Interpretation of cluster structures in pain-related phenotype data using explainable artificial intelligence (XAI)

Phenotyping peripheral neuropathies with and without pruritus: a cross-sectional multicenter study

ABSTRACT

Pruritus often escapes physicians' attention in patients with peripheral neuropathy (PNP). Here we aimed to characterize neuropathic pruritus in a cohort of 191 patients with PNP (large, mixed, or small fiber) and 57 control subjects with deep phenotyping in a multicenter cross-sectional observational study at 3 German sites. All participants underwent thorough neurological examination, nerve conduction studies, quantitative sensory testing, and skin biopsies to assess intraepidermal nerve fiber density. Patients filled in a set of questionnaires assessing the characteristics of pruritus and pain, the presence of depression and anxiety, and quality of life. Based on the severity of pruritus and pain, patients were grouped into 4 groups: "pruritus," "pain," "pruritus and pain," and "no pruritus/no pain." Although 11% (21/191) of patients reported pruritus as their only symptom, further 34.6% (66/191) reported pruritus and pain. Patients with pain (with or without pruritus) were more affected by anxiety, depression, and reduced quality of life than control subjects. Patients with pruritus (with and without pain) had increases in cold detection threshold, showing Aδ-fiber dysfunction. The pruritus group had lower intraepidermal nerve fiber density at the thigh, concomitant with a more proximal distribution of symptoms compared with the other PNP groups. Stratification of patients with PNP by using cross-sectional datasets and multinominal logistic regression analysis revealed distinct patterns for the patient groups. Together, our study sheds light on the presence of neuropathic pruritus in patients with PNP and its relationship with neuropathic pain, outlines the sensory and structural abnormalities associated with neuropathic pruritus, and highlights its impact on anxiety levels.

Cracking the Chronic Pain code: A scoping review of Artificial Intelligence in Chronic Pain research

OBJECTIVE

The aim of this review is to identify gaps and provide a direction for future research in the utilization of Artificial Intelligence (AI) in chronic pain (CP) management.

METHODS

A comprehensive literature search was conducted using various databases, including Ovid MEDLINE, Web of Science Core Collection, IEEE Xplore, and ACM Digital Library. The search was limited to studies on AI in CP research, focusing on diagnosis, prognosis, clinical decision support, self-management, and rehabilitation. The studies were evaluated based on predefined inclusion criteria, including the reporting quality of AI algorithms used.

RESULTS

After the screening process, 60 studies were reviewed, highlighting AI's effectiveness in diagnosing and classifying CP while revealing gaps in the attention given to treatment and rehabilitation. It was found that the most commonly used algorithms in CP research were support vector machines, logistic regression and random forest classifiers. The review also pointed out that attention to CP mechanisms is negligible despite being the most effective way to treat CP.

CONCLUSION

The review concludes that to achieve more effective outcomes in CP management, future research should prioritize identifying CP mechanisms, CP management, and rehabilitation while leveraging a wider range of algorithms and architectures.

SIGNIFICANCE

This review highlights the potential of AI in improving the management of CP, which is a significant personal and economic burden affecting more than 30% of the world's population. The identified gaps and future research directions provide valuable insights to researchers and practitioners in the field, with the potential to improve healthcare utilization.

Artificial intelligence and machine learning in clinical pharmacological research

BACKGROUND

Clinical pharmacology research has always involved computational analysis. With the abundance of drug-related data available, the integration of artificial intelligence (AI) and machine learning (ML) methods has emerged as a promising way to enhance clinical pharmacology research.

METHODS

Based on an accepted definition of clinical pharmacology as a field of research dealing with all aspects of drug-human interactions, the analysis included publications from institutes specializing in clinical pharmacology. Research topics and the most used machine learning methods in clinical pharmacology were retrieved from the PubMed database and summarized.

RESULTS

ML was identified in 674 publications attributed to clinical pharmacology research, with a significant increase in publication activity over the last decade. Notable research topics addressed by ML/AI included Covid-19-related clinical pharmacology research, clinical neuropharmacology, drug safety and risk assessment, clinical pharmacology related to cancer research, and antimicrobial and antiviral research unrelated to Covid-19. In terms of ML methods, neural networks, random forests, and support vector machines were frequently mentioned in the abstracts of the retrieved papers.

CONCLUSIONS

ML, and AI in general, is increasingly being used in various research areas within clinical pharmacology. This report presents specific examples of applications and highlights the most used ML methods.

KnAC: an approach for enhancing cluster analysis with background knowledge and explanations

Pattern discovery in multidimensional data sets has been the subject of research for decades. There exists a wide spectrum of clustering algorithms that can be used for this purpose. However, their practical applications share a common post-clustering phase, which concerns expert-based interpretation and analysis of the obtained results. We argue that this can be the bottleneck in the process, especially in cases where domain knowledge exists prior to clustering. Such a situation requires not only a proper analysis of automatically discovered clusters but also conformance checking with existing knowledge. In this work, we present Knowledge Augmented Clustering (KnAC). Its main goal is to confront expert-based labelling with automated clustering for the sake of updating and refining the former. Our solution is not restricted to any existing clustering algorithm. Instead, KnAC can serve as an augmentation of an arbitrary clustering algorithm, making the approach robust and a model-agnostic improvement of any state-of-the-art clustering method. We demonstrate the feasibility of our method on artificially, reproducible examples and in a real life use case scenario. In both cases, we achieved better results than classic clustering algorithms without augmentation.

Receptor tyrosine kinase MET ligand-interaction classified via machine learning from single-particle tracking data

Internalin B-mediated activation of the membrane-bound receptor tyrosine kinase MET is accompanied by a change in receptor mobility. Conversely, it should be possible to infer from receptor mobility whether a cell has been treated with internalin B. Here, we propose a method based on hidden Markov modeling and explainable artificial intelligence that machine-learns the key differences in MET mobility between internalin B-treated and -untreated cells from single-particle tracking data. Our method assigns receptor mobility to three diffusion modes (immobile, slow, and fast). It discriminates between internalin B-treated and -untreated cells with a balanced accuracy of >99% and identifies three parameters that are most affected by internalin B treatment: a decrease in the mobility of slow molecules (1) and a depopulation of the fast mode (2) caused by an increased transition of fast molecules to the slow mode (3). Our approach is based entirely on free software and is readily applicable to the analysis of other membrane receptors.

Machine Learning and Pathway Analysis-Based Discovery of Metabolomic Markers Relating to Chronic Pain Phenotypes

Recent scientific evidence suggests that chronic pain phenotypes are reflected in metabolomic changes. However, problems associated with chronic pain, such as sleep disorders or obesity, may complicate the metabolome pattern. Such a complex phenotype was investigated to identify common metabolomics markers at the interface of persistent pain, sleep, and obesity in 71 men and 122 women undergoing tertiary pain care. They were examined for patterns in d = 97 metabolomic markers that segregated patients with a relatively benign pain phenotype (low and little bothersome pain) from those with more severe clinical symptoms (high pain intensity, more bothersome pain, and co-occurring problems such as sleep disturbance). Two independent lines of data analysis were pursued. First, a data-driven supervised machine learning-based approach was used to identify the most informative metabolic markers for complex phenotype assignment. This pointed primarily at adenosine monophosphate (AMP), asparagine, deoxycytidine, glucuronic acid, and propionylcarnitine, and secondarily at cysteine and nicotinamide adenine dinucleotide (NAD) as informative for assigning patients to clinical pain phenotypes. After this, a hypothesis-driven analysis of metabolic pathways was performed, including sleep and obesity. In both the first and second line of analysis, three metabolic markers (NAD, AMP, and cysteine) were found to be relevant, including metabolic pathway analysis in obesity, associated with changes in amino acid metabolism, and sleep problems, associated with downregulated methionine metabolism. Taken together, present findings provide evidence that metabolomic changes associated with co-occurring problems may play a role in the development of severe pain. Co-occurring problems may influence each other at the metabolomic level. Because the methionine and glutathione metabolic pathways are physiologically linked, sleep problems appear to be associated with the first metabolic pathway, whereas obesity may be associated with the second.

Machine-Learning Points at Endoscopic, Quality of Life, and Olfactory Parameters as Outcome Criteria for Endoscopic Paranasal Sinus Surgery in Chronic Rhinosinusitis

Chronic rhinosinusitis (CRS) is often treated by functional endoscopic paranasal sinus surgery, which improves endoscopic parameters and quality of life, while olfactory function was suggested as a further criterion of treatment success. In a prospective cohort study, 37 parameters from four categories were recorded from 60 men and 98 women before and four months after endoscopic sinus surgery, including endoscopic measures of nasal anatomy/pathology, assessments of olfactory function, quality of life, and socio-demographic or concomitant conditions. Parameters containing relevant information about changes associated with surgery were examined using unsupervised and supervised methods, including machine-learning techniques for feature selection. The analyzed cohort included 52 men and 38 women. Changes in the endoscopic Lildholdt score allowed separation of baseline from postoperative data with a cross-validated accuracy of 85%. Further relevant information included primary nasal symptoms from SNOT-20 assessments, and self-assessments of olfactory function. Overall improvement in these relevant parameters was observed in 95% of patients. A ranked list of criteria was developed as a proposal to assess the outcome of functional endoscopic sinus surgery in CRS patients with nasal polyposis. Three different facets were captured, including the Lildholdt score as an endoscopic measure and, in addition, disease-specific quality of life and subjectively perceived olfactory function.