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Integrating multi-modal clinical data, such as electronic health records (EHR) and chest X-ray images (CXR), is particularly beneficial for clinical prediction tasks. However, in a temporal setting, multi-modal data are often inherently asynchronous. EHR can be continuously collected but CXR is generally taken with a much longer interval due to its high cost and radiation dose. When clinical prediction is needed, the last available CXR image might have been outdated, leading to suboptimal predictions. To address this challenge, we propose DDL-CXR, a method that dynamically generates an up-to-date latent representation of the individualized CXR images. Our approach leverages latent diffusion models for patient-specific generation strategically conditioned on a previous CXR image and EHR time series, providing information regarding anatomical structures and disease progressions, respectively. In this way, the interaction across modalities could be better captured by the latent CXR generation process, ultimately improving the prediction performance. Experiments using MIMIC datasets show that the proposed model could effectively address asynchronicity in multimodal fusion and consistently outperform existing methods., Comment: Accepted by NeurIPS-24

As the importance of comprehensive evaluation in workshop courses increases, there is a growing demand for efficient and fair assessment methods that reduce the workload for faculty members. This paper presents an evaluation conducted with Large Language Models (LLMs) using actual student essays in three scenarios: 1) without providing guidance such as rubrics, 2) with pre-specified rubrics, and 3) through pairwise comparison of essays. Quantitative analysis of the results revealed a strong correlation between LLM and faculty member assessments in the pairwise comparison scenario with pre-specified rubrics, although concerns about the quality and stability of evaluations remained. Therefore, we conducted a qualitative analysis of LLM assessment comments, showing that: 1) LLMs can match the assessment capabilities of faculty members, 2) variations in LLM assessments should be interpreted as diversity rather than confusion, and 3) assessments by humans and LLMs can differ and complement each other. In conclusion, this paper suggests that LLMs should not be seen merely as assistants to faculty members but as partners in evaluation committees and outlines directions for further research.

The combination of electronic health records (EHR) and medical images is crucial for clinicians in making diagnoses and forecasting prognosis. Strategically fusing these two data modalities has great potential to improve the accuracy of machine learning models in clinical prediction tasks. However, the asynchronous and complementary nature of EHR and medical images presents unique challenges. Missing modalities due to clinical and administrative factors are inevitable in practice, and the significance of each data modality varies depending on the patient and the prediction target, resulting in inconsistent predictions and suboptimal model performance. To address these challenges, we propose DrFuse to achieve effective clinical multi-modal fusion. It tackles the missing modality issue by disentangling the features shared across modalities and those unique within each modality. Furthermore, we address the modal inconsistency issue via a disease-wise attention layer that produces the patient- and disease-wise weighting for each modality to make the final prediction. We validate the proposed method using real-world large-scale datasets, MIMIC-IV and MIMIC-CXR. Experimental results show that the proposed method significantly outperforms the state-of-the-art models. Our implementation is publicly available at https://github.com/dorothy-yao/drfuse., Comment: Accepted by AAAI-24

Aligning users across networks using graph representation learning has been found effective where the alignment is accomplished in a low-dimensional embedding space. Yet, achieving highly precise alignment is still challenging, especially when nodes with long-range connectivity to the labeled anchors are encountered. To alleviate this limitation, we purposefully designed WL-Align which adopts a regularized representation learning framework to learn distinctive node representations. It extends the Weisfeiler-Lehman Isormorphism Test and learns the alignment in alternating phases of "across-network Weisfeiler-Lehman relabeling" and "proximity-preserving representation learning". The across-network Weisfeiler-Lehman relabeling is achieved through iterating the anchor-based label propagation and a similarity-based hashing to exploit the known anchors' connectivity to different nodes in an efficient and robust manner. The representation learning module preserves the second-order proximity within individual networks and is regularized by the across-network Weisfeiler-Lehman hash labels. Extensive experiments on real-world and synthetic datasets have demonstrated that our proposed WL-Align outperforms the state-of-the-art methods, achieving significant performance improvements in the "exact matching" scenario. Data and code of WL-Align are available at https://github.com/ChenPengGang/WLAlignCode.

Automatic generation of medical reports from X-ray images can assist radiologists to perform the time-consuming and yet important reporting task. Yet, achieving clinically accurate generated reports remains challenging. Modeling the underlying abnormalities using the knowledge graph approach has been found promising in enhancing the clinical accuracy. In this paper, we introduce a novel fined-grained knowledge graph structure called an attributed abnormality graph (ATAG). The ATAG consists of interconnected abnormality nodes and attribute nodes, allowing it to better capture the abnormality details. In contrast to the existing methods where the abnormality graph was constructed manually, we propose a methodology to automatically construct the fine-grained graph structure based on annotations, medical reports in X-ray datasets, and the RadLex radiology lexicon. We then learn the ATAG embedding using a deep model with an encoder-decoder architecture for the report generation. In particular, graph attention networks are explored to encode the relationships among the abnormalities and their attributes. A gating mechanism is adopted and integrated with various decoders for the generation. We carry out extensive experiments based on the benchmark datasets, and show that the proposed ATAG-based deep model outperforms the SOTA methods by a large margin and can improve the clinical accuracy of the generated reports., Comment: 14 pages, 7 figures

Social network alignment aims at aligning person identities across social networks. Embedding based models have been shown effective for the alignment where the structural proximity preserving objective is typically adopted for the model training. With the observation that ``overly-close'' user embeddings are unavoidable for such models causing alignment inaccuracy, we propose a novel learning framework which tries to enforce the resulting embeddings to be more widely apart among the users via the introduction of carefully implanted pseudo anchors. We further proposed a meta-learning algorithm to guide the updating of the pseudo anchor embeddings during the learning process. The proposed intervention via the use of pseudo anchors and meta-learning allows the learning framework to be applicable to a wide spectrum of network alignment methods. We have incorporated the proposed learning framework into several state-of-the-art models. Our experimental results demonstrate its efficacy where the methods with the pseudo anchors implanted can outperform their counterparts without pseudo anchors by a fairly large margin, especially when there only exist very few labeled anchors.

Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to those that can be cultured in the lab. But it excluded a huge portion of the microbiome that could not survive on lab conditions. In the past few years, the culture-independent metagenomic sequencing enabled us to explore the complex microbial community coexisting within and on us. Metagenomics has equipped us with new avenues of investigating the microbiome, from studying a single species to a complex community in a dynamic ecosystem. Thus, identifying the involved microbes and their genomes becomes one of the core tasks in metagenomic sequencing. Metagenome-assembled genomes are groups of contigs with similar sequence characteristics from de novo assembly and could represent the microbial genomes from metagenomic sequencing. In this paper, we reviewed a spectrum of tools for producing and annotating metagenome-assembled genomes from metagenomic sequencing data and discussed their technical and biological perspectives.

In few-shot domain adaptation (FDA), classifiers for the target domain are trained with accessible labeled data in the source domain (SD) and few labeled data in the target domain (TD). However, data usually contain private information in the current era, e.g., data distributed on personal phones. Thus, the private information will be leaked if we directly access data in SD to train a target-domain classifier (required by FDA methods). In this paper, to thoroughly prevent the privacy leakage in SD, we consider a very challenging problem setting, where the classifier for the TD has to be trained using few labeled target data and a well-trained SD classifier, named few-shot hypothesis adaptation (FHA). In FHA, we cannot access data in SD, as a result, the private information in SD will be protected well. To this end, we propose a target orientated hypothesis adaptation network (TOHAN) to solve the FHA problem, where we generate highly-compatible unlabeled data (i.e., an intermediate domain) to help train a target-domain classifier. TOHAN maintains two deep networks simultaneously, where one focuses on learning an intermediate domain and the other takes care of the intermediate-to-target distributional adaptation and the target-risk minimization. Experimental results show that TOHAN outperforms competitive baselines significantly.

In semantic segmentation, we aim to train a pixel-level classifier to assign category labels to all pixels in an image, where labeled training images and unlabeled test images are from the same distribution and share the same label set. However, in an open world, the unlabeled test images probably contain unknown categories and have different distributions from the labeled images. Hence, in this paper, we consider a new, more realistic, and more challenging problem setting where the pixel-level classifier has to be trained with labeled images and unlabeled open-world images -- we name it open-set domain adaptation segmentation (OSDAS). In OSDAS, the trained classifier is expected to identify unknown-class pixels and classify known-class pixels well. To solve OSDAS, we first investigate which distribution that unknown-class pixels obey. Then, motivated by the goodness-of-fit test, we use statistical measurements to show how a pixel fits the distribution of an unknown class and select highly-fitted pixels to form the unknown region in each test image. Eventually, we propose an end-to-end learning framework, known-region-aware domain alignment (KRADA), to distinguish unknown classes while aligning the distributions of known classes in labeled and unlabeled open-world images. The effectiveness of KRADA has been verified on two synthetic tasks and one COVID-19 segmentation task., Comment: 18 pages

Non-negative tensor factorization has been shown a practical solution to automatically discover phenotypes from the electronic health records (EHR) with minimal human supervision. Such methods generally require an input tensor describing the inter-modal interactions to be pre-established; however, the correspondence between different modalities (e.g., correspondence between medications and diagnoses) can often be missing in practice. Although heuristic methods can be applied to estimate them, they inevitably introduce errors, and leads to sub-optimal phenotype quality. This is particularly important for patients with complex health conditions (e.g., in critical care) as multiple diagnoses and medications are simultaneously present in the records. To alleviate this problem and discover phenotypes from EHR with unobserved inter-modal correspondence, we propose the collective hidden interaction tensor factorization (cHITF) to infer the correspondence between multiple modalities jointly with the phenotype discovery. We assume that the observed matrix for each modality is marginalization of the unobserved inter-modal correspondence, which are reconstructed by maximizing the likelihood of the observed matrices. Extensive experiments conducted on the real-world MIMIC-III dataset demonstrate that cHITF effectively infers clinically meaningful inter-modal correspondence, discovers phenotypes that are more clinically relevant and diverse, and achieves better predictive performance compared with a number of state-of-the-art computational phenotyping models., Comment: Accepted by IEEE Transactions on Knowledge and Data Engineering (TKDE)

Data summarization that presents a small subset of a dataset to users has been widely applied in numerous applications and systems. Many datasets are coded with hierarchical terminologies, e.g., the international classification of Diseases-9, Medical Subject Heading, and Gene Ontology, to name a few. In this paper, we study the problem of selecting a diverse set of k elements to summarize an input dataset with hierarchical terminologies, and visualize the summary in an ontology structure. We propose an efficient greedy algorithm to solve the problem with (1-1/e) = 62% -approximation guarantee. Although this greedy solution achieves quality-guaranteed answers approximately but it is still not optimal. To tackle the problem optimally, we further develop a dynamic programming algorithm to obtain optimal answers for graph visualization of log-data using ontology terminologies called OVDO . The complexity and correctness of OVDO are theoretically analyzed. In addition, we propose a useful optimization technique of tree reduction to remove useless nodes with zero weights and shrink the tree into a smaller one, which ensures the efficiency acceleration of OVDO in many real-world applications. Extensive experimental results on real-world datasets show the effectiveness and efficiency of our proposed approximate and exact algorithms for tree data summarization.

Most of the existing multi-relational network embedding methods, e.g., TransE, are formulated to preserve pair-wise connectivity structures in the networks. With the observations that significant triangular connectivity structures and parallelogram connectivity structures found in many real multi-relational networks are often ignored and that a hard-constraint commonly adopted by most of the network embedding methods is inaccurate by design, we propose a novel representation learning model for multi-relational networks which can alleviate both fundamental limitations. Scalable learning algorithms are derived using the stochastic gradient descent algorithm and negative sampling. Extensive experiments on real multi-relational network datasets of WordNet and Freebase demonstrate the efficacy of the proposed model when compared with the state-of-the-art embedding methods.

Semi-supervised learning plays an important role in large-scale machine learning. Properly using additional unlabeled data (largely available nowadays) often can improve the machine learning accuracy. However, if the machine learning model is misspecified for the underlying true data distribution, the model performance could be seriously jeopardized. This issue is known as model misspecification. To address this issue, we focus on generative models and propose a criterion to detect the onset of model misspecification by measuring the performance difference between models obtained using supervised and semi-supervised learning. Then, we propose to automatically modify the generative models during model training to achieve an unbiased generative model. Rigorous experiments were carried out to evaluate the proposed method using two image classification data sets PASCAL VOC'07 and MIR Flickr. Our proposed method has been demonstrated to outperform a number of state-of-the-art semi-supervised learning approaches for the classification task.

Authorship analysis (AA) is the study of unveiling the hidden properties of authors from a body of exponentially exploding textual data. It extracts an author's identity and sociolinguistic characteristics based on the reflected writing styles in the text. It is an essential process for various areas, such as cybercrime investigation, psycholinguistics, political socialization, etc. However, most of the previous techniques critically depend on the manual feature engineering process. Consequently, the choice of feature set has been shown to be scenario- or dataset-dependent. In this paper, to mimic the human sentence composition process using a neural network approach, we propose to incorporate different categories of linguistic features into distributed representation of words in order to learn simultaneously the writing style representations based on unlabeled texts for authorship analysis. In particular, the proposed models allow topical, lexical, syntactical, and character-level feature vectors of each document to be extracted as stylometrics. We evaluate the performance of our approach on the problems of authorship characterization and authorship verification with the Twitter, novel, and essay datasets. The experiments suggest that our proposed text representation outperforms the bag-of-lexical-n-grams, Latent Dirichlet Allocation, Latent Semantic Analysis, PVDM, PVDBOW, and word2vec representations.

This paper studies the topic modeling problem of tagged documents and images. Higher-order relations among tagged documents and images are major and ubiquitous characteristics, and play positive roles in extracting reliable and interpretable topics. In this paper, we propose the tag-topic models (TTM) to depict such higher-order topic structural dependencies within the Markov random field (MRF) framework. First, we use the novel factor graph representation of latent Dirichlet allocation (LDA)-based topic models from the MRF perspective, and present an efficient loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Second, we propose the factor hypergraph representation of TTM, and focus on both pairwise and higher-order relation modeling among tagged documents and images. Efficient loopy BP algorithm is developed to learn TTM, which encourages the topic labeling smoothness among tagged documents and images. Extensive experimental results confirm the incorporation of higher-order relations to be effective in enhancing the overall topic modeling performance, when compared with current state-of-the-art topic models, in many text and image mining tasks of broad interests such as word and link prediction, document classification, and tag recommendation., Comment: 13 pages, 9 figures

Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interests and touches on many important applications in text mining, computer vision and computational biology. This paper represents LDA as a factor graph within the Markov random field (MRF) framework, which enables the classic loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Although two commonly-used approximate inference methods, such as variational Bayes (VB) and collapsed Gibbs sampling (GS), have gained great successes in learning LDA, the proposed BP is competitive in both speed and accuracy as validated by encouraging experimental results on four large-scale document data sets. Furthermore, the BP algorithm has the potential to become a generic learning scheme for variants of LDA-based topic models. To this end, we show how to learn two typical variants of LDA-based topic models, such as author-topic models (ATM) and relational topic models (RTM), using BP based on the factor graph representation., Comment: 14 pages, 17 figures