Serguei Pakhomov

Changye Li, Weizhe Xu, Trevor Cohen et al. · uw

The evidence is growing that machine and deep learning methods can learn the subtle differences between the language produced by people with various forms of cognitive impairment such as dementia and cognitively healthy individuals. Valuable public data repositories such as TalkBank have made it possible for researchers in the computational community to join forces and learn from each other to make significant advances in this area. However, due to variability in approaches and data selection strategies used by various researchers, results obtained by different groups have been difficult to compare directly. In this paper, we present TRESTLE (\textbf{T}oolkit for \textbf{R}eproducible \textbf{E}xecution of \textbf{S}peech \textbf{T}ext and \textbf{L}anguage \textbf{E}xperiments), an open source platform that focuses on two datasets from the TalkBank repository with dementia detection as an illustrative domain. Successfully deployed in the hackallenge (Hackathon/Challenge) of the International Workshop on Health Intelligence at AAAI 2022, TRESTLE provides a precise digital blueprint of the data pre-processing and selection strategies that can be reused via TRESTLE by other researchers seeking comparable results with their peers and current state-of-the-art (SOTA) approaches.

Changye Li, David Knopman, Weizhe Xu et al. · uw

Deep learning (DL) techniques involving fine-tuning large numbers of model parameters have delivered impressive performance on the task of discriminating between language produced by cognitively healthy individuals, and those with Alzheimer's disease (AD). However, questions remain about their ability to generalize beyond the small reference sets that are publicly available for research. As an alternative to fitting model parameters directly, we propose a novel method by which a Transformer DL model (GPT-2) pre-trained on general English text is paired with an artificially degraded version of itself (GPT-D), to compute the ratio between these two models' \textit{perplexities} on language from cognitively healthy and impaired individuals. This technique approaches state-of-the-art performance on text data from a widely used "Cookie Theft" picture description task, and unlike established alternatives also generalizes well to spontaneous conversations. Furthermore, GPT-D generates text with characteristics known to be associated with AD, demonstrating the induction of dementia-related linguistic anomalies. Our study is a step toward better understanding of the relationships between the inner workings of generative neural language models, the language that they produce, and the deleterious effects of dementia on human speech and language characteristics.

Yongsen Tan, Zhecheng Sheng, Xiruo Ding et al.

Despite the burgeoning body of work on distribution shifts, provenance shift-where the relationship between data source and label changes at deployment-remains poorly understood and under-addressed. In this paper, we establish a formal connection between provenance shift, counterfactual invariance, and invariant learning to derive a learning objective for robustness. We then introduce \textsc{DeconDTN-Toolkit}, a specialized evaluation and remediation suite designed to simulate provenance shifts of varying degrees while maintaining the training protocol and the infrastructure of existing benchmarks. We reveal the vulnerability of Empirical Risk Minimization under provenance shift, introduce a robust out-of-distribution performance indicator, and conduct a comprehensive evaluation on existing algorithms. Our work provides both the theoretical grounding and the practical tools necessary to characterize the problem of confounding by provenance, and implementations of methods to mitigate it.

Changye Li, Trevor Cohen, Serguei Pakhomov · uw

Linguistic anomalies detectable in spontaneous speech have shown promise for various clinical applications including screening for dementia and other forms of cognitive impairment. The feasibility of deploying automated tools that can classify language samples obtained from speech in large-scale clinical settings depends on the ability to capture and automatically transcribe the speech for subsequent analysis. However, the impressive performance of self-supervised learning (SSL) automatic speech recognition (ASR) models with curated speech data is not apparent with challenging speech samples from clinical settings. One of the key questions for successfully applying ASR models for clinical applications is whether imperfect transcripts they generate provide sufficient information for downstream tasks to operate at an acceptable level of accuracy. In this study, we examine the relationship between the errors produced by several deep learning ASR systems and their impact on the downstream task of dementia classification. One of our key findings is that, paradoxically, ASR systems with relatively high error rates can produce transcripts that result in better downstream classification accuracy than classification based on verbatim transcripts.

Zhecheng Sheng, Raymond Finzel, Michael Lucke et al.

In healthcare, the ability to care for oneself is reflected in the "Activities of Daily Living (ADL)," which serve as a measure of functional ability (functioning). A lack of functioning may lead to poor living conditions requiring personal care and assistance. To accurately identify those in need of support, assistance programs continuously evaluate participants' functioning across various domains. However, the assessment process may encounter consistency issues when multiple assessors with varying levels of expertise are involved. Novice assessors, in particular, may lack the necessary preparation for real-world interactions with participants. To address this issue, we developed a dialogue system that simulates interactions between assessors and individuals of varying functioning in a natural and reproducible way. The dialogue system consists of two major modules, one for natural language understanding (NLU) and one for natural language generation (NLG), respectively. In order to generate responses consistent with the underlying knowledge base, the dialogue system requires both an understanding of the user's query and of biographical details of an individual being simulated. To fulfill this requirement, we experimented with query classification and generated responses based on those biographical details using some recently released InstructGPT-like models.

Xiruo Ding, Zhecheng Sheng, Meliha Yetişgen et al.

Natural Language Processing (NLP) methods have been broadly applied to clinical tasks. Machine learning and deep learning approaches have been used to improve the performance of clinical NLP. However, these approaches require sufficiently large datasets for training, and trained models have been shown to transfer poorly across sites. These issues have led to the promotion of data collection and integration across different institutions for accurate and portable models. However, this can introduce a form of bias called confounding by provenance. When source-specific data distributions differ at deployment, this may harm model performance. To address this issue, we evaluate the utility of backdoor adjustment for text classification in a multi-site dataset of clinical notes annotated for mentions of substance abuse. Using an evaluation framework devised to measure robustness to distributional shifts, we assess the utility of backdoor adjustment. Our results indicate that backdoor adjustment can effectively mitigate for confounding shift.

Changye Li, Trevor Cohen, Serguei Pakhomov · uw

Automatic speech recognition (ASR) models trained on large amounts of audio data are now widely used to convert speech to written text in a variety of applications from video captioning to automated assistants used in healthcare and other domains. As such, it is important that ASR models and their use is fair and equitable. Prior work examining the performance of commercial ASR systems on the Corpus of Regional African American Language (CORAAL) demonstrated significantly worse ASR performance on African American English (AAE). The current study seeks to understand the factors underlying this disparity by examining the performance of the current state-of-the-art neural network based ASR system (Whisper, OpenAI) on the CORAAL dataset. Two key findings have been identified as a result of the current study. The first confirms prior findings of significant dialectal variation even across neighboring communities, and worse ASR performance on AAE that can be improved to some extent with fine-tuning of ASR models. The second is a novel finding not discussed in prior work on CORAAL: differences in audio recording practices within the dataset have a significant impact on ASR accuracy resulting in a ``confounding by provenance'' effect in which both language use and recording quality differ by study location. These findings highlight the need for further systematic investigation to disentangle the effects of recording quality and inherent linguistic diversity when examining the fairness and bias present in neural ASR models, as any bias in ASR accuracy may have negative downstream effects on disparities in various domains of life in which ASR technology is used.

Changye Li, Weizhe Xu, Trevor Cohen et al. · uw

\textbf{Objectives}: We aimed to investigate how errors from automatic speech recognition (ASR) systems affect dementia classification accuracy, specifically in the ``Cookie Theft'' picture description task. We aimed to assess whether imperfect ASR-generated transcripts could provide valuable information for distinguishing between language samples from cognitively healthy individuals and those with Alzheimer's disease (AD). \textbf{Methods}: We conducted experiments using various ASR models, refining their transcripts with post-editing techniques. Both these imperfect ASR transcripts and manually transcribed ones were used as inputs for the downstream dementia classification. We conducted comprehensive error analysis to compare model performance and assess ASR-generated transcript effectiveness in dementia classification. \textbf{Results}: Imperfect ASR-generated transcripts surprisingly outperformed manual transcription for distinguishing between individuals with AD and those without in the ``Cookie Theft'' task. These ASR-based models surpassed the previous state-of-the-art approach, indicating that ASR errors may contain valuable cues related to dementia. The synergy between ASR and classification models improved overall accuracy in dementia classification. \textbf{Conclusion}: Imperfect ASR transcripts effectively capture linguistic anomalies linked to dementia, improving accuracy in classification tasks. This synergy between ASR and classification models underscores ASR's potential as a valuable tool in assessing cognitive impairment and related clinical applications.

Feng Chen, Weizhe Xu, Changye Li et al.

Formal thought disorder (FTD), a hallmark of schizophrenia spectrum disorders, manifests as incoherent speech and poses challenges for clinical assessment. Traditional clinical rating scales, though validated, are resource-intensive and lack scalability. Automated speech analysis with automatic speech recognition (ASR) allows for objective quantification of linguistic and temporal features of speech, offering scalable alternatives. The use of utterance timestamps in ASR captures pause dynamics, which are thought to reflect the cognitive processes underlying speech production. However, the utility of integrating these ASR-derived features for assessing FTD severity requires further evaluation. This study integrates pause features with semantic coherence metrics across three datasets: naturalistic self-recorded diaries (AVH, n = 140), structured picture descriptions (TOPSY, n = 72), and dream narratives (PsyCL, n = 43). We evaluated pause related features alongside established coherence measures, using support vector regression (SVR) to predict clinical FTD scores. Key findings demonstrate that pause features alone robustly predict the severity of FTD. Integrating pause features with semantic coherence metrics enhanced predictive performance compared to semantic-only models, with integration of independent models achieving correlations up to \r{ho} = 0.649 and AUC = 83.71% for severe cases detection (TOPSY, with best \r{ho} = 0.584 and AUC = 79.23% for semantic-only models). The performance gains from semantic and pause features integration held consistently across all contexts, though the nature of pause patterns was dataset-dependent. These findings suggest that frameworks combining temporal and semantic analyses provide a roadmap for refining the assessment of disorganized speech and advance automated speech analysis in psychosis.

Changye Li, Weizhe Xu, Serguei Pakhomov et al. · uw

Disorganized thinking is a key diagnostic indicator of schizophrenia-spectrum disorders. Recently, clinical estimates of the severity of disorganized thinking have been shown to correlate with measures of how difficult speech transcripts would be for large language models (LLMs) to predict. However, LLMs' deployment challenges -- including privacy concerns, computational and financial costs, and lack of transparency of training data -- limit their clinical utility. We investigate whether smaller neural language models can serve as effective alternatives for detecting positive formal thought disorder, using the same sliding window based perplexity measurements that proved effective with larger models. Surprisingly, our results show that smaller models are more sensitive to linguistic differences associated with formal thought disorder than their larger counterparts. Detection capability declines beyond a certain model size and context length, challenging the common assumption of ``bigger is better'' for LLM-based applications. Our findings generalize across audio diaries and clinical interview speech samples from individuals with psychotic symptoms, suggesting a promising direction for developing efficient, cost-effective, and privacy-preserving screening tools that can be deployed in both clinical and naturalistic settings.

Xiruo Ding, Zhecheng Sheng, Brian Hur et al.

Foundation models are a current focus of attention in both industry and academia. While they have shown their capabilities in a variety of tasks, in-depth research is required to determine their robustness to distribution shift when used as a basis for supervised machine learning. This is especially important in the context of clinical data, with particular limitations related to data accessibility, lack of pretraining materials, and limited availability of high-quality annotations. In this work, we examine the stability of models based on representations from foundation models under distribution shift. We focus on confounding by provenance, a form of distribution shift that emerges in the context of multi-institutional datasets when there are differences in source-specific language use and class distributions. Using a sampling strategy that synthetically induces varying degrees of distribution shift, we evaluate the extent to which representations from foundation models result in predictions that are inherently robust to confounding by provenance. Additionally, we examine the effectiveness of a straightforward confounding adjustment method inspired by Pearl's conception of backdoor adjustment. Results indicate that while foundation models do show some out-of-the-box robustness to confounding-by-provenance related distribution shifts, this can be considerably improved through adjustment. These findings suggest a need for deliberate adjustment of predictive models using representations from foundation models in the context of source-specific distributional differences.

Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz et al.

Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts. We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations including UMLS concept unique identifiers), and Fairview Health Services corpus (44,530 annotations). Our results showed that for UMLS concept matching, Boolean ensembling of the MiPACQ corpus trended towards higher performance over individual systems. Use of an approximate grid-search can help optimize the precision-recall tradeoff and can provide a set of heuristics for choosing an optimal set of ensembles.

Esha Singh, Anu Bompelli, Ruyuan Wan et al.

Dietary supplements (DS) have been widely used by consumers, but the information around the efficacy and safety of DS is disparate or incomplete, thus creating barriers for consumers to find information effectively. Conversational agent (CA) systems have been applied to the healthcare domain, but there is no such a system to answer consumers regarding DS use, although widespread use of DS. In this study, we develop the first CA system for DS use

Trevor Cohen, Serguei Pakhomov

In recent years there has been a burgeoning interest in the use of computational methods to distinguish between elicited speech samples produced by patients with dementia, and those from healthy controls. The difference between perplexity estimates from two neural language models (LMs) - one trained on transcripts of speech produced by healthy participants and the other trained on transcripts from patients with dementia - as a single feature for diagnostic classification of unseen transcripts has been shown to produce state-of-the-art performance. However, little is known about why this approach is effective, and on account of the lack of case/control matching in the most widely-used evaluation set of transcripts (DementiaBank), it is unclear if these approaches are truly diagnostic, or are sensitive to other variables. In this paper, we interrogate neural LMs trained on participants with and without dementia using synthetic narratives previously developed to simulate progressive semantic dementia by manipulating lexical frequency. We find that perplexity of neural LMs is strongly and differentially associated with lexical frequency, and that a mixture model resulting from interpolating control and dementia LMs improves upon the current state-of-the-art for models trained on transcript text exclusively.