of Artificial Intelligence (AI) from the perspective of geographic distance. We obtained 1,584,175 AI related publications during 1950-2019 from the Microsoft Academic Graph. Three latitude-and-longitude-based indicators were employed to quantify the geographic distance of collaborations in AI over time at domestic and international levels. The results show team collaborations in AI has been more popular in the field over time with around 42,000 (38.4%) multiple-affiliation AI publications in 2019. The changes in geographic distances of team collaborations indicate the increase of breadth and density for both domestic and international collaborations in AI over time. In addition, the United States produced the largest number of single-country and internationally collaborated AI publications, and China has played an important role in international collaborations in AI after 2010.

Islam Akef Ebeid, Majdi Hassan, Tingyi Wanyan et al.

Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug discovery rely on incorporating information from different biomedical databases. These databases contain various biological entities and relations such as proteins (PDB), genes (Gene Ontology), drugs (DrugBank), diseases (DDB), and protein-protein interactions (BioGRID). The process of semantically integrating heterogeneous biomedical databases is often riddled with imperfections. The quality of data-driven drug discovery relies on the accuracy of the mining methods used and the data's quality as well. Thus, having complete and refined biomedical knowledge graphs is central to achieving more accurate drug discovery outcomes. Here we propose using the latest graph representation learning and embedding models to refine and complete biomedical knowledge graphs. This preliminary work demonstrates learning discrete representations of the integrated biomedical knowledge graph Chem2Bio2RD [3]. We perform a knowledge graph completion and refinement task using a simple top-K cosine similarity measure between the learned embedding vectors to predict missing links between drugs and targets present in the data. We show that this simple procedure can be used alternatively to binary classifiers in link prediction.

Chongyan Chen, Islam Akef Ebeid, Yi Bu et al.

The emergence of the novel COVID-19 pandemic has had a significant impact on global healthcare and the economy over the past few months. The virus's rapid widespread has led to a proliferation in biomedical research addressing the pandemic and its related topics. One of the essential Knowledge Discovery tools that could help the biomedical research community understand and eventually find a cure for COVID-19 are Knowledge Graphs. The CORD-19 dataset is a collection of publicly available full-text research articles that have been recently published on COVID-19 and coronavirus topics. Here, we use several Machine Learning, Deep Learning, and Knowledge Graph construction and mining techniques to formalize and extract insights from the PubMed dataset and the CORD-19 dataset to identify COVID-19 related experts and bio-entities. Besides, we suggest possible techniques to predict related diseases, drug candidates, gene, gene mutations, and related compounds as part of a systematic effort to apply Knowledge Discovery methods to help biomedical researchers tackle the pandemic.

Tingyi Wanyan, Chenwei Zhang, Ariful Azad et al.

We present a multi-filtering Graph Convolution Neural Network (GCN) framework for network embedding task. It uses multiple local GCN filters to do feature extraction in every propagation layer. We show this approach could capture different important aspects of node features against the existing attribute embedding based method. We also show that with multi-filtering GCN approach, we can achieve significant improvement against baseline methods when training data is limited. We also perform many empirical experiments and demonstrate the benefit of using multiple filters against single filter as well as most current existing network embedding methods for both the link prediction and node classification tasks.

Chao Lu, Yi Bu, Xianlei Dong et al.

The number of publications and the number of citations received have become the most common indicators of scholarly success. In this context, scientific writing increasingly plays an important role in scholars' scientific careers. To understand the relationship between scientific writing and scientific impact, this paper selected 12 variables of linguistic complexity as a proxy for depicting scientific writing. We then analyzed these features from 36,400 full-text Biology articles and 1,797 full-text Psychology articles. These features were compared to the scientific impact of articles, grouped into high, medium, and low categories. The results suggested no practical significant relationship between linguistic complexity and citation strata in either discipline. This suggests that textual complexity plays little role in scientific impact in our data sets.

Zheng Gao, Gang Fu, Chunping Ouyang et al.

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.

Chao Lu, Yi Bu, Jie Wang et al.

Publishing articles in high-impact English journals is difficult for scholars around the world, especially for non-native English-speaking scholars (NNESs), most of whom struggle with proficiency in English. In order to uncover the differences in English scientific writing between native English-speaking scholars (NESs) and NNESs, we collected a large-scale data set containing more than 150,000 full-text articles published in PLoS between 2006 and 2015. We divided these articles into three groups according to the ethnic backgrounds of the first and corresponding authors, obtained by Ethnea, and examined the scientific writing styles in English from a two-fold perspective of linguistic complexity: (1) syntactic complexity, including measurements of sentence length and sentence complexity; and (2) lexical complexity, including measurements of lexical diversity, lexical density, and lexical sophistication. The observations suggest marginal differences between groups in syntactical and lexical complexity.

Zhiyong Cheng, Ying Ding, Lei Zhu et al.

Although latent factor models (e.g., matrix factorization) achieve good accuracy in rating prediction, they suffer from several problems including cold-start, non-transparency, and suboptimal recommendation for local users or items. In this paper, we employ textual review information with ratings to tackle these limitations. Firstly, we apply a proposed aspect-aware topic model (ATM) on the review text to model user preferences and item features from different aspects, and estimate the aspect importance of a user towards an item. The aspect importance is then integrated into a novel aspect-aware latent factor model (ALFM), which learns user's and item's latent factors based on ratings. In particular, ALFM introduces a weighted matrix to associate those latent factors with the same set of aspects discovered by ATM, such that the latent factors could be used to estimate aspect ratings. Finally, the overall rating is computed via a linear combination of the aspect ratings, which are weighted by the corresponding aspect importance. To this end, our model could alleviate the data sparsity problem and gain good interpretability for recommendation. Besides, an aspect rating is weighted by an aspect importance, which is dependent on the targeted user's preferences and targeted item's features. Therefore, it is expected that the proposed method can model a user's preferences on an item more accurately for each user-item pair locally. Comprehensive experimental studies have been conducted on 19 datasets from Amazon and Yelp 2017 Challenge dataset. Results show that our method achieves significant improvement compared with strong baseline methods, especially for users with only few ratings. Moreover, our model could interpret the recommendation results in depth.

Xiangnan Kong, Bokai Cao, Philip S. Yu et al.

Collective classification has been intensively studied due to its impact in many important applications, such as web mining, bioinformatics and citation analysis. Collective classification approaches exploit the dependencies of a group of linked objects whose class labels are correlated and need to be predicted simultaneously. In this paper, we focus on studying the collective classification problem in heterogeneous networks, which involves multiple types of data objects interconnected by multiple types of links. Intuitively, two objects are correlated if they are linked by many paths in the network. However, most existing approaches measure the dependencies among objects through directly links or indirect links without considering the different semantic meanings behind different paths. In this paper, we study the collective classification problem taht is defined among the same type of objects in heterogenous networks. Moreover, by considering different linkage paths in the network, one can capture the subtlety of different types of dependencies among objects. We introduce the concept of meta-path based dependencies among objects, where a meta path is a path consisting a certain sequence of linke types. We show that the quality of collective classification results strongly depends upon the meta paths used. To accommodate the large network size, a novel solution, called HCC (meta-path based Heterogenous Collective Classification), is developed to effectively assign labels to a group of instances that are interconnected through different meta-paths. The proposed HCC model can capture different types of dependencies among objects with respect to different meta paths. Empirical studies on real-world networks demonstrate that effectiveness of the proposed meta path-based collective classification approach.

Daifeng Li, Ying Ding, Xin Shuai et al.

Mining user opinion from Micro-Blogging has been extensively studied on the most popular social networking sites such as Twitter and Facebook in the U.S., but few studies have been done on Micro-Blogging websites in other countries (e.g. China). In this paper, we analyze the social opinion influence on Tencent, one of the largest Micro-Blogging websites in China, endeavoring to unveil the behavior patterns of Chinese Micro-Blogging users. This paper proposes a Topic-Level Opinion Influence Model (TOIM) that simultaneously incorporates topic factor and social direct influence in a unified probabilistic framework. Based on TOIM, two topic level opinion influence propagation and aggregation algorithms are developed to consider the indirect influence: CP (Conservative Propagation) and NCP (None Conservative Propagation). Users' historical social interaction records are leveraged by TOIM to construct their progressive opinions and neighbors' opinion influence through a statistical learning process, which can be further utilized to predict users' future opinions on some specific topics. To evaluate and test this proposed model, an experiment was designed and a sub-dataset from Tencent Micro-Blogging was used. The experimental results show that TOIM outperforms baseline methods on predicting users' opinion. The applications of CP and NCP have no significant differences and could significantly improve recall and F1-measure of TOIM.