Michael Moor

Michael Moor, Qian Huang, Shirley Wu et al.

Medicine, by its nature, is a multifaceted domain that requires the synthesis of information across various modalities. Medical generative vision-language models (VLMs) make a first step in this direction and promise many exciting clinical applications. However, existing models typically have to be fine-tuned on sizeable down-stream datasets, which poses a significant limitation as in many medical applications data is scarce, necessitating models that are capable of learning from few examples in real-time. Here we propose Med-Flamingo, a multimodal few-shot learner adapted to the medical domain. Based on OpenFlamingo-9B, we continue pre-training on paired and interleaved medical image-text data from publications and textbooks. Med-Flamingo unlocks few-shot generative medical visual question answering (VQA) abilities, which we evaluate on several datasets including a novel challenging open-ended VQA dataset of visual USMLE-style problems. Furthermore, we conduct the first human evaluation for generative medical VQA where physicians review the problems and blinded generations in an interactive app. Med-Flamingo improves performance in generative medical VQA by up to 20\% in clinician's rating and firstly enables multimodal medical few-shot adaptations, such as rationale generation. We release our model, code, and evaluation app under https://github.com/snap-stanford/med-flamingo.

Hamed Nilforoshan, Michael Moor, Yusuf Roohani et al.

Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. There are a large number of methods to predict the effect of an existing intervention based on historical data from individuals who received it. However, in many settings it is important to predict the effects of novel interventions (e.g., a newly invented drug), which these methods do not address. Here, we consider zero-shot causal learning: predicting the personalized effects of a novel intervention. We propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention's effect as a task. CaML trains a single meta-model across thousands of tasks, each constructed by sampling an intervention, its recipients, and its nonrecipients. By leveraging both intervention information (e.g., a drug's attributes) and individual features~(e.g., a patient's history), CaML is able to predict the personalized effects of novel interventions that do not exist at the time of training. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, \method's zero-shot predictions outperform even strong baselines trained directly on data from the test interventions.

Benjamin Yan, Ruochen Liu, David E. Kuo et al.

Automatically generated reports from medical images promise to improve the workflow of radiologists. Existing methods consider an image-to-report modeling task by directly generating a fully-fledged report from an image. However, this conflates the content of the report (e.g., findings and their attributes) with its style (e.g., format and choice of words), which can lead to clinically inaccurate reports. To address this, we propose a two-step approach for radiology report generation. First, we extract the content from an image; then, we verbalize the extracted content into a report that matches the style of a specific radiologist. For this, we leverage RadGraph -- a graph representation of reports -- together with large language models (LLMs). In our quantitative evaluations, we find that our approach leads to beneficial performance. Our human evaluation with clinical raters highlights that the AI-generated reports are indistinguishably tailored to the style of individual radiologist despite leveraging only a few examples as context.

Benjamin Gundersen, Nicolas Deperrois, Samuel Ruiperez-Campillo et al.

Recent advances in vision-language models (VLMs) have improved Chest X-ray (CXR) interpretation in multiple aspects. However, many medical VLMs rely solely on supervised fine-tuning (SFT), which optimizes next-token prediction without evaluating answer quality. In contrast, reinforcement learning (RL) can incorporate task-specific feedback, and its combination with explicit intermediate reasoning ("thinking") has demonstrated substantial gains on verifiable math and coding tasks. To investigate the effects of RL and thinking in a CXR VLM, we perform large-scale SFT on CXR data to build an updated RadVLM based on Qwen3-VL, followed by a cold-start SFT stage that equips the model with basic thinking ability. We then apply Group Relative Policy Optimization (GRPO) with clinically grounded, task-specific rewards for report generation and visual grounding, and run matched RL experiments on both domain-specific and general-domain Qwen3-VL variants, with and without thinking. Across these settings, we find that while strong SFT remains crucial for high base performance, RL provides additional gains on both tasks, whereas explicit thinking does not appear to further improve results. Under a unified evaluation pipeline, the RL-optimized RadVLM models outperform their baseline counterparts and reach state-of-the-art performance on both report generation and grounding, highlighting clinically aligned RL as a powerful complement to SFT for medical VLMs.

Jaehoon Yun, Jiwoong Sohn, Jungwoo Park et al.

Large language models have shown promise in clinical decision making, but current approaches struggle to localize and correct errors at specific steps of the reasoning process. This limitation is critical in medicine, where identifying and addressing reasoning errors is essential for accurate diagnosis and effective patient care. We introduce Med-PRM, a process reward modeling framework that leverages retrieval-augmented generation to verify each reasoning step against established medical knowledge bases. By verifying intermediate reasoning steps with evidence retrieved from clinical guidelines and literature, our model can precisely assess the reasoning quality in a fine-grained manner. Evaluations on five medical QA benchmarks and two open-ended diagnostic tasks demonstrate that Med-PRM achieves state-of-the-art performance, with improving the performance of base models by up to 13.50% using Med-PRM. Moreover, we demonstrate the generality of Med-PRM by integrating it in a plug-and-play fashion with strong policy models such as Meerkat, achieving over 80\% accuracy on MedQA for the first time using small-scale models of 8 billion parameters. Our code and data are available at: https://med-prm.github.io/

Samuel Schmidgall, Rojin Ziaei, Carl Harris et al.

Evaluating large language models (LLM) in clinical scenarios is crucial to assessing their potential clinical utility. Existing benchmarks rely heavily on static question-answering, which does not accurately depict the complex, sequential nature of clinical decision-making. Here, we introduce AgentClinic, a multimodal agent benchmark for evaluating LLMs in simulated clinical environments that include patient interactions, multimodal data collection under incomplete information, and the usage of various tools, resulting in an in-depth evaluation across nine medical specialties and seven languages. We find that solving MedQA problems in the sequential decision-making format of AgentClinic is considerably more challenging, resulting in diagnostic accuracies that can drop to below a tenth of the original accuracy. Overall, we observe that agents sourced from Claude-3.5 outperform other LLM backbones in most settings. Nevertheless, we see stark differences in the LLMs' ability to make use of tools, such as experiential learning, adaptive retrieval, and reflection cycles. Strikingly, Llama-3 shows up to 92% relative improvements with the notebook tool that allows for writing and editing notes that persist across cases. To further scrutinize our clinical simulations, we leverage real-world electronic health records, perform a clinical reader study, perturb agents with biases, and explore novel patient-centric metrics that this interactive environment firstly enables.

Cyril Zakka, Joseph Cho, Gracia Fahed et al.

Clinicians spend large amounts of time on clinical documentation, and inefficiencies impact quality of care and increase clinician burnout. Despite the promise of electronic medical records (EMR), the transition from paper-based records has been negatively associated with clinician wellness, in part due to poor user experience, increased burden of documentation, and alert fatigue. In this study, we present Almanac Copilot, an autonomous agent capable of assisting clinicians with EMR-specific tasks such as information retrieval and order placement. On EHR-QA, a synthetic evaluation dataset of 300 common EHR queries based on real patient data, Almanac Copilot obtains a successful task completion rate of 74% (n = 221 tasks) with a mean score of 2.45 over 3 (95% CI:2.34-2.56). By automating routine tasks and streamlining the documentation process, our findings highlight the significant potential of autonomous agents to mitigate the cognitive load imposed on clinicians by current EMR systems.

Melanie Rieff, Maya Varma, Ossian Rabow et al.

Multimodal in-context learning (ICL) remains underexplored despite significant potential for domains such as medicine. Clinicians routinely encounter diverse, specialized tasks requiring adaptation from limited examples, such as drawing insights from a few relevant prior cases or considering a constrained set of differential diagnoses. While multimodal large language models (MLLMs) have shown advances in medical visual question answering (VQA), their ability to learn multimodal tasks from context is largely unknown. We introduce SMMILE, the first expert-driven multimodal ICL benchmark for medical tasks. Eleven medical experts curated problems, each including a multimodal query and multimodal in-context examples as task demonstrations. SMMILE encompasses 111 problems (517 question-image-answer triplets) covering 6 medical specialties and 13 imaging modalities. We further introduce SMMILE++, an augmented variant with 1038 permuted problems. A comprehensive evaluation of 15 MLLMs demonstrates that most models exhibit moderate to poor multimodal ICL ability in medical tasks. In open-ended evaluations, ICL contributes only an 8% average improvement over zero-shot on SMMILE and 9.4% on SMMILE++. We observe a susceptibility for irrelevant in-context examples: even a single noisy or irrelevant example can degrade performance by up to 9.5%. Moreover, we observe that MLLMs are affected by a recency bias, where placing the most relevant example last can lead to substantial performance improvements of up to 71%. Our findings highlight critical limitations and biases in current MLLMs when learning multimodal medical tasks from context. SMMILE is available at https://smmile-benchmark.github.io.

Yulun Jiang, Yekun Chai, Maria Brbić et al.

The ability to process information from multiple modalities and to reason through it step-by-step remains a critical challenge in advancing artificial intelligence. However, existing reasoning benchmarks focus on text-only reasoning, or employ multimodal questions that can be answered by directly retrieving information from a non-text modality. Thus, complex reasoning remains poorly understood in multimodal domains. Here, we present MARBLE, a challenging multimodal reasoning benchmark that is designed to scrutinize multimodal language models (MLLMs) in their ability to carefully reason step-by-step through complex multimodal problems and environments. MARBLE is composed of two highly challenging tasks, M-Portal and M-Cube, that require the crafting and understanding of multistep plans under spatial, visual, and physical constraints. We find that current MLLMs perform poorly on MARBLE -- all the 12 advanced models obtain near-random performance on M-Portal and 0% accuracy on M-Cube. Only in simplified subtasks some models outperform the random baseline, indicating that complex reasoning is still a challenge for existing MLLMs. Moreover, we show that perception remains a bottleneck, where MLLMs occasionally fail to extract information from the visual inputs. By shedding a light on the limitations of MLLMs, we hope that MARBLE will spur the development of the next generation of models with the ability to reason and plan across many, multimodal reasoning steps.

Michael Moor, Nicolas Bennet, Drago Plecko et al.

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains $156,309$ unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to $26,734$ ($17.1\%$) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of $0.847 \pm 0.050$ (internal out-of sample validation) and $0.761 \pm 0.052$ (external validation). For a harmonised prevalence of $17\%$, at $80\%$ recall our model detects septic patients with $39\%$ precision 3.7 hours in advance.

Max Horn, Edward De Brouwer, Michael Moor et al.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

Jannis Born, Nina Wiedemann, Gabriel Brändle et al.

Controlling the COVID-19 pandemic largely hinges upon the existence of fast, safe, and highly-available diagnostic tools. Ultrasound, in contrast to CT or X-Ray, has many practical advantages and can serve as a globally-applicable first-line examination technique. We provide the largest publicly available lung ultrasound (US) dataset for COVID-19 consisting of 106 videos from three classes (COVID-19, bacterial pneumonia, and healthy controls); curated and approved by medical experts. On this dataset, we perform an in-depth study of the value of deep learning methods for differential diagnosis of COVID-19. We propose a frame-based convolutional neural network that correctly classifies COVID-19 US videos with a sensitivity of 0.98+-0.04 and a specificity of 0.91+-08 (frame-based sensitivity 0.93+-0.05, specificity 0.87+-0.07). We further employ class activation maps for the spatio-temporal localization of pulmonary biomarkers, which we subsequently validate for human-in-the-loop scenarios in a blindfolded study with medical experts. Aiming for scalability and robustness, we perform ablation studies comparing mobile-friendly, frame- and video-based architectures and show reliability of the best model by aleatoric and epistemic uncertainty estimates. We hope to pave the road for a community effort toward an accessible, efficient and interpretable screening method and we have started to work on a clinical validation of the proposed method. Data and code are publicly available.

Zhiliang Wu, Yinchong Yang, Yunpu Ma et al.

Randomized controlled trials typically analyze the effectiveness of treatments with the goal of making treatment recommendations for patient subgroups. With the advance of electronic health records, a great variety of data has been collected in clinical practice, enabling the evaluation of treatments and treatment policies based on observational data. In this paper, we focus on learning individualized treatment rules (ITRs) to derive a treatment policy that is expected to generate a better outcome for an individual patient. In our framework, we cast ITRs learning as a contextual bandit problem and minimize the expected risk of the treatment policy. We conduct experiments with the proposed framework both in a simulation study and based on a real-world dataset. In the latter case, we apply our proposed method to learn the optimal ITRs for the administration of intravenous (IV) fluids and vasopressors (VP). Based on various offline evaluation methods, we could show that the policy derived in our framework demonstrates better performance compared to both the physicians and other baselines, including a simple treatment prediction approach. As a long-term goal, our derived policy might eventually lead to better clinical guidelines for the administration of IV and VP.

Michael Moor, Max Horn, Christian Bock et al.

The signature transform is a 'universal nonlinearity' on the space of continuous vector-valued paths, and has received attention for use in machine learning on time series. However, real-world temporal data is typically observed at discrete points in time, and must first be transformed into a continuous path before signature techniques can be applied. We make this step explicit by characterising it as an imputation problem, and empirically assess the impact of various imputation strategies when applying signature-based neural nets to irregular time series data. For one of these strategies, Gaussian process (GP) adapters, we propose an extension~(GP-PoM) that makes uncertainty information directly available to the subsequent classifier while at the same time preventing costly Monte-Carlo (MC) sampling. In our experiments, we find that the choice of imputation drastically affects shallow signature models, whereas deeper architectures are more robust. Next, we observe that uncertainty-aware predictions (based on GP-PoM or indicator imputations) are beneficial for predictive performance, even compared to the uncertainty-aware training of conventional GP adapters. In conclusion, we have demonstrated that the path construction is indeed crucial for signature models and that our proposed strategy leads to competitive performance in general, while improving robustness of signature models in particular.

Max Horn, Michael Moor, Christian Bock et al.

Despite the eminent successes of deep neural networks, many architectures are often hard to transfer to irregularly-sampled and asynchronous time series that commonly occur in real-world datasets, especially in healthcare applications. This paper proposes a novel approach for classifying irregularly-sampled time series with unaligned measurements, focusing on high scalability and data efficiency. Our method SeFT (Set Functions for Time Series) is based on recent advances in differentiable set function learning, extremely parallelizable with a beneficial memory footprint, thus scaling well to large datasets of long time series and online monitoring scenarios. Furthermore, our approach permits quantifying per-observation contributions to the classification outcome. We extensively compare our method with existing algorithms on multiple healthcare time series datasets and demonstrate that it performs competitively whilst significantly reducing runtime.

Michael Moor, Max Horn, Bastian Rieck et al.

We propose a novel approach for preserving topological structures of the input space in latent representations of autoencoders. Using persistent homology, a technique from topological data analysis, we calculate topological signatures of both the input and latent space to derive a topological loss term. Under weak theoretical assumptions, we construct this loss in a differentiable manner, such that the encoding learns to retain multi-scale connectivity information. We show that our approach is theoretically well-founded and that it exhibits favourable latent representations on a synthetic manifold as well as on real-world image data sets, while preserving low reconstruction errors.

Stephanie L. Hyland, Martin Faltys, Matthias Hüser et al.

Intensive care clinicians are presented with large quantities of patient information and measurements from a multitude of monitoring systems. The limited ability of humans to process such complex information hinders physicians to readily recognize and act on early signs of patient deterioration. We used machine learning to develop an early warning system for circulatory failure based on a high-resolution ICU database with 240 patient years of data. This automatic system predicts 90.0% of circulatory failure events (prevalence 3.1%), with 81.8% identified more than two hours in advance, resulting in an area under the receiver operating characteristic curve of 94.0% and area under the precision-recall curve of 63.0%. The model was externally validated in a large independent patient cohort.

Michael Moor, Max Horn, Bastian Rieck et al.

Sepsis is a life-threatening host response to infection associated with high mortality, morbidity, and health costs. Its management is highly time-sensitive since each hour of delayed treatment increases mortality due to irreversible organ damage. Meanwhile, despite decades of clinical research, robust biomarkers for sepsis are missing. Therefore, detecting sepsis early by utilizing the affluence of high-resolution intensive care records has become a challenging machine learning problem. Recent advances in deep learning and data mining promise to deliver a powerful set of tools to efficiently address this task. This empirical study proposes two novel approaches for the early detection of sepsis: a deep learning model and a lazy learner based on time series distances. Our deep learning model employs a temporal convolutional network that is embedded in a Multi-task Gaussian Process Adapter framework, making it directly applicable to irregularly-spaced time series data. Our lazy learner, by contrast, is an ensemble approach that employs dynamic time warping. We frame the timely detection of sepsis as a supervised time series classification task. For this, we derive the most recent sepsis definition in an hourly resolution to provide the first fully accessible early sepsis detection environment. Seven hours before sepsis onset, our methods improve area under the precision--recall curve from 0.25 to 0.35/0.40 over the state of the art. This demonstrates that they are well-suited for detecting sepsis in the crucial earlier stages when management is most effective.