Electronic Health Record (EHR) provides abundant information through various modalities. However, learning multi-modal EHR is currently facing two major challenges, namely, 1) data embedding and 2) cases with missing modality. A lack of shared embedding function across modalities can discard the temporal relationship between different EHR modalities. On the other hand, most EHR studies are limited to relying only on EHR Times-series, and therefore, missing modality in EHR has not been well-explored. Therefore, in this study, we introduce a Unified Multi-modal Set Embedding (UMSE) and Modality-Aware Attention (MAA) with Skip Bottleneck (SB). UMSE treats all EHR modalities without a separate imputation module or error-prone carry-forward, whereas MAA with SB learns missing modal EHR with effective modality-aware attention. Our model outperforms other baseline models in mortality, vasopressor need, and intubation need prediction with the MIMIC-IV dataset.

Accurate time prediction of patients' critical events is crucial in urgent scenarios where timely decision-making is important. Though many studies have proposed automatic prediction methods using Electronic Health Records (EHR), their coarse-grained time resolutions limit their practical usage in urgent environments such as the emergency department (ED) and intensive care unit (ICU). Therefore, in this study, we propose an hourly prediction method based on self-supervised predictive coding and multi-modal fusion for two critical tasks: mortality and vasopressor need prediction. Through extensive experiments, we prove significant performance gains from both multi-modal fusion and self-supervised predictive regularization, most notably in far-future prediction, which becomes especially important in practice. Our uni-modal/bi-modal/bi-modal self-supervision scored 0.846/0.877/0.897

Generated synthetic data in medical research can substitute privacy and security-sensitive data with a large-scale curated dataset, reducing data collection and annotation costs. As part of this effort, we propose UniXGen, a unified chest X-ray and report generation model, with the following contributions. First, we design a unified model for bidirectional chest X-ray and report generation by adopting a vector quantization method to discretize chest X-rays into discrete visual tokens and formulating both tasks as sequence generation tasks. Second, we introduce several special tokens to generate chest X-rays with specific views that can be useful when the desired views are unavailable. Furthermore, UniXGen can flexibly take various inputs from single to multiple views to take advantage of the additional findings available in other X-ray views. We adopt an efficient transformer for computational and memory efficiency to handle the long-range input sequence of multi-view chest X-rays with high resolution and long paragraph reports. In extensive experiments, we show that our unified model has a synergistic effect on both generation tasks, as opposed to training only the task-specific models. We also find that view-specific special tokens can distinguish between different views and properly generate specific views even if they do not exist in the dataset, and utilizing multi-view chest X-rays can faithfully capture the abnormal findings in the additional X-rays. The source code is publicly available at: https://github.com/ttumyche/UniXGen.

Deep neural networks have been successfully adopted to diverse domains including pathology classification based on medical images. However, large-scale and high-quality data to train powerful neural networks are rare in the medical domain as the labeling must be done by qualified experts. Researchers recently tackled this problem with some success by taking advantage of models pre-trained on large-scale general domain data. Specifically, researchers took contrastive image-text encoders (e.g., CLIP) and fine-tuned it with chest X-ray images and paired reports to perform zero-shot pathology classification, thus completely removing the need for pathology-annotated images to train a classification model. Existing studies, however, fine-tuned the pre-trained model with the same contrastive learning objective, and failed to exploit the multi-labeled nature of medical image-report pairs. In this paper, we propose a new fine-tuning strategy based on sentence sampling and positive pair loss relaxation for improving the downstream zero-shot pathology classification performance, which can be applied to any pre-trained contrastive image-text encoders. Our method consistently showed dramatically improved zero-shot pathology classification performance on four different chest X-ray datasets and 3 different pre-trained models (5.77% average AUROC increase). In particular, fine-tuning CLIP with our method showed much comparable or marginally outperformed to board-certified radiologists (0.619 vs 0.625 in F1 score and 0.530 vs 0.544 in MCC) in zero-shot classification of five prominent diseases from the CheXpert dataset.

Electrocardiogram (ECG) synthesis is the area of research focused on generating realistic synthetic ECG signals for medical use without concerns over annotation costs or clinical data privacy restrictions. Traditional ECG generation models consider a single ECG lead and utilize GAN-based generative models. These models can only generate single lead samples and require separate training for each diagnosis class. The diagnosis classes of ECGs are insufficient to capture the intricate differences between ECGs depending on various features (e.g. patient demographic details, co-existing diagnosis classes, etc.). To alleviate these challenges, we present a text-to-ECG task, in which textual inputs are used to produce ECG outputs. Then we propose Auto-TTE, an autoregressive generative model conditioned on clinical text reports to synthesize 12-lead ECGs, for the first time to our knowledge. We compare the performance of our model with other representative models in text-to-speech and text-to-image. Experimental results show the superiority of our model in various quantitative evaluations and qualitative analysis. Finally, we conduct a user study with three board-certified cardiologists to confirm the fidelity and semantic alignment of generated samples. our code will be available at https://github.com/TClife/text_to_ecg

This is an exploratory study that discovers the current image quantization (vector quantization) do not satisfy translation equivariance in the quantized space due to aliasing. Instead of focusing on anti-aliasing, we propose a simple yet effective way to achieve translation-equivariant image quantization by enforcing orthogonality among the codebook embeddings. To explore the advantages of translation-equivariant image quantization, we conduct three proof-of-concept experiments with a carefully controlled dataset: (1) text-to-image generation, where the quantized image indices are the target to predict, (2) image-to-text generation, where the quantized image indices are given as a condition, (3) using a smaller training set to analyze sample efficiency. From the strictly controlled experiments, we empirically verify that the translation-equivariant image quantizer improves not only sample efficiency but also the accuracy over VQGAN up to +11.9% in text-to-image generation and +3.9% in image-to-text generation.

In order to perform unconditional video generation, we must learn the distribution of the real-world videos. In an effort to synthesize high-quality videos, various studies attempted to learn a mapping function between noise and videos, including recent efforts to separate motion distribution and appearance distribution. Previous methods, however, learn motion dynamics in discretized, fixed-interval timesteps, which is contrary to the continuous nature of motion of a physical body. In this paper, we propose a novel video generation approach that learns separate distributions for motion and appearance, the former modeled by neural ODE to learn natural motion dynamics. Specifically, we employ a two-stage approach where the first stage converts a noise vector to a sequence of keypoints in arbitrary frame rates, and the second stage synthesizes videos based on the given keypoints sequence and the appearance noise vector. Our model not only quantitatively outperforms recent baselines for video generation, but also demonstrates versatile functionality such as dynamic frame rate manipulation and motion transfer between two datasets, thus opening new doors to diverse video generation applications.

An intelligent machine that can answer human questions based on electronic health records (EHR-QA) has a great practical value, such as supporting clinical decisions, managing hospital administration, and medical chatbots. Previous table-based QA studies focusing on translating natural questions into table queries (NLQ2SQL), however, suffer from the unique nature of EHR data due to complex and specialized medical terminology, hence increased decoding difficulty. In this paper, we design UniQA, a unified encoder-decoder architecture for EHR-QA where natural language questions are converted to queries such as SQL or SPARQL. We also propose input masking (IM), a simple and effective method to cope with complex medical terms and various typos and better learn the SQL/SPARQL syntax. Combining the unified architecture with an effective auxiliary training objective, UniQA demonstrated a significant performance improvement against the previous state-of-the-art model for MIMICSQL* (14.2% gain), the most complex NLQ2SQL dataset in the EHR domain, and its typo-ridden versions (approximately 28.8% gain). In addition, we confirmed consistent results for the graph-based EHR-QA dataset, MIMICSPARQL*.

Generating accurate terminology is a crucial component for the practicality and reliability of neural machine translation (NMT) systems. To address this, lexically constrained NMT explores various methods to ensure pre-specified words and phrases to appear in the translations. In many cases, however, those methods are evaluated on general domain corpora, where the terms are mostly uni- and bi-grams (>98%). In this paper, we instead tackle a more challenging setup consisting of domain-specific corpora with much longer n-gram and highly specialized terms. To encourage span-level representations in generation, we additionally impose a source-sentence conditioned masked span prediction loss in the decoder and observe improvements on both terminology translation as well as BLEU scores. Experimental results on three domain-specific corpora in two language pairs demonstrate that the proposed training scheme can improve the performance of existing lexically constrained methods that can operate both with or without a term dictionary at test time.

Sophisticated cyber attacks have plagued many high-profile businesses. To remain aware of the fast-evolving threat landscape, open-source Cyber Threat Intelligence (OSCTI) has received growing attention from the community. Commonly, knowledge about threats is presented in a vast number of OSCTI reports. Despite the pressing need for high-quality OSCTI, existing OSCTI gathering and management platforms, however, have primarily focused on isolated, low-level Indicators of Compromise. On the other hand, higher-level concepts (e.g., adversary tactics, techniques, and procedures) and their relationships have been overlooked, which contain essential knowledge about threat behaviors that is critical to uncovering the complete threat scenario. To bridge the gap, we propose SecurityKG, a system for automated OSCTI gathering and management. SecurityKG collects OSCTI reports from various sources, uses a combination of AI and NLP techniques to extract high-fidelity knowledge about threat behaviors, and constructs a security knowledge graph. SecurityKG also provides a UI that supports various types of interactivity to facilitate knowledge graph exploration.