Yu‐Wen Chen

Helen Zhou, Yuwen Chen, Zachary C. Lipton

Machine learning models deployed in healthcare systems face data drawn from continually evolving environments. However, researchers proposing such models typically evaluate them in a time-agnostic manner, with train and test splits sampling patients throughout the entire study period. We introduce the Evaluation on Medical Datasets Over Time (EMDOT) framework and Python package, which evaluates the performance of a model class over time. Across five medical datasets and a variety of models, we compare two training strategies: (1) using all historical data, and (2) using a window of the most recent data. We note changes in performance over time, and identify possible explanations for these shocks.

Yuwen Chen, Helen Zhou, Zachary C. Lipton

Medical imaging data is often siloed within hospitals, limiting the amount of data available for specialized model development. With limited in-domain data, one might hope to leverage larger datasets from related domains. In this paper, we analyze the benefit of transferring self-supervised contrastive representations from moment contrast (MoCo) pretraining on out-of-distribution data to settings with limited data. We consider two X-ray datasets which image different parts of the body, and compare transferring from each other to transferring from ImageNet. We find that depending on quantity of labeled and unlabeled data, contrastive pretraining on larger out-of-distribution datasets can perform nearly as well or better than MoCo pretraining in-domain, and pretraining on related domains leads to higher performance than if one were to use the ImageNet pretrained weights. Finally, we provide a preliminary way of quantifying similarity between datasets.

Yu-Wen Chen, Hsin-Min Wang, Yu Tsao

The performance of speech-processing models is heavily influenced by the speech corpus that is used for training and evaluation. In this study, we propose BAlanced Script PROducer (BASPRO) system, which can automatically construct a phonetically balanced and rich set of Chinese sentences for collecting Mandarin Chinese speech data. First, we used pretrained natural language processing systems to extract ten-character candidate sentences from a large corpus of Chinese news texts. Then, we applied a genetic algorithm-based method to select 20 phonetically balanced sentence sets, each containing 20 sentences, from the candidate sentences. Using BASPRO, we obtained a recording script called TMNews, which contains 400 ten-character sentences. TMNews covers 84% of the syllables used in the real world. Moreover, the syllable distribution has 0.96 cosine similarity to the real-world syllable distribution. We converted the script into a speech corpus using two text-to-speech systems. Using the designed speech corpus, we tested the performances of speech enhancement (SE) and automatic speech recognition (ASR), which are one of the most important regression- and classification-based speech processing tasks, respectively. The experimental results show that the SE and ASR models trained on the designed speech corpus outperform their counterparts trained on a randomly composed speech corpus.

Hui Su, Xiao Zhou, Houjin Yu et al.

Large Language Models pre-trained with self-supervised learning have demonstrated impressive zero-shot generalization capabilities on a wide spectrum of tasks. In this work, we present WeLM: a well-read pre-trained language model for Chinese that is able to seamlessly perform different types of tasks with zero or few-shot demonstrations. WeLM is trained with 10B parameters by "reading" a curated high-quality corpus covering a wide range of topics. We show that WeLM is equipped with broad knowledge on various domains and languages. On 18 monolingual (Chinese) tasks, WeLM can significantly outperform existing pre-trained models with similar sizes and match the performance of models up to 25 times larger. WeLM also exhibits strong capabilities in multi-lingual and code-switching understanding, outperforming existing multilingual language models pre-trained on 30 languages. Furthermore, We collected human-written prompts for a large set of supervised datasets in Chinese and fine-tuned WeLM with multi-prompted training. The resulting model can attain strong generalization on unseen types of tasks and outperform the unsupervised WeLM in zero-shot learning. Finally, we demonstrate that WeLM has basic skills at explaining and calibrating the decisions from itself, which can be promising directions for future research. Our models can be applied from https://welm.weixin.qq.com/docs/api/.

Hsuan-Kung Yang, Tsu-Ching Hsiao, Ting-Hsuan Liao et al.

In this paper, we introduce a new concept of incorporating factorized flow maps as mid-level representations, for bridging the perception and the control modules in modular learning based robotic frameworks. To investigate the advantages of factorized flow maps and examine their interplay with the other types of mid-level representations, we further develop a configurable framework, along with four different environments that contain both static and dynamic objects, for analyzing the impacts of factorized optical flow maps on the performance of deep reinforcement learning agents. Based on this framework, we report our experimental results on various scenarios, and offer a set of analyses to justify our hypothesis. Finally, we validate flow factorization in real world scenarios.

Ye Su, Hezhe Qiao, Di Wu et al.

The imputation of the Multivariate time series (MTS) is particularly challenging since the MTS typically contains irregular patterns of missing values due to various factors such as instrument failures, interference from irrelevant data, and privacy regulations. Existing statistical methods and deep learning methods have shown promising results in time series imputation. In this paper, we propose a Temporal Gaussian Copula Model (TGC) for three-order MTS imputation. The key idea is to leverage the Gaussian Copula to explore the cross-variable and temporal relationships based on the latent Gaussian representation. Subsequently, we employ an Expectation-Maximization (EM) algorithm to improve robustness in managing data with varying missing rates. Comprehensive experiments were conducted on three real-world MTS datasets. The results demonstrate that our TGC substantially outperforms the state-of-the-art imputation methods. Additionally, the TGC model exhibits stronger robustness to the varying missing ratios in the test dataset. Our code is available at https://github.com/MVL-Lab/TGC-MTS.

Haoyu Dong, Yuwen Chen, Hanxue Gu et al.

The widespread use of Magnetic Resonance Imaging (MRI) in combination with deep learning shows promise for many high-impact automated diagnostic and prognostic tools. However, training new models requires large amounts of labeled data, a challenge due to high cost of precise annotations and data privacy. To address this issue, we introduce the MRI-CORE, a vision foundation model trained using more than 6 million slices from over 110 thousand MRI volumes across 18 body locations. Our experiments show notable improvements in performance over state-of-the-art methods in 13 data-restricted segmentation tasks, as well as in image classification, and zero-shot segmentation, showing the strong potential of MRI-CORE to enable data-efficient development of artificial intelligence models. We also present data on which strategies yield most useful foundation models and a novel analysis relating similarity between pre-training and downstream task data with transfer learning performance. Our model is publicly available with a permissive license.

Nicholas Konz, Yuwen Chen, Hanxue Gu et al.

Modern medical image translation methods use generative models for tasks such as the conversion of CT images to MRI. Evaluating these methods typically relies on some chosen downstream task in the target domain, such as segmentation. On the other hand, task-agnostic metrics are attractive, such as the network feature-based perceptual metrics (e.g., FID) that are common to image translation in general computer vision. In this paper, we investigate evaluation metrics for medical image translation on two medical image translation tasks (GE breast MRI to Siemens breast MRI and lumbar spine MRI to CT), tested on various state-of-the-art translation methods. We show that perceptual metrics do not generally correlate with segmentation metrics due to them extending poorly to the anatomical constraints of this sub-field, with FID being especially inconsistent. However, we find that the lesser-used pixel-level SWD metric may be useful for subtle intra-modality translation. Our results demonstrate the need for further research into helpful metrics for medical image translation.

Yaqian Chen, Hanxue Gu, Haoyu Dong et al.

Accurately registering breast MR images from different time points enables the alignment of anatomical structures and tracking of tumor progression, supporting more effective breast cancer detection, diagnosis, and treatment planning. However, the complexity of dense tissue and its highly non-rigid nature pose challenges for conventional registration methods, which primarily focus on aligning general structures while overlooking intricate internal details. To address this, we propose \textbf{GuidedMorph}, a novel two-stage registration framework designed to better align dense tissue. In addition to a single-scale network for global structure alignment, we introduce a framework that utilizes dense tissue information to track breast movement. The learned transformation fields are fused by introducing the Dual Spatial Transformer Network (DSTN), improving overall alignment accuracy. A novel warping method based on the Euclidean distance transform (EDT) is also proposed to accurately warp the registered dense tissue and breast masks, preserving fine structural details during deformation. The framework supports paradigms that require external segmentation models and with image data only. It also operates effectively with the VoxelMorph and TransMorph backbones, offering a versatile solution for breast registration. We validate our method on ISPY2 and internal dataset, demonstrating superior performance in dense tissue, overall breast alignment, and breast structural similarity index measure (SSIM), with notable improvements by over 13.01% in dense tissue Dice, 3.13% in breast Dice, and 1.21% in breast SSIM compared to the best learning-based baseline.

Helen Zhou, Yuwen Chen, Zachary C. Lipton

Machine learning (ML) models deployed in healthcare systems must face data drawn from continually evolving environments. However, researchers proposing such models typically evaluate them in a time-agnostic manner, splitting datasets according to patients sampled randomly throughout the entire study time period. This work proposes the Evaluation on Medical Datasets Over Time (EMDOT) framework, which evaluates the performance of a model class across time. Inspired by the concept of backtesting, EMDOT simulates possible training procedures that practitioners might have been able to execute at each point in time and evaluates the resulting models on all future time points. Evaluating both linear and more complex models on six distinct medical data sources (tabular and imaging), we show how depending on the dataset, using all historical data may be ideal in many cases, whereas using a window of the most recent data could be advantageous in others. In datasets where models suffer from sudden degradations in performance, we investigate plausible explanations for these shocks. We release the EMDOT package to help facilitate further works in deployment-oriented evaluation over time.

Yu-Wen Chen, Yu Tsao

Speech intelligibility and quality assessment models are essential tools for researchers to evaluate and improve speech processing models. However, only a few studies have investigated multi-task models for intelligibility and quality assessment due to the limitations of available data. In this study, we released TMHINT-QI, the first Chinese speech dataset that records the quality and intelligibility scores of clean, noisy, and enhanced utterances. Then, we propose InQSS, a non-intrusive multi-task learning framework for intelligibility and quality assessment. We evaluated the InQSS on both the training-from-scratch and the pretrained models. The experimental results confirm the effectiveness of the InQSS framework. In addition, the resulting model can predict not only the intelligibility scores but also the quality scores of a speech signal.

Yu-Wen Chen, Kuo-Hsuan Hung, Shang-Yi Chuang et al.

Synthesized speech from articulatory movements can have real-world use for patients with vocal cord disorders, situations requiring silent speech, or in high-noise environments. In this work, we present EMA2S, an end-to-end multimodal articulatory-to-speech system that directly converts articulatory movements to speech signals. We use a neural-network-based vocoder combined with multimodal joint-training, incorporating spectrogram, mel-spectrogram, and deep features. The experimental results confirm that the multimodal approach of EMA2S outperforms the baseline system in terms of both objective evaluation and subjective evaluation metrics. Moreover, results demonstrate that joint mel-spectrogram and deep feature loss training can effectively improve system performance.