Leveraging natural language processing to study emotional coherence in psychotherapy

The association between emotional experience and expression, known as emotional coherence, is considered important for individual functioning. Recent advances in natural language processing (NLP) make it possible to automatically recognize verbally expressed emotions in psychotherapy dialogues and to explore emotional coherence with larger samples and finer granularity than previously. The present study used state-of-the-art emotion recognition models to automatically label clients' emotions at the utterance level, employed these labeled data to examine the coherence between verbally expressed emotions and self-reported emotions, and examined the associations between emotional coherence and clients' improvement in functioning throughout treatment. The data comprised 872 transcribed sessions from 68 clients. Clients self-reported their functioning before each session and their emotions after each. A subsample of 196 sessions were manually coded. A transformer-based approach was used to automatically label the remaining data for a total of 139,061 utterances. Multilevel modeling was used to assess emotional coherence and determine whether it was associated with changes in clients' functioning throughout treatment. The emotion recognition model demonstrated moderate performance. The findings indicated a significant association between verbally expressed emotions and self-reported emotions. Coherence in clients' negative emotions was associated with improvement in functioning. The results suggest an association between clients' subjective experience and their verbal expression of emotions and underscore the importance of this coherence to functioning. NLP may uncover crucial emotional processes in psychotherapy. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Comparative Magnitude and Persistence of Humoral SARS-CoV-2 Vaccination Responses in the Adult Population in Germany

Recent increases in SARS-CoV-2 infections have led to questions about duration and quality of vaccine-induced immune protection. While numerous studies have been published on immune responses triggered by vaccination, these often focus on studying the impact of one or two immunisation schemes within subpopulations such as immunocompromised individuals or healthcare workers. To provide information on the duration and quality of vaccine-induced immune responses against SARS-CoV-2, we analyzed antibody titres against various SARS-CoV-2 antigens and ACE2 binding inhibition against SARS-CoV-2 wild-type and variants of concern in samples from a large German population-based seroprevalence study (MuSPAD) who had received all currently available immunisation schemes. We found that homologous mRNA-based or heterologous prime-boost vaccination produced significantly higher antibody responses than vector-based homologous vaccination. Ad26.CoV2S.2 performance was particularly concerning with reduced titres and 91.7% of samples classified as non-responsive for ACE2 binding inhibition, suggesting that recipients require a booster mRNA vaccination. While mRNA vaccination induced a higher ratio of RBD- and S1-targeting antibodies, vector-based vaccines resulted in an increased proportion of S2-targeting antibodies. Given the role of RBD- and S1-specific antibodies in neutralizing SARS-CoV-2, their relative over-representation after mRNA vaccination may explain why these vaccines have increased efficacy compared to vector-based formulations. Previously infected individuals had a robust immune response once vaccinated, regardless of which vaccine they received, which could aid future dose allocation should shortages arise for certain manufacturers. Overall, both titres and ACE2 binding inhibition peaked approximately 28 days post-second vaccination and then decreased.

LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations

MOTIVATION

Natural Language Processing techniques are constantly being advanced to accommodate the influx of data as well as to provide exhaustive and structured knowledge dissemination. Within the biomedical domain, relation detection between bio-entities known as the Bio-Entity Relation Extraction (BRE) task has a critical function in knowledge structuring. Although recent advances in deep learning-based biomedical domain embedding have improved BRE predictive analytics, these works are often task selective or use external knowledge-based pre-/post-processing. In addition, deep learning-based models do not account for local syntactic contexts, which have improved data representation in many kernel classifier-based models. In this study, we propose a universal BRE model, i.e. LBERT, which is a Lexically aware Transformer-based Bidirectional Encoder Representation model, and which explores both local and global contexts representations for sentence-level classification tasks.

RESULTS

This article presents one of the most exhaustive BRE studies ever conducted over five different bio-entity relation types. Our model outperforms state-of-the-art deep learning models in protein-protein interaction (PPI), drug-drug interaction and protein-bio-entity relation classification tasks by 0.02%, 11.2% and 41.4%, respectively. LBERT representations show a statistically significant improvement over BioBERT in detecting true bio-entity relation for large corpora like PPI. Our ablation studies clearly indicate the contribution of the lexical features and distance-adjusted attention in improving prediction performance by learning additional local semantic context along with bi-directionally learned global context.

AVAILABILITY AND IMPLEMENTATION

Github. https://github.com/warikoone/LBERT.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Medical knowledge infused convolutional neural networks for cohort selection in clinical trials

OBJECTIVE

In this era of digitized health records, there has been a marked interest in using de-identified patient records for conducting various health related surveys. To assist in this research effort, we developed a novel clinical data representation model entitled medical knowledge-infused convolutional neural network (MKCNN), which is used for learning the clinical trial criteria eligibility status of patients to participate in cohort studies.

MATERIALS AND METHODS

In this study, we propose a clinical text representation infused with medical knowledge (MK). First, we isolate the noise from the relevant data using a medically relevant description extractor; then we utilize log-likelihood ratio based weights from selected sentences to highlight "met" and "not-met" knowledge-infused representations in bichannel setting for each instance. The combined medical knowledge-infused representation (MK) from these modules helps identify significant clinical criteria semantics, which in turn renders effective learning when used with a convolutional neural network architecture.

RESULTS

MKCNN outperforms other Medical Knowledge (MK) relevant learning architectures by approximately 3%; notably SVM and XGBoost implementations developed in this study. MKCNN scored 86.1% on F1metric, a gain of 6% above the average performance assessed from the submissions for n2c2 task. Although pattern/rule-based methods show a higher average performance for the n2c2 clinical data set, MKCNN significantly improves performance of machine learning implementations for clinical datasets.

CONCLUSION

MKCNN scored 86.1% on the F1 score metric. In contrast to many of the rule-based systems introduced during the n2c2 challenge workshop, our system presents a model that heavily draws on machine-based learning. In addition, the MK representations add more value to clinical comprehension and interpretation of natural texts.

LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task

Identifying the interactions between chemical compounds and genes from biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this paper, we describe Linguistic Pattern-Aware Dependency Tree Kernel, a linguistic interaction pattern learning method developed for CHEMPROT task-BioCreative VI, to capture chemical-protein interaction (CPI) patterns within biomedical literatures. We also introduce a framework to integrate these linguistic patterns with smooth partial tree kernel to extract the CPIs. This new method of feature representation models aspects of linguistic probability in geometric representation, which not only optimizes the sufficiency of feature dimension for classification, but also defines features as interpretable contexts rather than long vectors of numbers. In order to test the robustness and efficiency of our system in identifying different kinds of biological interactions, we evaluated our framework on three separate data sets, i.e. CHEMPROT corpus, Chemical-Disease Relation corpus and Protein-Protein Interaction corpus. Corresponding experiment results demonstrate that our method is effective and outperforms several compared systems for each data set.