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Applications · Health / Medicine

Alexander Capstick, Rahul G. Krishnan, Payam Barnaghi

Large language models (LLMs) acquire a breadth of information across various domains. However, their computational complexity, cost, and lack of transparency often hinder their direct application for predictive tasks where privacy and interpretability are paramount. In fields such as healthcare, biology, and finance, specialised and interpretable linear models still hold considerable value. In such domains, labelled data may be scarce or expensive to obtain. Well-specified prior distributions over model parameters can reduce the sample complexity of learning through Bayesian inference; however, eliciting expert priors can be time-consuming. We therefore introduce AutoElicit to extract knowledge from LLMs and construct priors for predictive models. We show these priors are informative and can be refined using natural language. We perform a careful study contrasting AutoElicit with in-context learning and demonstrate how to perform model selection between the two methods. We find that AutoElicit yields priors that can substantially reduce error over uninformative priors, using fewer labels, and consistently outperform in-context learning. We show that AutoElicit saves over 6 months of labelling effort when building a new predictive model for urinary tract infections from sensor recordings of people living with dementia.

Applications · Health / Medicine

Kaicheng Fu, Changde Du, Jie Peng, Kunpeng Wang, Shuangchen Zhao, Xiaoyu Chen, Huiguang He

Emotion recognition systems face significant challenges in real-world applications, where novel emotion categories continually emerge and multiple emotions often co-occur. This paper introduces multi-label fine-grained class incremental emotion decoding, which aims to develop models capable of incrementally learning new emotion categories while maintaining the ability to recognize multiple concurrent emotions. We propose an Augmented Emotional Semantics Learning (AESL) framework to address two critical challenges: past- and future-missing partial label problems. AESL incorporates an augmented Emotional Relation Graph (ERG) for reliable soft label generation and affective dimension-based knowledge distillation for future-aware feature learning. We evaluate our approach on three datasets spanning brain activity and multimedia domains, demonstrating its effectiveness in decoding up to 28 fine-grained emotion categories. Results show that AESL significantly outperforms existing methods while effectively mitigating catastrophic forgetting. Our code is available at https://github.com/ChangdeDu/EmoGrowth.

Applications · Health / Medicine

Clara Fannjiang, Ji Won Park

Algorithms for machine learning-guided design, or *design algorithms*, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task—for example, to design novel proteins with high binding affinity to a therapeutic target—one must choose a design algorithm and specify any hyperparameters and predictive and/or generative models involved. How can these decisions be made such that the resulting designs are successful? This paper proposes a method for *design algorithm selection*, which aims to select design algorithms that will produce a distribution of design labels satisfying a user-specified success criterion—for example, that at least ten percent of designs’ labels exceed a threshold. It does so by combining designs’ predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms, building upon techniques from prediction-powered inference (Angelopoulos et al., 2023). The method is guaranteed with high probability to return design algorithms that yield successful label distributions (or the null set if none exist), if the density ratios between the design and labeled data distributions are known. We demonstrate the method’s effectiveness in simulated protein and RNA design tasks, in settings with either known or estimated density ratios.

Applications · Health / Medicine

Piyush Lalitkumar Tiwary, Kinjawl Bhattacharyya, Prathosh AP

Medical image segmentation models often struggle to generalize across different domains due to various reasons. Domain Generalization (DG) methods overcome this either through representation learning or data augmentation (DA). While representation learning methods seek domain-invariant features, they often rely on ad-hoc techniques and lack formal guarantees. DA methods, which enrich model representations through synthetic samples, have shown comparable or superior performance to representation learning approaches. We propose LangDAug, a novel **Lang**evin **D**ata **Aug**mentation for multi-source domain generalization in 2D medical image segmentation. LangDAug leverages Energy-Based Models (EBMs) trained via contrastive divergence to traverse between source domains, generating intermediate samples through Langevin dynamics. Theoretical analysis shows that LangDAug induces a regularization effect, and for GLMs, it upper-bounds the Rademacher complexity by the intrinsic dimensionality of the data manifold. Through extensive experiments on Fundus segmentation and 2D MRI prostate segmentation benchmarks, we show that LangDAug outperforms state-of-the-art domain generalization methods and effectively complements existing domain-randomization approaches. The codebase for our method is available at https://github.com/backpropagator/LangDAug.

Applications · Health / Medicine

Olga Ovcharenko, Florian Barkmann, Philip Toma, Imant Daunhawer, Julia Vogt, Sebastian Schelter, Valentina Boeva

Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present scSSL-Bench, a comprehensive benchmark that evaluates nineteen SSL methods. Our evaluation spans nine datasets and focuses on three common downstream tasks: batch correction, cell type annotation, and missing modality prediction. Furthermore, we systematically assess various data augmentation strategies. Our analysis reveals task-specific trade-offs: the specialized single-cell frameworks, scVI, CLAIRE, and the finetuned scGPT excel at uni-modal batch correction, while generic SSL methods, such as VICReg and SimCLR, demonstrate superior performance in cell typing and multi-modal data integration. Random masking emerges as the most effective augmentation technique across all tasks, surpassing domain-specific augmentations. Notably, our results indicate the need for a specialized single-cell multi-modal data integration framework. scSSL-Bench provides a standardized evaluation platform and concrete recommendations for applying SSL to single-cell analysis, advancing the convergence of deep learning and single-cell genomics.

Applications · Health / Medicine

Yanchao Tan, Hang Lv, Yunfei Zhan, Guofang Ma, Bo Xiong, Carl Yang

Language Models (LMs) have advanced diagnosis prediction by leveraging the semantic understanding of medical concepts in Electronic Health Records (EHRs). Despite these advancements, existing LM-based methods often fail to capture the structures of medical concepts (e.g., hierarchy structure from domain knowledge). In this paper, we propose BoxLM, a novel framework that unifies the structures and semantics of medical concepts for diagnosis prediction. Specifically, we propose a structure-semantic fusion mechanism via box embeddings, which integrates both ontology-driven and EHR-driven hierarchical structures with LM-based semantic embeddings, enabling interpretable medical concept representations.Furthermore, in the box-aware diagnosis prediction module, an evolve-and-memorize patient box learning mechanism is proposed to model the temporal dynamics of patient visits, and a volume-based similarity measurement is proposed to enable accurate diagnosis prediction. Extensive experiments demonstrate that BoxLM consistently outperforms state-of-the-art baselines, especially achieving strong performance in few-shot learning scenarios, showcasing its practical utility in real-world clinical settings.

Applications · Health / Medicine

Aaron Wenteler, Martina Occhetta, Nikhil Branson, Victor Curean, Magdalena Huebner, William Dee, William Connell, Siu Chung, Alex Hawkins-Hooker, Yasha Ektefaie 等

*In silico* modeling of transcriptional responses to perturbations is crucial for advancing our understanding of cellular processes and disease mechanisms. We present PertEval-scFM, a standardized framework designed to evaluate models for perturbation effect prediction. We apply PertEval-scFM to benchmark zero-shot single-cell foundation model (scFM) embeddings against baseline models to assess whether these contextualized representations enhance perturbation effect prediction. Our results show that scFM embeddings offer limited improvement over simple baseline models in the zero-shot setting, particularly under distribution shift. Overall, this study provides a systematic evaluation of zero-shot scFM embeddings for perturbation effect prediction, highlighting the challenges of this task and the limitations of current-generation scFMs. Our findings underscore the need for specialized models and high-quality datasets that capture a broader range of cellular states. Source code and documentation can be found at: https://github.com/aaronwtr/PertEval.

Applications · Health / Medicine

Alessandro Palma, Sergei Rybakov, Leon Hetzel, Stephan Günnemann, Fabian Theis

Latent space interpolations are a powerful tool for navigating deep generative models in applied settings. An example is single-cell RNA sequencing, where existing methods model cellular state transitions as latent space interpolations with variational autoencoders, often assuming linear shifts and Euclidean geometry. However, unless explicitly enforced, linear interpolations in the latent space may not correspond to geodesic paths on the data manifold, limiting methods that assume Euclidean geometry in the data representations. We introduce FlatVI, a novel training framework that regularises the latent manifold of discrete-likelihood variational autoencoders towards Euclidean geometry, specifically tailored for modelling single-cell count data. By encouraging straight lines in the latent space to approximate geodesic interpolations on the decoded single-cell manifold, FlatVI enhances compatibility with downstream approaches that assume Euclidean latent geometry. Experiments on synthetic data support the theoretical soundness of our approach, while applications to time-resolved single-cell RNA sequencing data demonstrate improved trajectory reconstruction and manifold interpolation.

Applications · Health / Medicine

Kian Kenyon-Dean, Zitong Jerry Wang, John Urbanik, Konstantin Donhauser, Jason Hartford, Saber Saberian, Nil Sahin, Ihab Bendidi, Safiye Celik, Juan Vera 等

Deriving insights from experimentally generated datasets requires methods that can account for random and systematic measurement errors and remove them in order to accurately represent the underlying effects of the conditions being tested. Here we present a framework for pretraining on large-scale microscopy datasets that includes three steps: (1) curating a set of diverse and self-consistent training samples, (2) scaling training of an appropriate foundation model architecture on this dataset, (3) evaluating intermediate layers of the trained model to identify the best representation for downstream tasks. Using this strategy, we present the largest foundation model for cell microscopy data to our knowledge, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60\% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome relationship recall, batch correction replicate consistency, and compound-gene activity prediction benchmarks.

Applications · Health / Medicine

Changshuo Liu, Lingze Zeng, Kaiping Zheng, Shaofeng Cai, Beng Chin Ooi, James Yip

Electronic health records (EHR) aggregate extensive data critical for advancing patient care and refining intervention strategies. EHR data is essential for epidemiological study, more commonly referred to as cohort study, where patients with shared characteristics or similar diseases are analyzed over time. Unfortunately, existing studies on cohort modeling are limited, struggling to derive fine-grained cohorts or effectively utilize cohort information, which hinders their ability to uncover intrinsic relationships between cohorts. To this end, we propose NeuralCohort, a cohort-aware neural representation learning method that precisely segments patients into finer-grained cohorts via an innovative cohort contextualization mechanism and captures both intra- and inter-cohort information using a Biscale Cohort Learning Module. Designed as a plug-in, NeuralCohort integrates seamlessly with existing backbone models, enhancing their cohort analysis capabilities by infusing deep cohort insights into the representation learning processes. The effectiveness and generalizability of NeuralCohort are validated across extensive real-world EHR datasets. Experimental results demonstrate that NeuralCohort consistently improves the performance of various backbone models, achieving up to an 8.1% increase in AUROC.

Applications · Health / Medicine

Ihab Bendidi, Yassir El Mesbahi, Alisandra Denton, Karush Suri, Kian Kenyon-Dean, Auguste Genovesio, Emmanuel Noutahi

Understanding cellular responses to stimuli is crucial for biological discovery and drug development. Transcriptomics provides interpretable, gene-level insights, while microscopy imaging offers rich predictive features but is harder to interpret. Weakly paired datasets, where samples share biological states, enable multimodal learning but are scarce, limiting their utility for training and multimodal inference. We propose a framework to enhance transcriptomics by distilling knowledge from microscopy images. Using weakly paired data, our method aligns and binds modalities, enriching gene expression representations with morphological information. To address data scarcity, we introduce (1) *Semi-Clipped*, an adaptation of CLIP for cross-modal distillation using pretrained foundation models, achieving state-of-the-art results, and (2) *PEA* (**P**erturbation **E**mbedding **A**ugmentation), a novel augmentation technique that enhances transcriptomics data while preserving inherent biological information. These strategies improve the predictive power and retain the interpretability of transcriptomics, enabling rich unimodal representations for complex biological tasks.

Applications · Health / Medicine

Jason Qin, Hans-Hermann Wessels, Carlos Fernandez-Granda, Yuhan Hao

Combinatorial CRISPR screening enables large-scale identification of synergistic gene pairs for combination therapies, but exhaustive experimentation is infeasible. We introduce NAIAD, an active learning framework that efficiently discovers optimal gene pairs by leveraging single-gene perturbation effects and adaptive gene embeddings that scale with the training data size, mitigating overfitting in small-sample learning while capturing complex gene interactions as more data is collected. Evaluated on four CRISPR datasets with over 350,000 interactions, NAIAD trained on small datasets outperforms existing models by up to 40\%. Its recommendation system prioritizes gene pairs with maximum predicted effects, accelerating discovery with fewer experiments. We also extend NAIAD to optimal drug combination identification among 2,000 candidates. Overall, NAIAD enhances combinatorial perturbation design and drives advances in genomics research and therapeutic development in combination therapy. Our code is publicly available at: https://github.com/NeptuneBio/NAIAD

Applications · Health / Medicine

Zhengrui Guo, Qichen Sun, Jiabo MA, Lishuang Feng, Jinzhuo Wang, Hao Chen

Whole slide image (WSI) analysis presents significant computational challenges due to the massive number of patches in gigapixel images. While transformer architectures excel at modeling long-range correlations through self-attention, their quadratic computational complexity makes them impractical for computational pathology applications. Existing solutions like local-global or linear self-attention reduce computational costs but compromise the strong modeling capabilities of full self-attention. In this work, we propose **Querent**, *i.e.*, the **quer**y-awar**e** long co**nt**extual dynamic modeling framework, which achieves a theoretically bounded approximation of full self-attention while delivering practical efficiency. Our method adaptively predicts which surrounding regions are most relevant for each patch, enabling focused yet unrestricted attention computation only with potentially important contexts. By using efficient region-wise metadata computation and importance estimation, our approach dramatically reduces computational overhead while preserving global perception to model fine-grained patch correlations. Through comprehensive experiments on biomarker prediction, gene mutation prediction, cancer subtyping, and survival analysis across over 10 WSI datasets, our method demonstrates superior performance compared to the state-of-the-art approaches. Codes are available at https://github.com/dddavid4real/Querent.

Applications · Health / Medicine

Justin Lee, Behnaz Moradi-Jamei, Heman Shakeri

Modeling the evolution of high-dimensional systems from limited snapshot observations at irregular time points poses a significant challenge in quantitative biology and related fields. Traditional approaches often rely on dimensionality reduction techniques, which can oversimplify the dynamics and fail to capture critical transient behaviors in non-equilibrium systems. We present Multi-Marginal Stochastic Flow Matching (MMSFM), a novel extension of simulation-free score and flow matching methods to the multi-marginal setting, enabling the alignment of high-dimensional data measured at non-equidistant time points without reducing dimensionality. The use of measure-valued splines enhances robustness to irregular snapshot timing, and score matching prevents overfitting in high-dimensional spaces. We validate our framework on several synthetic and benchmark datasets and apply it to single-cell perturbation data from melanoma cell lines and gene expression data collected at uneven time points.

Miscellaneous Aspects of Machine Learning · Causality

Andrew Ying, Zhichen Zhao, Ronghui Xu

We consider time to treatment initialization. This can commonly occur in preventive medicine, such as disease screening and vaccination; it can also occur with non-fatal health conditions such as HIV infection without the onset of AIDS. While traditional causal inference focused on ‘when to treat’ and its effects, including their possible dependence on subject characteristics, we consider the incremental causal effect when the intensity of time to treatment initialization is intervened upon. We provide identification of the incremental causal effect without the commonly required positivity assumption, as well as an estimation framework using inverse probability weighting. We illustrate our approach via simulation, and apply it to a rheumatoid arthritis study to evaluate the incremental effect of time to start methotrexate on joint pain.

Applications · Genetics, Cell Biology, Health, etc

Lazar Atanackovic, Xi (Nicole) Zhang, Brandon Amos, Mathieu Blanchette, Leo J Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depend on the microenvironment of cells specific to each patient. We propose *Meta Flow Matching* (MFM), a practical approach to integrate along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions, unlike previously proposed methods. We demonstrate the ability of MFM to improve the prediction of individual treatment responses on a large-scale multi-patient single-cell drug screen dataset.

Hieu Phan, Loc Le, Mao Nguyen, Phat Nguyen, Sang Nguyen, Minh-Triet Tran, Tho Quan

This research introduces XGA-Osteo, an innovative approach that leverages Explainable Artificial Intelligence (XAI) to enhance the accuracy and interpretability of knee osteoarthritis diagnosis. Recent studies have utilized AI approaches to automate the diagnosis using knee joint X-ray images. However, these studies have primarily focused on predicting the severity of osteoarthritis without providing additional information to assist doctors in their diagnoses. In addition to accurately diagnosing the severity of the condition, XGA-Osteo generates an anomaly map, produced from a reconstructed image of a healthy knee using adversarial learning. Thus, the abnormal regions in X-ray images can be highlighted, offering valuable supplementary information to medical experts during the diagnosis process.

Bum Chul Kwon, Simona Rabinovici-Cohen, Beldine Moturi, Ruth Mwaura, Kezia Wahome, Oliver Njeru, Miguel Shinyenyi, Catherine Wanjiru, Sekou Remy, William Ogallo 等

Biomedical foundation models, trained on diverse sources of small molecule data, hold great potential for accelerating drug discovery. However, their complex nature often presents a barrier for researchers seeking scientific insights and drug candidate generation. SPARK addresses this challenge by providing a user-friendly, web-based interface that empowers researchers to leverage these powerful models in their scientific workflows. Through SPARK, users can specify target proteins and desired molecule properties, adjust pre-trained models for tailored inferences, generate lists of potential drug candidates, analyze and compare molecules through interactive visualizations, and filter candidates based on key metrics (e.g., toxicity). By seamlessly integrating human knowledge and biomedical AI models' capabilities through an interactive web-based system, SPARK can improve the efficiency of collaboration between human experts and AI, thereby accelerating drug candidate discovery and ultimately leading to breakthroughs in finding cures for various diseases.

Pavel Blinov, Konstantin Egorov, Ivan Sviridov, Nikolay Ivanov, Stepan Botman, Evgeniy Tagin, Stepan Kudin, Galina Zubkova, Andrey V. Savchenko

Building an intelligent and efficient medical assistant is still a challenging AI problem. The major limitation comes from the data modality scarceness, which reduces comprehensive patient perception. This demo paper presents GigaPevt, the first multimodal medical assistant that combines the dialog capabilities of large language models with specialized medical models. Such an approach shows immediate advantages in dialog quality and metric performance, with a 1.18% accuracy improvement in the question-answering task.

Yixuan Wu, Kaiyuan Hu, Danny Z. Chen, Jian Wu

With the rapid advance of computer graphics and artificial intelligence technologies, the ways we interact with the world have undergone a transformative shift. Virtual Reality (VR) technology, aided by artificial intelligence (AI), has emerged as a dominant interaction media in multiple application areas, thanks to its advantage of providing users with immersive experiences. Among those applications, medicine is considered one of the most promising areas. In this paper, we present a comprehensive examination of the burgeoning field of AI-enhanced VR applications in medical care and services. By introducing a systematic taxonomy, we meticulously classify the pertinent techniques and applications into three well-defined categories based on different phases of medical diagnosis and treatment: Visualization Enhancement, VR-related Medical Data Processing, and VR-assisted Intervention. This categorization enables a structured exploration of the diverse roles that AI-powered VR plays in the medical domain, providing a framework for a more comprehensive understanding and evaluation of these technologies.nTo our best knowledge, this work is the first systematic survey of AI-powered VR systems in medical settings, laying a foundation for future research in this interdisciplinary domain.