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Medical coding is the task of assigning medical codes to clinical free-text documentation. Healthcare professionals manually assign such codes to track patient diagnoses and treatments. Automated medical coding can considerably alleviate this administrative burden. In this paper, we reproduce, compare, and analyze state-of-the-art automated medical coding machine learning models. We show that several models underperform due to weak configurations, poorly sampled train-test splits, and insufficient evaluation. In previous work, the macro F1 score has been calculated sub-optimally, and our correction doubles it. We contribute a revised model comparison using stratified sampling and identical experimental setups, including hyperparameters and decision boundary tuning. We analyze prediction errors to validate and falsify assumptions of previous works. The analysis confirms that all models struggle with rare codes, while long documents only have a negligible impact. Finally, we present the first comprehensive results on the newly released MIMIC-IV dataset using the reproduced models. We release our code, model parameters, and new MIMIC-III and MIMIC-IV training and evaluation pipelines to accommodate fair future comparisons., Comment: 11 pages, 6 figures, to be published in Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '23), July 23--27, 2023, Taipei, Taiwan

Medical coding is the task of assigning medical codes to clinical free-text documentation. Healthcare professionals manually assign such codes to track patient diagnoses and treatments. Automated medical coding can considerably alleviate this administrative burden. In this paper, we reproduce, compare, and analyze state-of-the-art automated medical coding machine learning models. We show that several models underperform due to weak configurations, poorly sampled train-test splits, and insufficient evaluation. In previous work, the macro F1 score has been calculated sub-optimally, and our correction doubles it. We contribute a revised model comparison using stratified sampling and identical experimental setups, including hyperparameters and decision boundary tuning. We analyze prediction errors to validate and falsify assumptions of previous works. The analysis confirms that all models struggle with rare codes, while long documents only have a negligible impact. Finally, we present the first comprehensive results on the newly released MIMIC-IV dataset using the reproduced models. We release our code, model parameters, and new MIMIC-III and MIMIC-IV training and evaluation pipelines to accommodate fair future comparisons.

Medical coding is the task of assigning medical codes to clinical free-text documentation. Healthcare professionals manually assign such codes to track patient diagnoses and treatments. Automated medical coding can considerably alleviate this administrative burden. In this paper, we reproduce, compare, and analyze state-of-the-art automated medical coding machine learning models. We show that several models underperform due to weak configurations, poorly sampled train-test splits, and insufficient evaluation. In previous work, the macro F1 score has been calculated sub-optimally, and our correction doubles it. We contribute a revised model comparison using stratified sampling and identical experimental setups, including hyperparameters and decision boundary tuning. We analyze prediction errors to validate and falsify assumptions of previous works. The analysis confirms that all models struggle with rare codes, while long documents only have a negligible impact. Finally, we present the first comprehensive results on the newly released MIMIC-IV dataset using the reproduced models. We release our code, model parameters, and new MIMIC-III and MIMIC-IV training and evaluation pipelines to accommodate fair future comparisons.

Unsupervised representation learning for speech processing has matured greatly in the last few years. Work in computer vision and natural language processing has paved the way, but speech data offers unique challenges. As a result, methods from other domains rarely translate directly. We review the development of unsupervised representation learning for speech over the last decade. We identify two primary model categories: self-supervised methods and probabilistic latent variable models. We describe the models and develop a comprehensive taxonomy. Finally, we discuss and compare models from the two categories.

Unsupervised representation learning for speech processing has matured greatly in the last few years. Work in computer vision and natural language processing has paved the way, but speech data offers unique challenges. As a result, methods from other domains rarely translate directly. We review the development of unsupervised representation learning for speech over the last decade. We identify two primary model categories: self-supervised methods and probabilistic latent variable models. We describe the models and develop a comprehensive taxonomy. Finally, we discuss and compare models from the two categories.

We present simple methods for out-of-distribution detection using a trainedgenerative model. These techniques, based on classical statistical tests, aremodel-agnostic in the sense that they can be applied to any differentiablegenerative model. The idea is to combine a classical parametric test (Rao'sscore test) with the recently introduced typicality test. These two teststatistics are both theoretically well-founded and exploit different sources ofinformation based on the likelihood for the typicality test and its gradientfor the score test. We show that combining them using Fisher's method overallleads to a more accurate out-of-distribution test. We also discuss the benefitsof casting out-of-distribution detection as a statistical testing problem,noting in particular that false positive rate control can be valuable forpractical out-of-distribution detection. Despite their simplicity andgenerality, these methods can be competitive with model-specificout-of-distribution detection algorithms without any assumptions on the out-distribution.

Although supervised deep learning has revolutionized speech and audio processing, it has necessitated the building of specialist models for individual tasks and application scenarios. It is likewise difficult to apply this to dialects and languages for which only limited labeled data is available. Self-supervised representation learning methods promise a single universal model that would benefit a wide variety of tasks and domains. Such methods have shown success in natural language processing and computer vision domains, achieving new levels of performance while reducing the number of labels required for many downstream scenarios. Speech representation learning is experiencing similar progress in three main categories: generative, contrastive, and predictive methods. Other approaches rely on multi-modal data for pre-training, mixing text or visual data streams with speech. Although self-supervised speech representation is still a nascent research area, it is closely related to acoustic word embedding and learning with zero lexical resources, both of which have seen active research for many years. This review presents approaches for self-supervised speech representation learning and their connection to other research areas. Since many current methods focus solely on automatic speech recognition as a downstream task, we review recent efforts on benchmarking learned representations to extend the application beyond speech recognition.

Stochastic latent variable models (LVMs) achieve state-of-the-art performance on natural image generation but are still inferior to deterministic models on speech. In this paper, we develop a speech benchmark of popular temporal LVMs and compare them against state-of-the-art deterministic models. We report the likelihood, which is a much used metric in the image domain, but rarely, or incomparably, reported for speech models. To assess the quality of the learned representations, we also compare their usefulness for phoneme recognition. Finally, we adapt the Clockwork VAE, a state-of-the-art temporal LVM for video generation, to the speech domain. Despite being autoregressive only in latent space, we find that the Clockwork VAE can outperform previous LVMs and reduce the gap to deterministic models by using a hierarchy of latent variables.

Although supervised deep learning has revolutionized speech and audio processing, it has necessitated the building of specialist models for individual tasks and application scenarios. It is likewise difficult to apply this to dialects and languages for which only limited labeled data is available. Self-supervised representation learning methods promise a single universal model that would benefit a wide variety of tasks and domains. Such methods have shown success in natural language processing and computer vision domains, achieving new levels of performance while reducing the number of labels required for many downstream scenarios. Speech representation learning is experiencing similar progress in three main categories: generative, contrastive, and predictive methods. Other approaches rely on multi-modal data for pre-training, mixing text or visual data streams with speech. Although self-supervised speech representation is still a nascent research area, it is closely related to acoustic word embedding and learning with zero lexical resources, both of which have seen active research for many years. This review presents approaches for self-supervised speech representation learning and their connection to other research areas. Since many current methods focus solely on automatic speech recognition as a downstream task, we review recent efforts on benchmarking learned representations to extend the application beyond speech recognition.

Although supervised deep learning has revolutionized speech and audio processing, it has necessitated the building of specialist models for individual tasks and application scenarios. It is likewise difficult to apply this to dialects and languages for which only limited labeled data is available. Self-supervised representation learning methods promise a single universal model that would benefit a wide variety of tasks and domains. Such methods have shown success in natural language processing and computer vision domains, achieving new levels of performance while reducing the number of labels required for many downstream scenarios. Speech representation learning is experiencing similar progress in three main categories: generative, contrastive, and predictive methods. Other approaches rely on multi-modal data for pre-training, mixing text or visual data streams with speech. Although self-supervised speech representation is still a nascent research area, it is closely related to acoustic word embedding and learning with zero lexical resources, both of which have seen active research for many years. This review presents approaches for self-supervised speech representation learning and their connection to other research areas. Since many current methods focus solely on automatic speech recognition as a downstream task, we review recent efforts on benchmarking learned representations to extend the application beyond speech recognition.

We present simple methods for out-of-distribution detection using a trained generative model. These techniques, based on classical statistical tests, are model-agnostic in the sense that they can be applied to any differentiable generative model. The idea is to combine a classical parametric test (Rao's score test) with the recently introduced typicality test. These two test statistics are both theoretically well-founded and exploit different sources of information based on the likelihood for the typicality test and its gradient for the score test. We show that combining them using Fisher's method overall leads to a more accurate out-of-distribution test. We also discuss the benefits of casting out-of-distribution detection as a statistical testing problem, noting in particular that false positive rate control can be valuable for practical out-of-distribution detection. Despite their simplicity and generality, these methods can be competitive with model-specific out-of-distribution detection algorithms without any assumptions on the out-distribution., Comment: Accepted at the 25th International Conference on Artificial Intelligence and Statistics (AISTATS), 2022

Stochastic latent variable models (LVMs) achieve state-of-the-art performance on natural image generation but are still inferior to deterministic models on speech. In this paper, we develop a speech benchmark of popular temporal LVMs and compare them against state-of-the-art deterministic models. We report the likelihood, which is a much used metric in the image domain, but rarely, or incomparably, reported for speech models. To assess the quality of the learned representations, we also compare their usefulness for phoneme recognition. Finally, we adapt the Clockwork VAE, a state-of-the-art temporal LVM for video generation, to the speech domain. Despite being autoregressive only in latent space, we find that the Clockwork VAE can outperform previous LVMs and reduce the gap to deterministic models by using a hierarchy of latent variables., Comment: Accepted at the 2022 ICLR workshop on Deep Generative Models for Highly Structured Data (https://deep-gen-struct.github.io)

Recent advances in self-supervised learning through contrastive training have shown that it is possible to learn a competitive speech recognition system with as little as 10 minutes of labeled data. However, these systems are computationally expensive since they require pre-training followed by fine-tuning in a large parameter space. We explore the performance of such systems without fine-tuning by training a stateof- the-art speech recognizer on the fixed representations from the computationally demanding wav2vec 2.0 framework. We find performance to decrease without fine-tuning and, in the extreme low-resource setting, wav2vec 2.0 is inferior to its predecessor. In addition, we find that wav2vec 2.0 representations live in a low dimensional subspace and that decorrelating the features of the representations can stabilize training of the automatic speech recognizer. Finally, we propose a bidirectional extension to the original wav2vec framework that consistently improves performance.

Deep generative models have been demonstrated as state-of-the-art density estimators. Yet, recent work has found that they often assign a higher likelihood to data from outside the training distribution. This seemingly paradoxical behavior has caused concerns over the quality of the attained density estimates. In the context of hierarchical variational autoencoders, we provide evidence to explain this behavior by out-of-distribution data having in-distribution low-level features. We argue that this is both expected and desirable behavior. With this insight in hand, we develop a fast, scalable and fully unsupervised likelihood-ratio score for OOD detection that requires data to be in-distribution across all feature-levels. We benchmark the method on a vast set of data and model combinations and achieve state-of-the-art results on out-of-distribution detection.

Recent advances in self-supervised learning through contrastive training have shown that it is possible to learn a competitive speech recognition system with as little as 10 minutes of labeled data. However, these systems are computationally expensive since they require pre-training followed by fine-tuning in a large parameter space. We explore the performance of such systems without fine-tuning by training a stateof- the-art speech recognizer on the fixed representations from the computationally demanding wav2vec 2.0 framework. We find performance to decrease without fine-tuning and, in the extreme low-resource setting, wav2vec 2.0 is inferior to its predecessor. In addition, we find that wav2vec 2.0 representations live in a low dimensional subspace and that decorrelating the features of the representations can stabilize training of the automatic speech recognizer. Finally, we propose a bidirectional extension to the original wav2vec framework that consistently improves performance.

Deep generative models have been demonstrated as state-of-the-art density estimators. Yet, recent work has found that they often assign a higher likelihood to data from outside the training distribution. This seemingly paradoxical behavior has caused concerns over the quality of the attained density estimates. In the context of hierarchical variational autoencoders, we provide evidence to explain this behavior by out-of-distribution data having in-distribution low-level features. We argue that this is both expected and desirable behavior. With this insight in hand, we develop a fast, scalable and fully unsupervised likelihood-ratio score for OOD detection that requires data to be in-distribution across all feature-levels. We benchmark the method on a vast set of data and model combinations and achieve state-of-the-art results on out-of-distribution detection., Comment: Appeared in Proceedings of the 38th International Conference on Machine Learning (ICML 2021). 18 pages, source code available at https://github.com/JakobHavtorn/hvae-oodd, https://github.com/vlievin/biva-pytorch and https://github.com/larsmaaloee/BIVA

The two most common paradigms for end-to-end speech recognition are connectionist temporal classification (CTC) and attention-based encoder-decoder (AED) models. It has been argued that the latter is better suited for learning an implicit language model. We test this hypothesis by measuring temporal context sensitivity and evaluate how the models perform when we constrain the amount of contextual information in the audio input. We find that the AED model is indeed more context sensitive, but that the gap can be closed by adding self-attention to the CTC model. Furthermore, the two models perform similarly when contextual information is constrained. Finally, in contrast to previous research, our results show that the CTC model is highly competitive on WSJ and LibriSpeech without the help of an external language model.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning., Comment: Accepted at ACL 2020

The two most common paradigms for end-to-end speech recognition are connectionist temporal classification (CTC) and attention-based encoder-decoder (AED) models. It has been argued that the latter is better suited for learning an implicit language model. We test this hypothesis by measuring temporal context sensitivity and evaluate how the models perform when we constrain the amount of contextual information in the audio input. We find that the AED model is indeed more context sensitive, but that the gap can be closed by adding self-attention to the CTC model. Furthermore, the two models perform similarly when contextual information is constrained. Finally, in contrast to previous research, our results show that the CTC model is highly competitive on WSJ and LibriSpeech without the help of an external language model.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning.

The two most common paradigms for end-to-end speech recognition are connectionist temporal classification (CTC) and attention-based encoder-decoder (AED) models. It has been argued that the latter is better suited for learning an implicit language model. We test this hypothesis by measuring temporal context sensitivity and evaluate how the models perform when we constrain the amount of contextual information in the audio input. We find that the AED model is indeed more context sensitive, but that the gap can be closed by adding self-attention to the CTC model. Furthermore, the two models perform similarly when contextual information is constrained. Finally, in contrast to previous research, our results show that the CTC model is highly competitive on WSJ and LibriSpeech without the help of an external language model.