As machine learning systems become increasingly integrated into human-centered domains such as healthcare, ensuring fairness while maintaining high predictive performance is critical. Existing bias mitigation techniques often impose a trade-off between fairness and accuracy, inadvertently degrading performance for certain demographic groups. In high-stakes domains like clinical diagnosis, such trade-offs are ethically and practically unacceptable. In this study, we propose a fairness-without-harm approach by learning distinct representations for different demographic groups and selectively applying demographic experts consisting of group-specific representations and personalized classifiers through a no-harm constrained selection. We evaluate our approach on three real-world medical datasets—covering eye disease, skin cancer, and X-ray diagnosis—as well as two face datasets. Extensive empirical results demonstrate the effectiveness of our approach in achieving fairness without harm.

Domain adaptation (DA) tackles the issue of distribution shift by learning a model from a source domain that generalizes to a target domain. However, most existing DA methods are designed for scenarios where the source and target domain data lie within the same feature space, which limits their applicability in real-world situations. Recently, heterogeneous DA (HeDA) methods have been introduced to address the challenges posed by heterogeneous feature space between source and target domains. Despite their successes, current HeDA techniques fall short when there is a mismatch in both feature and label spaces. To address this, this paper explores a new DA scenario called open-set HeDA (OSHeDA). In OSHeDA, the model must not only handle heterogeneity in feature space but also identify samples belonging to novel classes. To tackle this challenge, we first develop a novel theoretical framework that constructs learning bounds for prediction error on target domain. Guided by this framework, we propose a new DA method called Representation Learning for OSHeDA (RL-OSHeDA). This method is designed to simultaneously transfer knowledge between heterogeneous data sources and identify novel classes. Experiments across text, image, and clinical data demonstrate the effectiveness of our algorithm. Model implementation is available at https://github.com/pth1993/OSHeDA.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

., the six-organ dysfunction assessment of SOFA in Figure 1) play a vital role in sepsis identification within clinicians' workflow, providing evidence-based risk assessments essential for sepsis diagnosis. However, artificial intelligence (AI) sepsis prediction models typically generate a single sepsis risk score without incorporating clinical calculators for assessing organ dysfunctions, making the models less convincing and transparent to clinicians. To bridge the gap, we propose to mimic clinicians' workflow with a novel framework SepsisCalc to integrate clinical calculators into the predictive model, yielding a clinically transparent and precise model for utilization in clinical settings. Practically, clinical calculators usually combine information from multiple component variables in Electronic Health Records (EHR), and might not be applicable when the variables are (partially) missing. We mitigate this issue by representing EHRs as temporal graphs and integrating a learning module to dynamically add the accurately estimated calculator to the graphs. Experimental results on real-world datasets show that the proposed model outperforms state-of-the-art methods on sepsis prediction tasks. Moreover, we developed a system to identify organ dysfunctions and potential sepsis risks, providing a human-AI interaction tool for deployment, which can help clinicians understand the prediction outputs and prepare timely interventions for the corresponding dysfunctions, paving the way for actionable clinical decision-making support for early intervention.

As machine learning (ML) algorithms are increasingly used in medical image analysis, concerns have emerged about their potential biases against certain social groups. Although many approaches have been proposed to ensure the fairness of ML models, most existing works focus only on medical image diagnosis tasks, such as image classification and segmentation, and overlooked prognosis scenarios, which involve predicting the likely outcome or progression of a medical condition over time. To address this gap, we introduce FairTTE, the first comprehensive framework for assessing fairness in time-to-event (TTE) prediction in medical imaging. FairTTE encompasses a diverse range of imaging modalities and TTE outcomes, integrating cutting-edge TTE prediction and fairness algorithms to enable systematic and fine-grained analysis of fairness in medical image prognosis. Leveraging causal analysis techniques, FairTTE uncovers and quantifies distinct sources of bias embedded within medical imaging datasets. Our large-scale evaluation reveals that bias is pervasive across different imaging modalities and that current fairness methods offer limited mitigation. We further demonstrate a strong association between underlying bias sources and model disparities, emphasizing the need for holistic approaches that target all forms of bias. Notably, we find that fairness becomes increasingly difficult to maintain under distribution shifts, underscoring the limitations of existing solutions and the pressing need for more robust, equitable prognostic models.

Sleep staging has become a critical task in diagnosing and treating sleep disorders to prevent sleep-related diseases. With growing large-scale sleep databases, significant progress has been made toward automatic sleep staging. However, previous studies face critical problems in sleep studies; the heterogeneity of subjects' physiological signals, the inability to extract meaningful information from unlabeled data to improve predictive performances, the difficulty in modeling correlations between sleep stages, and the lack of an effective mechanism to quantify predictive uncertainty. In this study, we propose a neural network-based sleep staging model, DREAM, to learn domain generalized representations from physiological signals and model sleep dynamics. DREAM learns sleep-related and subject-invariant representations from diverse subjects' sleep signals and models sleep dynamics by capturing interactions between sequential signal segments and between sleep stages. We conducted a comprehensive empirical study to demonstrate the superiority of DREAM, including sleep stage prediction experiments, a case study, the usage of unlabeled data, and uncertainty. Notably, the case study validates DREAM's ability to learn the generalized decision function for new subjects, especially in case there are differences between testing and training subjects. Uncertainty quantification shows that DREAM provides prediction uncertainty, making the model reliable and helping sleep experts in real-world applications.

Although recent advances in machine learning have shown its success to learn from independent and identically distributed (IID) data, it is vulnerable to out-of-distribution (OOD) data in an open world. Domain generalization (DG) deals with such an issue and it aims to learn a model from multiple source domains that can be generalized to unseen target domains. Existing studies on DG have largely focused on stationary settings with homogeneous source domains. However, in many applications, domains may evolve along a specific direction (e.g., time, space). Without accounting for such non-stationary patterns, models trained with existing methods may fail to generalize on OOD data. In this paper, we study domain generalization in non-stationary environment. We first examine the impact of environmental non-stationarity on model performance and establish the theoretical upper bounds for the model error at target domains. Then, we propose a novel algorithm based on adaptive invariant representation learning, which leverages the non-stationary pattern to train a model that attains good performance on target domains. Experiments on both synthetic and real data validate the proposed algorithm.

Sleep staging is a key challenge in diagnosing and treating sleep-related diseases due to its labor-intensive, time-consuming, costly, and error-prone. With the availability of large-scale sleep signal data, many deep learning methods are proposed for automatic sleep staging. However, these existing methods face several challenges including the heterogeneity of patients’ underlying health conditions and the difficulty modeling complex interactions between sleep stages. In this paper, we propose a neural network architecture named DREAM to tackle these issues for automatic sleep staging. DREAM consists of (i) a feature representation network that generates robust representations for sleep signals via the variational auto-encoder framework and contrastive learning and (ii) a sleep stage classification network that explicitly models the interactions between sleep stages in the sequential context at both feature representation and label classification levels via Transformer and conditional random field architectures. Our experimental results indicate that DREAM significantly outperforms existing methods for automatic sleep staging on three sleep signal datasets.

molecular design is a key challenge in drug discovery due to the complexity of chemical space. With the availability of molecular datasets and advances in machine learning, many deep generative models are proposed for generating novel molecules with desired properties. However, most of the existing models focus only on molecular distribution learning and target-based molecular design, thereby hindering their potentials in real-world applications. In drug discovery, phenotypic molecular design has advantages over target-based molecular design, especially in first-in-class drug discovery. In this work, we propose the first deep graph generative model (FAME) targeting phenotypic molecular design, in particular gene expression-based molecular design. FAME leverages a conditional variational autoencoder framework to learn the conditional distribution generating molecules from gene expression profiles. However, this distribution is difficult to learn due to the complexity of the molecular space and the noisy phenomenon in gene expression data. To tackle these issues, a gene expression denoising (GED) model that employs contrastive objective function is first proposed to reduce noise from gene expression data. FAME is then designed to treat molecules as the sequences of fragments and learn to generate these fragments in autoregressive manner. By leveraging this fragment-based generation strategy and the denoised gene expression profiles, FAME can generate novel molecules with a high validity rate and desired biological activity. The experimental results show that FAME outperforms existing methods including both SMILES-based and graph-based deep generative models for phenotypic molecular design. Furthermore, the effective mechanism for reducing noise in gene expression data proposed in our study can be applied to omics data modeling in general for facilitating phenotypic drug discovery.

Complication risk profiling is a key challenge in the healthcare domain due to the complex interaction between heterogeneous entities (e.g., visit, disease, medication) in clinical data. With the availability of real-world clinical data such as electronic health records and insurance claims, many deep learning methods are proposed for complication risk profiling. However, these existing methods face two open challenges. First, data heterogeneity relates to those methods leveraging clinical data from a single view only while the data can be considered from multiple views (e.g., sequence of clinical visits, set of clinical features). Second, generalized prediction relates to most of those methods focusing on single-task learning, whereas each complication onset is predicted independently, leading to suboptimal models. We propose a multi-view multi-task network (MuViTaNet) for predicting the onset of multiple complications to tackle these issues. In particular, MuViTaNet complements patient representation by using a multi-view encoder to effectively extract information by considering clinical data as both sequences of clinical visits and sets of clinical features. In addition, it leverages additional information from both related labeled and unlabeled datasets to generate more generalized representations by using a new multi-task learning scheme for making more accurate predictions. The experimental results show that MuViTaNet outperforms existing methods for profiling the development of cardiac complications in breast cancer survivors. Furthermore, thanks to its multi-view multi-task architecture, MuViTaNet also provides an effective mechanism for interpreting its predictions in multiple perspectives, thereby helping clinicians discover the underlying mechanism triggering the onset and for making better clinical treatments in real-world scenarios.

Named entity recognition (NER) has attracted a substantial amount of research. Recently, several neural network-based models have been proposed and achieved high performance. However, there is little research on fine-grained NER (FG-NER), in which hundreds of named entity categories must be recognized, especially for non-English languages. It is still an open question whether there is a model that is robust across various settings or the proper model varies depending on the language, the number of named entity categories, and the size of training datasets. This paper first presents an empirical comparison of FG-NER models for English and Japanese and demonstrates that LSTM+CNN+CRF (Ma and Hovy, 2016), one of the state-of-the-art methods for English NER, also works well for English FG-NER but does not work well for Japanese, a language that has a large number of character types. To tackle this problem, we propose a method to improve the neural network-based Japanese FG-NER performance by removing the CNN layer and utilizing dictionary and category embeddings. Experiment results show that the proposed method improves Japanese FG-NER F-score from 66.76% to 75.18%.