Alexander Geiger

Alexander Geiger, Lars Wagner, Daniel Rueckert et al.

Diagnosing esophageal motility disorders pose significant challenges due to the complexity of high-resolution impedance manometry (HRIM) data and variability in clinical interpretation. This work explores the feasibility of a multimodal Machine Learning (ML)-based classification approach that combines HRIM recordings with patient-specific information and incorporates a graph-based modeling of esophageal physiology. We analyze HRIM recordings with corresponding patient information from 104 patients with esophageal motility disorders. Patient data includes demographic, clinical, and symptom information extracted from structured questionnaires and free-text notes using keyword detection and large language model-based processing. HRIM data is represented as spatio-temporal graphs, where nodes correspond to pressure values along the esophagus and edges encode spatial adjacency and impedance dynamics. A graph neural network (GNN) is applied to learn physiologically meaningful representations, which are fused with patient embeddings for multi-category, multi-class classification of swallow events. The impact of patient features and graph-based modeling is evaluated by ablation studies and comparison to vision-based classifier baselines. The proposed multimodal approach indicates improvements over models that rely solely on HRIM-derived features across all classification categories. Additionally, the graph-based modeling provides gains compared to vision-based baselines. Our experiments systematically assess the complementary contribution of multiple modalities, as well as demonstrate the feasibility of our proposed graph-based approach. Our initial findings demonstrate that integrating patient-level data with graph-based representations of HRIM signals appears to be a promising direction for more accurate classification of esophageal motility disorders.

Alexander Geiger, Dongyu Liu, Sarah Alnegheimish et al.

Time series anomalies can offer information relevant to critical situations facing various fields, from finance and aerospace to the IT, security, and medical domains. However, detecting anomalies in time series data is particularly challenging due to the vague definition of anomalies and said data's frequent lack of labels and highly complex temporal correlations. Current state-of-the-art unsupervised machine learning methods for anomaly detection suffer from scalability and portability issues, and may have high false positive rates. In this paper, we propose TadGAN, an unsupervised anomaly detection approach built on Generative Adversarial Networks (GANs). To capture the temporal correlations of time series distributions, we use LSTM Recurrent Neural Networks as base models for Generators and Critics. TadGAN is trained with cycle consistency loss to allow for effective time-series data reconstruction. We further propose several novel methods to compute reconstruction errors, as well as different approaches to combine reconstruction errors and Critic outputs to compute anomaly scores. To demonstrate the performance and generalizability of our approach, we test several anomaly scoring techniques and report the best-suited one. We compare our approach to 8 baseline anomaly detection methods on 11 datasets from multiple reputable sources such as NASA, Yahoo, Numenta, Amazon, and Twitter. The results show that our approach can effectively detect anomalies and outperform baseline methods in most cases (6 out of 11). Notably, our method has the highest averaged F1 score across all the datasets. Our code is open source and is available as a benchmarking tool.

Alexander Geiger, Lars Wagner, Daniel Rueckert et al.

High-resolution manometry (HRM) is the gold standard in diagnosing esophageal motility disorders. As HRM is typically conducted under short-term laboratory settings, intermittently occurring disorders are likely to be missed. Therefore, long-term (up to 24h) HRM (LTHRM) is used to gain detailed insights into the swallowing behavior. However, analyzing the extensive data from LTHRM is challenging and time consuming as medical experts have to analyze the data manually, which is slow and prone to errors. To address this challenge, we propose a Deep Learning based swallowing detection method to accurately identify swallowing events and secondary non-deglutitive-induced esophageal motility disorders in LTHRM data. We then proceed with clustering the identified swallows into distinct classes, which are analyzed by highly experienced clinicians to validate the different swallowing patterns. We evaluate our computational pipeline on a total of 25 LTHRMs, which were meticulously annotated by medical experts. By detecting more than 94% of all relevant swallow events and providing all relevant clusters for a more reliable diagnostic process among experienced clinicians, we are able to demonstrate the effectiveness as well as positive clinical impact of our approach to make LTHRM feasible in clinical care.

Alexander Geiger, Lars Wagner, Daniel Rueckert et al.

The explainability of deep learning models remains a significant challenge, particularly in the medical domain where interpretable outputs are critical for clinical trust and transparency. Path attribution methods such as Integrated Gradients rely on a baseline representing the absence of relevant features ("missingness"). Commonly used baselines, such as all-zero inputs, are often semantically meaningless, especially in medical contexts. While alternative baseline choices have been explored, existing methods lack a principled approach to dynamically select baselines tailored to each input. In this work, we examine the notion of missingness in the medical context, analyze its implications for baseline selection, and introduce a counterfactual-guided approach to address the limitations of conventional baselines. We argue that a generated counterfactual (i.e. clinically "normal" variation of the pathological input) represents a more accurate representation of a meaningful absence of features. We use a Variational Autoencoder in our implementation, though our concept is model-agnostic and can be applied with any suitable counterfactual method. We evaluate our concept on three distinct medical data sets and empirically demonstrate that counterfactual baselines yield more faithful and medically relevant attributions, outperforming standard baseline choices as well as other related methods.

Dongyu Liu, Kalyan Veeramachaneni, Alexander Geiger et al.

Anomaly detection plays a key role in air quality analysis by enhancing situational awareness and alerting users to potential hazards. However, existing anomaly detection approaches for air quality analysis have their own limitations regarding parameter selection (e.g., need for extensive domain knowledge), computational expense, general applicability (e.g., require labeled data), interpretability, and the efficiency of analysis. Furthermore, the poor quality of collected air quality data (inconsistently formatted and sometimes missing) also increases the difficulty of analysis substantially. In this paper, we systematically formulate design requirements for a system that can solve these limitations and then propose AQEyes, an integrated visual analytics system for efficiently monitoring, detecting, and examining anomalies in air quality data. In particular, we propose a unified end-to-end tunable machine learning pipeline that includes several data pre-processors and featurizers to deal with data quality issues. The pipeline integrates an efficient unsupervised anomaly detection method that works without the use of labeled data and overcomes the limitations of existing approaches. Further, we develop an interactive visualization system to visualize the outputs from the pipeline. The system incorporates a set of novel visualization and interaction designs, allowing analysts to visually examine air quality dynamics and anomalous events in multiple scales and from multiple facets. We demonstrate the performance of this pipeline through a quantitative evaluation and show the effectiveness of the visualization system using qualitative case studies on real-world datasets.