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Yifan Peng

Publications and source records attributed to Yifan Peng.

At least 163 records · Page 9Linked to original sources
arXiv2023

An empirical study of using radiology reports and images to improve ICU mortality prediction

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%).

cs.AI↗
arXiv2023

Reducing Barriers to Self-Supervised Learning: HuBERT Pre-training with Academic Compute

Self-supervised learning (SSL) has led to great strides in speech processing. However, the resources needed to train these models has become prohibitively large as they continue to scale. Currently, only a few groups with substantial resources are capable of creating SSL models, which harms reproducibility. In this work, we optimize HuBERT SSL to fit in academic constraints. We reproduce HuBERT independently from the original implementation, with no performance loss. Our code and training optimizations make SSL feasible with only 8 GPUs, instead of the 32 used in the original work. We also explore a semi-supervised route, using an ASR model to skip the first pre-training iteration. Within one iteration of pre-training, our models improve over HuBERT on several tasks. Furthermore, our HuBERT Large variant requires only 8 GPUs, achieving similar performance to the original trained on 128. As our contribution to the community, all models, configurations, and code are made open-source in ESPnet.

cs.CL↗
arXiv2023

Tensor decomposition for minimization of E2E SLU model toward on-device processing

Spoken Language Understanding (SLU) is a critical speech recognition application and is often deployed on edge devices. Consequently, on-device processing plays a significant role in the practical implementation of SLU. This paper focuses on the end-to-end (E2E) SLU model due to its small latency property, unlike a cascade system, and aims to minimize the computational cost. We reduce the model size by applying tensor decomposition to the Conformer and E-Branchformer architectures used in our E2E SLU models. We propose to apply singular value decomposition to linear layers and the Tucker decomposition to convolution layers, respectively. We also compare COMP/PARFAC decomposition and Tensor-Train decomposition to the Tucker decomposition. Since the E2E model is represented by a single neural network, our tensor decomposition can flexibly control the number of parameters without changing feature dimensions. On the STOP dataset, we achieved 70.9% exact match accuracy under the tight constraint of only 15 million parameters.

eess.AS↗
arXiv2023

Less Likely Brainstorming: Using Language Models to Generate Alternative Hypotheses

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.

cs.CL↗
arXiv2023

DPHuBERT: Joint Distillation and Pruning of Self-Supervised Speech Models

Self-supervised learning (SSL) has achieved notable success in many speech processing tasks, but the large model size and heavy computational cost hinder the deployment. Knowledge distillation trains a small student model to mimic the behavior of a large teacher model. However, the student architecture usually needs to be manually designed and will remain fixed during training, which requires prior knowledge and can lead to suboptimal performance. Inspired by recent success of task-specific structured pruning, we propose DPHuBERT, a novel task-agnostic compression method for speech SSL based on joint distillation and pruning. Experiments on SUPERB show that DPHuBERT outperforms pure distillation methods in almost all tasks. Moreover, DPHuBERT requires little training time and performs well with limited training data, making it suitable for resource-constrained applications. Our method can also be applied to various speech SSL models. Our code and models will be publicly available.

cs.CL↗
arXiv2023

A Comparative Study on E-Branchformer vs Conformer in Speech Recognition, Translation, and Understanding Tasks

Conformer, a convolution-augmented Transformer variant, has become the de facto encoder architecture for speech processing due to its superior performance in various tasks, including automatic speech recognition (ASR), speech translation (ST) and spoken language understanding (SLU). Recently, a new encoder called E-Branchformer has outperformed Conformer in the LibriSpeech ASR benchmark, making it promising for more general speech applications. This work compares E-Branchformer and Conformer through extensive experiments using different types of end-to-end sequence-to-sequence models. Results demonstrate that E-Branchformer achieves comparable or better performance than Conformer in almost all evaluation sets across 15 ASR, 2 ST, and 3 SLU benchmarks, while being more stable during training. We will release our training configurations and pre-trained models for reproducibility, which can benefit the speech community.

cs.CL↗
arXiv2023

SODA: A Natural Language Processing Package to Extract Social Determinants of Health for Cancer Studies

Objective: We aim to develop an open-source natural language processing (NLP) package, SODA (i.e., SOcial DeterminAnts), with pre-trained transformer models to extract social determinants of health (SDoH) for cancer patients, examine the generalizability of SODA to a new disease domain (i.e., opioid use), and evaluate the extraction rate of SDoH using cancer populations. Methods: We identified SDoH categories and attributes and developed an SDoH corpus using clinical notes from a general cancer cohort. We compared four transformer-based NLP models to extract SDoH, examined the generalizability of NLP models to a cohort of patients prescribed with opioids, and explored customization strategies to improve performance. We applied the best NLP model to extract 19 categories of SDoH from the breast (n=7,971), lung (n=11,804), and colorectal cancer (n=6,240) cohorts. Results and Conclusion: We developed a corpus of 629 cancer patients notes with annotations of 13,193 SDoH concepts/attributes from 19 categories of SDoH. The Bidirectional Encoder Representations from Transformers (BERT) model achieved the best strict/lenient F1 scores of 0.9216 and 0.9441 for SDoH concept extraction, 0.9617 and 0.9626 for linking attributes to SDoH concepts. Fine-tuning the NLP models using new annotations from opioid use patients improved the strict/lenient F1 scores from 0.8172/0.8502 to 0.8312/0.8679. The extraction rates among 19 categories of SDoH varied greatly, where 10 SDoH could be extracted from >70% of cancer patients, but 9 SDoH had a low extraction rate (<70% of cancer patients). The SODA package with pre-trained transformer models is publicly available at https://github.com/uf-hobiinformatics-lab/SDoH_SODA.

cs.CL↗
arXiv2023

The Pipeline System of ASR and NLU with MLM-based Data Augmentation toward STOP Low-resource Challenge

This paper describes our system for the low-resource domain adaptation track (Track 3) in Spoken Language Understanding Grand Challenge, which is a part of ICASSP Signal Processing Grand Challenge 2023. In the track, we adopt a pipeline approach of ASR and NLU. For ASR, we fine-tune Whisper for each domain with upsampling. For NLU, we fine-tune BART on all the Track3 data and then on low-resource domain data. We apply masked LM (MLM) -based data augmentation, where some of input tokens and corresponding target labels are replaced using MLM. We also apply a retrieval-based approach, where model input is augmented with similar training samples. As a result, we achieved exact match (EM) accuracy 63.3/75.0 (average: 69.15) for reminder/weather domain, and won the 1st place at the challenge.

cs.CL↗
arXiv2023

A Study on the Integration of Pipeline and E2E SLU systems for Spoken Semantic Parsing toward STOP Quality Challenge

Recently there have been efforts to introduce new benchmark tasks for spoken language understanding (SLU), like semantic parsing. In this paper, we describe our proposed spoken semantic parsing system for the quality track (Track 1) in Spoken Language Understanding Grand Challenge which is part of ICASSP Signal Processing Grand Challenge 2023. We experiment with both end-to-end and pipeline systems for this task. Strong automatic speech recognition (ASR) models like Whisper and pretrained Language models (LM) like BART are utilized inside our SLU framework to boost performance. We also investigate the output level combination of various models to get an exact match accuracy of 80.8, which won the 1st place at the challenge.

cs.CL↗
arXiv2023

FactReranker: Fact-guided Reranker for Faithful Radiology Report Summarization

Automatic radiology report summarization is a crucial clinical task, whose key challenge is to maintain factual accuracy between produced summaries and ground truth radiology findings. Existing research adopts reinforcement learning to directly optimize factual consistency metrics such as CheXBert or RadGraph score. However, their decoding method using greedy search or beam search considers no factual consistency when picking the optimal candidate, leading to limited factual consistency improvement. To address it, we propose a novel second-stage summarizing approach FactReranker, the first attempt that learns to choose the best summary from all candidates based on their estimated factual consistency score. We propose to extract medical facts of the input medical report, its gold summary, and candidate summaries based on the RadGraph schema and design the fact-guided reranker to efficiently incorporate the extracted medical facts for selecting the optimal summary. We decompose the fact-guided reranker into the factual knowledge graph generation and the factual scorer, which allows the reranker to model the mapping between the medical facts of the input text and its gold summary, thus can select the optimal summary even the gold summary can't be observed during inference. We also present a fact-based ranking metric (RadMRR) for measuring the ability of the reranker on selecting factual consistent candidates. Experimental results on two benchmark datasets demonstrate the superiority of our method in generating summaries with higher factual consistency scores when compared with existing methods.

cs.CL↗
arXiv2023

Learning a Room with the Occ-SDF Hybrid: Signed Distance Function Mingled with Occupancy Aids Scene Representation

Implicit neural rendering, which uses signed distance function (SDF) representation with geometric priors (such as depth or surface normal), has led to impressive progress in the surface reconstruction of large-scale scenes. However, applying this method to reconstruct a room-level scene from images may miss structures in low-intensity areas or small and thin objects. We conducted experiments on three datasets to identify limitations of the original color rendering loss and priors-embedded SDF scene representation. We found that the color rendering loss results in optimization bias against low-intensity areas, causing gradient vanishing and leaving these areas unoptimized. To address this issue, we propose a feature-based color rendering loss that utilizes non-zero feature values to bring back optimization signals. Additionally, the SDF representation can be influenced by objects along a ray path, disrupting the monotonic change of SDF values when a single object is present. To counteract this, we explore using the occupancy representation, which encodes each point separately and is unaffected by objects along a querying ray. Our experimental results demonstrate that the joint forces of the feature-based rendering loss and Occ-SDF hybrid representation scheme can provide high-quality reconstruction results, especially in challenging room-level scenarios. The code would be released.

cs.CV↗
arXiv2023

I3D: Transformer architectures with input-dependent dynamic depth for speech recognition

Transformer-based end-to-end speech recognition has achieved great success. However, the large footprint and computational overhead make it difficult to deploy these models in some real-world applications. Model compression techniques can reduce the model size and speed up inference, but the compressed model has a fixed architecture which might be suboptimal. We propose a novel Transformer encoder with Input-Dependent Dynamic Depth (I3D) to achieve strong performance-efficiency trade-offs. With a similar number of layers at inference time, I3D-based models outperform the vanilla Transformer and the static pruned model via iterative layer pruning. We also present interesting analysis on the gate probabilities and the input-dependency, which helps us better understand deep encoders.

cs.CL↗
arXiv2023

Improving Massively Multilingual ASR With Auxiliary CTC Objectives

Multilingual Automatic Speech Recognition (ASR) models have extended the usability of speech technologies to a wide variety of languages. With how many languages these models have to handle, however, a key to understanding their imbalanced performance across different languages is to examine if the model actually knows which language it should transcribe. In this paper, we introduce our work on improving performance on FLEURS, a 102-language open ASR benchmark, by conditioning the entire model on language identity (LID). We investigate techniques inspired from recent Connectionist Temporal Classification (CTC) studies to help the model handle the large number of languages, conditioning on the LID predictions of auxiliary tasks. Our experimental results demonstrate the effectiveness of our technique over standard CTC/Attention-based hybrid models. Furthermore, our state-of-the-art systems using self-supervised models with the Conformer architecture improve over the results of prior work on FLEURS by a relative 28.4% CER. Trained models and reproducible recipes are available at https://github.com/espnet/espnet/tree/master/egs2/fleurs/asr1 .

cs.CL↗
arXiv2023

Structured Pruning of Self-Supervised Pre-trained Models for Speech Recognition and Understanding

Self-supervised speech representation learning (SSL) has shown to be effective in various downstream tasks, but SSL models are usually large and slow. Model compression techniques such as pruning aim to reduce the model size and computation without degradation in accuracy. Prior studies focus on the pruning of Transformers; however, speech models not only utilize a stack of Transformer blocks, but also combine a frontend network based on multiple convolutional layers for low-level feature representation learning. This frontend has a small size but a heavy computational cost. In this work, we propose three task-specific structured pruning methods to deal with such heterogeneous networks. Experiments on LibriSpeech and SLURP show that the proposed method is more accurate than the original wav2vec2-base with 10% to 30% less computation, and is able to reduce the computation by 40% to 50% without any degradation.

cs.CL↗
arXiv2023

Evaluate underdiagnosis and overdiagnosis bias of deep learning model on primary open-angle glaucoma diagnosis in under-served patient populations

In the United States, primary open-angle glaucoma (POAG) is the leading cause of blindness, especially among African American and Hispanic individuals. Deep learning has been widely used to detect POAG using fundus images as its performance is comparable to or even surpasses diagnosis by clinicians. However, human bias in clinical diagnosis may be reflected and amplified in the widely-used deep learning models, thus impacting their performance. Biases may cause (1) underdiagnosis, increasing the risks of delayed or inadequate treatment, and (2) overdiagnosis, which may increase individuals' stress, fear, well-being, and unnecessary/costly treatment. In this study, we examined the underdiagnosis and overdiagnosis when applying deep learning in POAG detection based on the Ocular Hypertension Treatment Study (OHTS) from 22 centers across 16 states in the United States. Our results show that the widely-used deep learning model can underdiagnose or overdiagnose underserved populations. The most underdiagnosed group is female younger (< 60 yrs) group, and the most overdiagnosed group is Black older (>=60 yrs) group. Biased diagnosis through traditional deep learning methods may delay disease detection, treatment and create burdens among under-served populations, thereby, raising ethical concerns about using deep learning models in ophthalmology clinics.

cs.CV↗
arXiv2022

SpeechLMScore: Evaluating speech generation using speech language model

While human evaluation is the most reliable metric for evaluating speech generation systems, it is generally costly and time-consuming. Previous studies on automatic speech quality assessment address the problem by predicting human evaluation scores with machine learning models. However, they rely on supervised learning and thus suffer from high annotation costs and domain-shift problems. We propose SpeechLMScore, an unsupervised metric to evaluate generated speech using a speech-language model. SpeechLMScore computes the average log-probability of a speech signal by mapping it into discrete tokens and measures the average probability of generating the sequence of tokens. Therefore, it does not require human annotation and is a highly scalable framework. Evaluation results demonstrate that the proposed metric shows a promising correlation with human evaluation scores on different speech generation tasks including voice conversion, text-to-speech, and speech enhancement.

eess.AS↗
arXiv2022

Attend Who is Weak: Pruning-assisted Medical Image Localization under Sophisticated and Implicit Imbalances

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\%.

cs.CV↗
arXiv2022

RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging

AI-powered Medical Imaging has recently achieved enormous attention due to its ability to provide fast-paced healthcare diagnoses. However, it usually suffers from a lack of high-quality datasets due to high annotation cost, inter-observer variability, human annotator error, and errors in computer-generated labels. Deep learning models trained on noisy labelled datasets are sensitive to the noise type and lead to less generalization on the unseen samples. To address this challenge, we propose a Robust Stochastic Knowledge Distillation (RoS-KD) framework which mimics the notion of learning a topic from multiple sources to ensure deterrence in learning noisy information. More specifically, RoS-KD learns a smooth, well-informed, and robust student manifold by distilling knowledge from multiple teachers trained on overlapping subsets of training data. Our extensive experiments on popular medical imaging classification tasks (cardiopulmonary disease and lesion classification) using real-world datasets, show the performance benefit of RoS-KD, its ability to distill knowledge from many popular large networks (ResNet-50, DenseNet-121, MobileNet-V2) in a comparatively small network, and its robustness to adversarial attacks (PGD, FSGM). More specifically, RoS-KD achieves >2% and >4% improvement on F1-score for lesion classification and cardiopulmonary disease classification tasks, respectively, when the underlying student is ResNet-18 against recent competitive knowledge distillation baseline. Additionally, on cardiopulmonary disease classification task, RoS-KD outperforms most of the SOTA baselines by ~1% gain in AUC score.

cs.CV↗