Domain Adaptation of Attention Heads for Zero-shot Anomaly Detection

Zero-shot anomaly detection (ZSAD) in images is an approach that can detect anomalies without access to normal samples, which can be beneficial in various realistic scenarios where model training is not possible. However, existing ZSAD research has shown limitations by either not considering domain adaptation of general-purpose backbone models to anomaly detection domains or by implementing only partial adaptation to some model components. In this paper, we propose HeadCLIP to overcome these limitations by effectively adapting both text and image encoders to the domain. HeadCLIP generalizes the concepts of normality and abnormality through learnable prompts in the text encoder, and introduces learnable head weights to the image encoder to dynamically adjust the features held by each attention head according to domain characteristics. Additionally, we maximize the effect of domain adaptation by introducing a joint anomaly score that utilizes domain-adapted pixel-level information for image-level anomaly detection. Experimental results using multiple real datasets in both industrial and medical domains show that HeadCLIP outperforms existing ZSAD techniques at both pixel and image levels. In the industrial domain, improvements of up to 4.9%p in pixel-level mean anomaly detection score (mAD) and up to 3.0%p in image-level mAD were achieved, with similar improvements (3.2%p, 3.1%p) in the medical domain.

A Rule Based Solution to Co-reference Resolution in Clinical Text

Objective: The aim of this study was to build an effective co-reference resolution system tailored for the biomedical domain. Materials and Methods: Experiment materials used in this study is provided by the 2011 i2b2 Natural Language Processing Challenge. The 2011 i2b2 challenge involves coreference resolution in medical documents. Concept mentions have been annotated in clinical texts, and the mentions that co-refer in each document are to be linked by coreference chains. Normally, there are two ways of constructing a system to automatically discover co-referent links. One is to manually build rules for co-reference resolution, and the other category of approaches is to use machine learning systems to learn automatically from training datasets and then perform the resolution task on testing datasets. Results: Experiments show the existing co-reference resolution systems are able to find some of the co-referent links, and our rule based system performs well finding the majority of the co-referent links. Our system achieved 89.6% overall performance on multiple medical datasets. Conclusion: The experiment results show that manually crafted rules based on observation of training data is a valid way to accomplish high performance in this coreference resolution task for the critical biomedical domain.

Developing and Evaluating an AI-Assisted Prediction Model for Unplanned Intensive Care Admissions following Elective Neurosurgery using Natural Language Processing within an Electronic Healthcare Record System

Introduction: Timely care in a specialised neuro-intensive therapy unit (ITU) reduces mortality and hospital stays, with planned admissions being safer than unplanned ones. However, post-operative care decisions remain subjective. This study used artificial intelligence (AI), specifically natural language processing (NLP) to analyse electronic health records (EHRs) and predict ITU admissions for elective surgery patients. Methods: This study analysed the EHRs of elective neurosurgery patients from University College London Hospital (UCLH) using NLP. Patients were categorised into planned high dependency unit (HDU) or ITU admission; unplanned HDU or ITU admission; or ward / overnight recovery (ONR). The Medical Concept Annotation Tool (MedCAT) was used to identify SNOMED-CT concepts within the clinical notes. We then explored the utility of these identified concepts for a range of AI algorithms trained to predict ITU admission. Results: The CogStack-MedCAT NLP model, initially trained on hospital-wide EHRs, underwent two refinements: first with data from patients with Normal Pressure Hydrocephalus (NPH) and then with data from Vestibular Schwannoma (VS) patients, achieving a concept detection F1-score of 0.93. This refined model was then used to extract concepts from EHR notes of 2,268 eligible neurosurgical patients. We integrated the extracted concepts into AI models, including a decision tree model and a neural time-series model. Using the simpler decision tree model, we achieved a recall of 0.87 (CI 0.82 - 0.91) for ITU admissions, reducing the proportion of unplanned ITU cases missed by human experts from 36% to 4%. Conclusion: The NLP model, refined for accuracy, has proven its efficiency in extracting relevant concepts, providing a reliable basis for predictive AI models to use in clinically valid applications.

Disease Entity Recognition and Normalization is Improved with Large Language Model Derived Synthetic Normalized Mentions

Background: Machine learning methods for clinical named entity recognition and entity normalization systems can utilize both labeled corpora and Knowledge Graphs (KGs) for learning. However, infrequently occurring concepts may have few mentions in training corpora and lack detailed descriptions or synonyms, even in large KGs. For Disease Entity Recognition (DER) and Disease Entity Normalization (DEN), this can result in fewer high quality training examples relative to the number of known diseases. Large Language Model (LLM) generation of synthetic training examples could improve performance in these information extraction tasks. Methods: We fine-tuned a LLaMa-2 13B Chat LLM to generate a synthetic corpus containing normalized mentions of concepts from the Unified Medical Language System (UMLS) Disease Semantic Group. We measured overall and Out of Distribution (OOD) performance for DER and DEN, with and without synthetic data augmentation. We evaluated performance on 3 different disease corpora using 4 different data augmentation strategies, assessed using BioBERT for DER and SapBERT and KrissBERT for DEN. Results: Our synthetic data yielded a substantial improvement for DEN, in all 3 training corpora the top 1 accuracy of both SapBERT and KrissBERT improved by 3-9 points in overall performance and by 20-55 points in OOD data. A small improvement (1-2 points) was also seen for DER in overall performance, but only one dataset showed OOD improvement. Conclusion: LLM generation of normalized disease mentions can improve DEN relative to normalization approaches that do not utilize LLMs to augment data with synthetic mentions. Ablation studies indicate that performance gains for DEN were only partially attributable to improvements in OOD performance. The same approach has only a limited ability to improve DER. We make our software and dataset publicly available.

A Cost-effective, Stand-alone, and Real-time TinyML-Based Gait Diagnosis Unit Aimed at Lower-limb Robotic Prostheses and Exoskeletons

Robotic prostheses and exoskeletons can do wonders compared to their non-robotic counterpart. However, in a cost-soaring world where 1 in every 10 patients has access to normal medical prostheses, access to advanced ones is, unfortunately, extremely limited especially due to their high cost, a significant portion of which is contributed to by the diagnosis and controlling units. However, affordability is often not a major concern for developing such devices as with cost reduction, performance is also found to be deducted due to the cost vs. performance trade-off. Considering the gravity of such circumstances, the goal of this research was to propose an affordable wearable real-time gait diagnosis unit (GDU) aimed at robotic prostheses and exoskeletons. As a proof of concept, it has also developed the GDU prototype which leveraged TinyML to run two parallel quantized int8 models into an ESP32 NodeMCU development board (7.30 USD) to effectively classify five gait scenarios (idle, walk, run, hopping, and skip) and generate an anomaly score based on acceleration data received from two attached IMUs. The developed wearable gait diagnosis stand-alone unit could be fitted to any prosthesis or exoskeleton and could effectively classify the gait scenarios with an overall accuracy of 92% and provide anomaly scores within 95-96 ms with only 3 seconds of gait data in real-time.

Efficient Biomedical Entity Linking: Clinical Text Standardization with Low-Resource Techniques

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the Unified Medical Language System (UMLS) are developed and maintained to store millions of clinical entities including the definitions, relations and other corresponding information. These ontologies are used for standardization of clinical text by normalizing varying surface forms of a clinical term through Biomedical entity linking. With the introduction of transformer-based language models, there has been significant progress in Biomedical entity linking. In this work, we focus on learning through synonym pairs associated with the entities. As compared to the existing approaches, our approach significantly reduces the training data and resource consumption. Moreover, we propose a suite of context-based and context-less reranking techniques for performing the entity disambiguation. Overall, we achieve similar performance to the state-of-the-art zero-shot and distant supervised entity linking techniques on the Medmentions dataset, the largest annotated dataset on UMLS, without any domain-based training. Finally, we show that retrieval performance alone might not be sufficient as an evaluation metric and introduce an article level quantitative and qualitative analysis to reveal further insights on the performance of entity linking methods.

ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish

Advances in natural language processing techniques, such as named entity recognition and normalization to widely used standardized terminologies like UMLS or SNOMED-CT, along with the digitalization of electronic health records, have significantly advanced clinical text analysis. This study presents ClinLinker, a novel approach employing a two-phase pipeline for medical entity linking that leverages the potential of in-domain adapted language models for biomedical text mining: initial candidate retrieval using a SapBERT-based bi-encoder and subsequent re-ranking with a cross-encoder, trained by following a contrastive-learning strategy to be tailored to medical concepts in Spanish. This methodology, focused initially on content in Spanish, substantially outperforming multilingual language models designed for the same purpose. This is true even for complex scenarios involving heterogeneous medical terminologies and being trained on a subset of the original data. Our results, evaluated using top-k accuracy at 25 and other top-k metrics, demonstrate our approach's performance on two distinct clinical entity linking Gold Standard corpora, DisTEMIST (diseases) and MedProcNER (clinical procedures), outperforming previous benchmarks by 40 points in DisTEMIST and 43 points in MedProcNER, both normalized to SNOMED-CT codes. These findings highlight our approach's ability to address language-specific nuances and set a new benchmark in entity linking, offering a potent tool for enhancing the utility of digital medical records. The resulting system is of practical value, both for large scale automatic generation of structured data derived from clinical records, as well as for exhaustive extraction and harmonization of predefined clinical variables of interest.

A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models

Medical imaging is critical to the diagnosis, surveillance, and treatment of many health conditions, including oncological, neurological, cardiovascular, and musculoskeletal disorders, among others. Radiologists interpret these complex, unstructured images and articulate their assessments through narrative reports that remain largely unstructured. This unstructured narrative must be converted into a structured semantic representation to facilitate secondary applications such as retrospective analyses or clinical decision support. Here, we introduce the Corpus of Annotated Medical Imaging Reports (CAMIR), which includes 609 annotated radiology reports from three imaging modality types: Computed Tomography, Magnetic Resonance Imaging, and Positron Emission Tomography-Computed Tomography. Reports were annotated using an event-based schema that captures clinical indications, lesions, and medical problems. Each event consists of a trigger and multiple arguments, and a majority of the argument types, including anatomy, normalize the spans to pre-defined concepts to facilitate secondary use. CAMIR uniquely combines a granular event structure and concept normalization. To extract CAMIR events, we explored two BERT (Bi-directional Encoder Representation from Transformers)-based architectures, including an existing architecture (mSpERT) that jointly extracts all event information and a multi-step approach (PL-Marker++) that we augmented for the CAMIR schema.

A Survey on Visual Anomaly Detection: Challenge, Approach, and Prospect

Visual Anomaly Detection (VAD) endeavors to pinpoint deviations from the concept of normality in visual data, widely applied across diverse domains, e.g., industrial defect inspection, and medical lesion detection. This survey comprehensively examines recent advancements in VAD by identifying three primary challenges: 1) scarcity of training data, 2) diversity of visual modalities, and 3) complexity of hierarchical anomalies. Starting with a brief overview of the VAD background and its generic concept definitions, we progressively categorize, emphasize, and discuss the latest VAD progress from the perspective of sample number, data modality, and anomaly hierarchy. Through an in-depth analysis of the VAD field, we finally summarize future developments for VAD and conclude the key findings and contributions of this survey.

PM2: A New Prompting Multi-modal Model Paradigm for Few-shot Medical Image Classification

Few-shot learning has been successfully applied to medical image classification as only very few medical examples are available for training. Due to the challenging problem of limited number of annotated medical images, image representations should not be solely derived from a single image modality which is insufficient for characterizing concept classes. In this paper, we propose a new prompting multi-modal model paradigm on medical image classification based on multi-modal foundation models, called PM2. Besides image modality,PM2 introduces another supplementary text input, known as prompt, to further describe corresponding image or concept classes and facilitate few-shot learning across diverse modalities. To better explore the potential of prompt engineering, we empirically investigate five distinct prompt schemes under the new paradigm. Furthermore, linear probing in multi-modal models acts as a linear classification head taking as input only class token, which ignores completely merits of rich statistics inherent in high-level visual tokens. Thus, we alternatively perform a linear classification on feature distribution of visual tokens and class token simultaneously. To effectively mine such rich statistics, a global covariance pooling with efficient matrix power normalization is used to aggregate visual tokens. Then we study and combine two classification heads. One is shared for class token of image from vision encoder and prompt representation encoded by text encoder. The other is to classification on feature distribution of visual tokens from vision encoder. Extensive experiments on three medical datasets show that our PM2 significantly outperforms counterparts regardless of prompt schemes and achieves state-of-the-art performance.