Deep learning models have been widely used to assist doctors with clinical decision-making.

Tab. 4 provides detailed statistics of the two datasets. B.2 Clinical Predictive T asks We focus on two common clinical predictive tasks: readmission prediction and mortality prediction. In the case of the eICU dataset, the predictions are made 12 hours after admission. The overall prevalence for these tasks is 15% for readmission and 4% for mortality. For the MIMIC-IV dataset, the predictions are made at the time of discharge.

Clinical notes contain rich patient information, such as diagnoses or medications, making them valuable for patient representation learning. Recent advances in large language models have further improved the ability to extract meaningful representations from clinical texts. However, clinical notes are often missing. For example, in our analysis of the MIMIC-IV dataset, 24.5% of patients have no available discharge summaries. In such cases, representations can be learned from other modalities such as structured data, chest X-rays, or radiology reports. Yet the availability of these modalities is influenced by clinical decision-making and varies across patients, resulting in modality missing-not-at-random (MMNAR) patterns. We propose a causal representation learning framework that leverages observed data and informative missingness in multimodal clinical records. It consists of: (1) an MMNAR-aware modality fusion component that integrates structured data, imaging, and text while conditioning on missingness patterns to capture patient health and clinician-driven assignment; (2) a modality reconstruction component with contrastive learning to ensure semantic sufficiency in representation learning; and (3) a multitask outcome prediction model with a rectifier that corrects for residual bias from specific modality observation patterns. Comprehensive evaluations across MIMIC-IV and eICU show consistent gains over the strongest baselines, achieving up to 13.8% AUC improvement for hospital readmission and 13.1% for ICU admission.

Mapping clinical documents to standardised clinical vocabularies is an important task, as it provides structured data for information retrieval and analysis, which is essential to clinical research, hospital administration and improving patient care. However, manual coding is both difficult and time-consuming, making it impractical at scale. Automated coding can potentially alleviate this burden, improving the availability and accuracy of structured clinical data. The task is difficult to automate, as it requires mapping to high-dimensional and long-tailed target spaces, such as the International Classification of Diseases (ICD). While external knowledge sources have been readily utilised to enhance output code representation, the use of external resources for representing the input documents has been underexplored. In this work, we compute a structured representation of the input documents, making use of document-level knowledge graphs (KGs) that provide a comprehensive structured view of a patient's condition. The resulting knowledge graph efficiently represents the patient-centred input documents with 23\% of the original text while retaining 90\% of the information. We assess the effectiveness of this graph for automated ICD-9 coding by integrating it into the state-of-the-art ICD coding architecture PLM-ICD. Our experiments yield improved Macro-F1 scores by up to 3.20\% on popular benchmarks, while improving training efficiency. We attribute this improvement to different types of entities and relationships in the KG, and demonstrate the improved explainability potential of the approach over the text-only baseline.

Digital healthcare systems have enabled the collection of mass healthcare data in electronic healthcare records (EHRs), allowing artificial intelligence solutions for various healthcare prediction tasks. However, existing studies often focus on isolated components of EHR data, limiting their predictive performance and interpretability. To address this gap, we propose ProtoEHR, an interpretable hierarchical prototype learning framework that fully exploits the rich, multi-level structure of EHR data to enhance healthcare predictions. More specifically, ProtoEHR models relationships within and across three hierarchical levels of EHRs: medical codes, hospital visits, and patients. We first leverage large language models to extract semantic relationships among medical codes and construct a medical knowledge graph as the knowledge source. Building on this, we design a hierarchical representation learning framework that captures contextualized representations across three levels, while incorporating prototype information within each level to capture intrinsic similarities and improve generalization. To perform a comprehensive assessment, we evaluate ProtoEHR in two public datasets on five clinically significant tasks, including prediction of mortality, prediction of readmission, prediction of length of stay, drug recommendation, and prediction of phenotype. The results demonstrate the ability of ProtoEHR to make accurate, robust, and interpretable predictions compared to baselines in the literature. Furthermore, ProtoEHR offers interpretable insights on code, visit, and patient levels to aid in healthcare prediction.

Medication recommendation is a crucial task in healthcare, especially for patients with complex medical conditions. However, existing methods often struggle to effectively balance the reuse of historical medications with the introduction of new drugs in response to the changing patient conditions. In order to address this challenge, we propose an Adaptively Responsive network for Medication Recommendation ( ARMR), a new method which incorporates 1) a piecewise temporal learning component that distinguishes between recent and distant patient history, enabling more nuanced temporal understanding, and 2) an adaptively responsive mechanism that dynamically adjusts attention to new and existing drugs based on the patient's current health state and medication history. Experiments on the MIMIC-III and MIMIC-IV datasets indicate that ARMR has better performance compared with the state-of-the-art baselines in different evaluation metrics, which contributes to more personalized and accurate medication recommendations. The source code is publicly avaiable at: https://github.com/seucoin/armr2.

--A key challenge in learning from multimodal biological data is missing modalities, where all data from some modalities are missing for some patients. Current fusion methods address this by excluding patients with missing modalities, imputing missing modalities, or making predictions directly with partial modalities. T o address these limitations, we propose MAGNET (M issing-modality-A ware G raph neural NET work) for direct prediction with partial modalities, which introduces a patient-modality multi-head attention mechanism to fuse lower-dimensional modality em-beddings based on their importance and missingness. T o generate predictions, MAGNET further constructs a patient graph with fused multi-modal embeddings as node features and the connectivity determined by the modality missingness, followed by a conventional graph neural network. Experiments on three public multiomics datasets for cancer classification, with real-world instead of artificial missingness, show that MAGNET outperforms the state-of-the-art fusion methods. The data and code are available at https://github.com/SinaT ANCER development is a complex process driven by interactions across multiple molecular layers [1]-[3]. To unravel this complexity, cancer research increasingly profiles patients using these molecular modalities, known as multi-omics. Each omics modality provides unique value individually while multimodal fusion can offer complementary insights [4], [5]. Multimodal machine learning approaches integrate these biological modalities to construct a comprehensive patient profile for improving downstream predictive tasks, such as cancer classification and subtyping [6]-[8]. Despite the effectiveness of multimodal biological data fusion, conventional approaches often assume that all omics modalities are available for each patient [9], [10]. However, missing modalities, characterized by structured missingness where all data from some modalities are missing for some patients, are an unavoidable challenge in biomedical applications [11]. For example, some patients may have missing tran-scriptomic profiles due to sample degradation or insufficient RNA quality, while others may lack proteomic data because of cost constraints or technical limitations [12], [13].

Patient stratification--identifying clinically meaningful subgroups--is essential for advancing personalized medicine through improved diagnostics and treatment strategies. Electronic health records (EHRs), particularly those from intensive care units (ICUs), contain rich temporal clinical data that can be leveraged for this purpose. In this work, we introduce ICU-TSB (Temporal Stratification Benchmark), the first comprehensive benchmark for evaluating patient stratification based on temporal patient representation learning using three publicly available ICU EHR datasets. A key contribution of our benchmark is a novel hierarchical evaluation framework utilizing disease taxonomies to measure the alignment of discovered clusters with clinically validated disease groupings. In our experiments with ICU-TSB, we compared statistical methods and several recurrent neural networks, including LSTM and GRU, for their ability to generate effective patient representations for subsequent clustering of patient trajectories. Our results demonstrate that temporal representation learning can rediscover clinically meaningful patient cohorts; nevertheless, it remains a challenging task, with v-measuring varying from up to 0.46 at the top level of the taxonomy to up to 0.40 at the lowest level. To further enhance the practical utility of our findings, we also evaluate multiple strategies for assigning interpretable labels to the identified clusters.