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Applications/Health

Sanja Scepanovic, Ivica Obadic, Sagar Joglekar, Laura GIUSTARINI, Cristiano Nattero, Daniele Quercia, Xiaoxiang Zhu

As extreme weather events become more frequent, understanding their impact on human health becomes increasingly crucial. However, the utilization of Earth Observation to effectively analyze the environmental context in relation to health remains limited. This limitation is primarily due to the lack of fine-grained spatial and temporal data in public and population health studies, hindering a comprehensive understanding of health outcomes. Additionally, obtaining appropriate environmental indices across different geographical levels and timeframes poses a challenge. For the years 2019 (pre-COVID) and 2020 (COVID), we collected spatio-temporal indicators for all Lower Layer Super Output Areas in England. These indicators included: i) 111 sociodemographic features linked to health in existing literature, ii) 43 environmental point features (e.g., greenery and air pollution levels), iii) 4 seasonal composite satellite images each with 11 bands, and iv) prescription prevalence associated with five medical conditions (depression, anxiety, diabetes, hypertension, and asthma), opioids and total prescriptions. We combined these indicators into a single MedSat dataset, the availability of which presents an opportunity for the machine learning community to develop new techniques specific to public health. These techniques would address challenges such as handling large and complex data volumes, performing effective feature engineering on environmental and sociodemographic factors, capturing spatial and temporal dependencies in the models, addressing imbalanced data distributions, developing novel computer vision methods for health modeling based on satellite imagery, ensuring model explainability, and achieving generalization beyond the specific geographical region.

Applications/Health

Elena Sizikova, Niloufar Saharkhiz, Diksha Sharma, Miguel Lago, Berkman Sahiner, Jana Delfino, Aldo Badano

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

Applications/Health

Andy Zhou, Samuel Li, Pranav Sriram, Xiang Li, Jiahua Dong, Ansh Sharma, Yuanyi Zhong, Shirui Luo, Volodymyr Kindratenko, George Heintz 等

The healthcare and AI communities have witnessed a growing interest in the development of AI-assisted systems for automated diagnosis of Parkinson's Disease (PD), one of the most prevalent neurodegenerative disorders. However, the progress in this area has been significantly impeded by the absence of a unified, publicly available benchmark, which prevents comprehensive evaluation of existing PD analysis methods and the development of advanced models. This work overcomes these challenges by introducing YouTubePD -- the first publicly available multimodal benchmark designed for PD analysis. We crowd-source existing videos featured with PD from YouTube, exploit multimodal information including in-the-wild videos, audio data, and facial landmarks across 200+ subject videos, and provide dense and diverse annotations from clinical expert. Based on our benchmark, we propose three challenging and complementary tasks encompassing both discriminative and generative tasks, along with a comprehensive set of corresponding baselines. Experimental evaluation showcases the potential of modern deep learning and computer vision techniques, in particular the generalizability of the models developed on YouTubePD to real-world clinical settings, while revealing their limitations. We hope our work paves the way for future research in this direction.

Applications/Health

Wojciech Kusa, Oscar E. Mendoza, Matthias Samwald, Petr Knoth, Allan Hanbury

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMED, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMED serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMED-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMED, we conduct experiments and establish baselines on new datasets.

Applications/Health

Nina Montana-Brown, Shaheer U. Saeed, Ahmed Abdulaal, Thomas Dowrick, Yakup Kilic, Sophie Wilkinson, Jack Gao, Meghavi Mashar, Chloe He, Alkisti Stavropoulou 等

Minimally-invasive surgery (MIS) and robot-assisted minimally invasive (RAMIS) surgery offer well-documented benefits to patients such as reduced post-operative pain and shorter hospital stays.However, the automation of MIS and RAMIS through the use of AI has been slow due to difficulties in data acquisition and curation, partially caused by the ethical considerations of training, testing and deploying AI models in medical environments.We introduce \texttt{SARAMIS}, the first large-scale dataset of anatomically derived 3D rendering assets of the human abdominal anatomy.Using previously existing, open-source CT datasets of the human anatomy, we derive novel 3D meshes, tetrahedral volumes, textures and diffuse maps for over 104 different anatomical targets in the human body, representing the largest, open-source dataset of 3D rendering assets for synthetic simulation of vision tasks in MIS+RAMIS, increasing the availability of openly available 3D meshes in the literature by three orders of magnitude.We supplement our dataset with a series of GPU-enabled rendering environments, which can be used to generate datasets for realistic MIS/RAMIS tasks.Finally, we present an example of the use of \texttt{SARAMIS} assets for an autonomous navigation task in colonoscopy from CT abdomen-pelvis scans for the first time in the literature.\texttt{SARAMIS} is publically made available at https://github.com/NMontanaBrown/saramis/, with assets released under a CC-BY-NC-SA license.

Applications/Health

Chaoqi Yang, M Westover, Jimeng Sun

Biological signals, such as electroencephalograms (EEG), play a crucial role in numerous clinical applications, exhibiting diverse data formats and quality profiles. Current deep learning models for biosignals (based on CNN, RNN, and Transformers) are typically specialized for specific datasets and clinical settings, limiting their broader applicability. This paper explores the development of a flexible biosignal encoder architecture that can enable pre-training on multiple datasets and fine-tuned on downstream biosignal tasks with different formats.To overcome the unique challenges associated with biosignals of various formats, such as mismatched channels, variable sample lengths, and prevalent missing val- ues, we propose Biosignal Transformer (BIOT). The proposed BIOT model can enable cross-data learning with mismatched channels, variable lengths, and missing values by tokenizing different biosignals into unified "sentences" structure. Specifically, we tokenize each channel separately into fixed-length segments containing local signal features and then rearrange the segments to form a long "sentence". Channel embeddings and relative position embeddings are added to each segment (viewed as "token") to preserve spatio-temporal features.The BIOT model is versatile and applicable to various biosignal learning settings across different datasets, including joint pre-training for larger models. Comprehensive evaluations on EEG, electrocardiogram (ECG), and human activity sensory signals demonstrate that BIOT outperforms robust baselines in common settings and facilitates learning across multiple datasets with different formats. Using CHB-MIT seizure detection task as an example, our vanilla BIOT model shows 3% improvement over baselines in balanced accuracy, and the pre-trained BIOT models (optimized from other data sources) can further bring up to 4% improvements. Our repository is public at https://github.com/ycq091044/BIOT.

Applications/Health

Ruofan Wu, Jiawei Qiao, Mingzhe Wu, Wen Yu, Ming Zheng, Tengfei LIU, Tianyi Zhang, Weiqiang Wang

We present neural frailty machine (NFM), a powerful and flexible neural modeling framework for survival regressions. The NFM framework utilizes the classical idea of multiplicative frailty in survival analysis as a principled way of extending the proportional hazard assumption, at the same time being able to leverage the strong approximation power of neural architectures for handling nonlinear covariate dependence. Two concrete models are derived under the framework that extends neural proportional hazard models and nonparametric hazard regression models. Both models allow efficient training under the likelihood objective. Theoretically, for both proposed models, we establish statistical guarantees of neural function approximation with respect to nonparametric components via characterizing their rate of convergence. Empirically, we provide synthetic experiments that verify our theoretical statements. We also conduct experimental evaluations over $6$ benchmark datasets of different scales, showing that the proposed NFM models achieve predictive performance comparable to or sometimes surpassing state-of-the-art survival models. Our code is publicly availabel at https://github.com/Rorschach1989/nfm

Applications/Health

Shenghuan Sun, Greg Goldgof, Atul Butte, Ahmed Alaa

Generative models capable of precisely capturing nuanced clinical features in medical images hold great promise for facilitating clinical data sharing, enhancing rare disease datasets, and efficiently synthesizing (annotated) medical images at scale. Despite their potential, assessing the quality of synthetic medical images remains a challenge. While modern generative models can synthesize visually-realistic medical images, the clinical plausibility of these images may be called into question. Domain-agnostic scores, such as FID score, precision, and recall, cannot incorporate clinical knowledge and are, therefore, not suitable for assessing clinical sensibility. Additionally, there are numerous unpredictable ways in which generative models may fail to synthesize clinically plausible images, making it challenging to anticipate potential failures and design automated scores for their detection. To address these challenges, this paper introduces a pathologist-in-the-loop framework for generating clinically-plausible synthetic medical images. Our framework comprises three steps: (1) pretraining a conditional diffusion model to generate medical images conditioned on a clinical concept, (2) expert pathologist evaluation of the generated images to assess whether they satisfy clinical desiderata, and (3) training a reward model that predicts human feedback on new samples, which we use to incorporate expert knowledge into the finetuning objective of the diffusion model. Our results show that human feedback significantly improves the quality of synthetic images in terms of fidelity, diversity, utility in downstream applications, and plausibility as evaluated by experts. We also demonstrate that human feedback can teach the model new clinical concepts not annotated in the original training data. Our results demonstrate the value of incorporating human feedback in clinical applications where generative models may struggle to capture extensive domain knowledge from raw data alone.

Applications/Health

Hao Zheng, Hongming Li, Yong Fan

Accurate reconstruction of cortical surfaces from brain magnetic resonance images (MRIs) remains a challenging task due to the notorious partial volume effect in brain MRIs and the cerebral cortex's thin and highly folded patterns. Although many promising deep learning-based cortical surface reconstruction methods have been developed, they typically fail to model the interdependence between inner (white matter) and outer (pial) cortical surfaces, which can help generate cortical surfaces with spherical topology. To robustly reconstruct the cortical surfaces with topological correctness, we develop a new deep learning framework to jointly reconstruct the inner, outer, and their in-between (midthickness) surfaces and estimate cortical thickness directly from 3D MRIs. Our method first estimates the midthickness surface and then learns three diffeomorphic flows jointly to optimize the midthickness surface and deform it inward and outward to the inner and outer cortical surfaces respectively, regularized by topological correctness. Our method also outputs a cortex thickness value for each surface vertex, estimated from its diffeomorphic deformation trajectory. Our method has been evaluated on two large-scale neuroimaging datasets, including ADNI and OASIS, achieving state-of-the-art cortical surface reconstruction performance in terms of accuracy, surface regularity, and computation efficiency.

Applications/Health

Chang Lu, Chandan Reddy, Ping Wang, Yue Ning

Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural language processing (NLP) techniques, there are still challenges including limited availability of data due to privacy constraints and the high variability of clinical notes caused by different writing habits of medical professionals and various pathological features of patients. In this work, we investigate the semi-structured nature of clinical notes and propose an automatic algorithm to segment them into sections. To address the variability issues in existing ICD coding models with limited data, we introduce a contrastive pre-training approach on sections using a soft multi-label similarity metric based on tree edit distance. Additionally, we design a masked section training strategy to enable ICD coding models to locate sections related to ICD codes. Extensive experimental results demonstrate that our proposed training strategies effectively enhance the performance of existing ICD coding methods.

Applications/Health

Suman Bhoi, Mong Li Lee, Wynne Hsu, Ngiap Chuan Tan

Patients with co-morbidities often require multiple medications to manage their conditions. However, existing medication recommendation systems only offer class-level medications and regard all interactions among drugs to have the same level of severity. This limits their ability to provide personalized and safe recommendations tailored to individual needs. In this work, we introduce a deep learning-based fine-grained medication recommendation system called REFINE, which is designed to improve treatment outcomes and minimize adverse drug interactions. In order to better characterize patients’ health conditions, we model the trend in medication dosage titrations and lab test responses, and adapt the vision transformer to obtain effective patient representations. We also model drug interaction severity levels as weighted graphs to learn safe drug combinations and design a balanced loss function to avoid overly conservative recommendations and miss medications that might be needed for certain conditions. Extensive experiments on two real-world datasets show that REFINE outperforms state-of-the-art techniques.

Applications/Health

Zhizhang Yuan, Daoze Zhang, YANG YANG, Junru Chen, Yafeng Li

Automated seizure detection is of great importance to epilepsy diagnosis and treatment. An emerging method used in seizure detection, stereoelectroencephalography (SEEG), can provide detailed and stereoscopic brainwave information. However, modeling SEEG in clinical scenarios will face challenges like huge domain shift between different patients and dramatic pattern evolution among different brain areas. In this study, we propose a Pretraining-based model for Patient-independent seizure detection (PPi) to address these challenges. Firstly, we design two novel self-supervised tasks which can extract rich information from abundant SEEG data while preserving the unique characteristics between brain signals recorded from different brain areas. Then two techniques channel background subtraction and brain region enhancement are proposed to effectively tackle the domain shift problem. Extensive experiments show that PPi outperforms the SOTA baselines on two public datasets and a real-world clinical dataset collected by ourselves, which demonstrates the effectiveness and practicability of PPi. Finally, visualization analysis illustrates the rationality of the two domain generalization techniques.

Applications/Health

Jonas Schweisthal, Dennis Frauen, Valentyn Melnychuk, Stefan Feuerriegel

Decision-making in personalized medicine such as cancer therapy or critical care must often make choices for dosage combinations, i.e., multiple continuous treatments. Existing work for this task has modeled the effect of multiple treatments independently, while estimating the joint effect has received little attention but comes with non-trivial challenges. In this paper, we propose a novel method for reliable off-policy learning for dosage combinations. Our method proceeds along three steps: (1) We develop a tailored neural network that estimates the individualized dose-response function while accounting for the joint effect of multiple dependent dosages. (2) We estimate the generalized propensity score using conditional normalizing flows in order to detect regions with limited overlap in the shared covariate-treatment space. (3) We present a gradient-based learning algorithm to find the optimal, individualized dosage combinations. Here, we ensure reliable estimation of the policy value by avoiding regions with limited overlap. We finally perform an extensive evaluation of our method to show its effectiveness. To the best of our knowledge, ours is the first work to provide a method for reliable off-policy learning for optimal dosage combinations.

Applications/Health

Daoze Zhang, Zhizhang Yuan, YANG YANG, Junru Chen, Jingjing Wang, Yafeng Li

We propose a foundation model named Brant for modeling intracranial recordings, which learns powerful representations of intracranial neural signals by pre-training, providing a large-scale, off-the-shelf model for medicine. Brant is the largest model in the field of brain signals and is pre-trained on a large corpus of intracranial data collected by us. The design of Brant is to capture long-term temporal dependency and spatial correlation from neural signals, combining the information in both time and frequency domains. As a foundation model, Brant achieves SOTA performance on various downstream tasks (i.e. neural signal forecasting, frequency-phase forecasting, imputation and seizure detection), showing the generalization ability to a broad range of tasks. The low-resource label analysis and representation visualization further illustrate the effectiveness of our pre-training strategy. In addition, we explore the effect of model size to show that a larger model with a higher capacity can lead to performance improvements on our dataset. The source code and pre-trained weights are available at: https://zju-brainnet.github.io/Brant.github.io/.

Applications/Health

Hongzheng Yang, Cheng Chen, Yueyao CHEN, Scheppach, Hon Chi Yip, DOU QI

Uncertainty estimation plays an important role for future reliable deployment of deep segmentation models in safety-critical scenarios such as medical applications. However, existing methods for uncertainty estimation have been limited by the lack of explicit guidance for calibrating the prediction risk and model confidence. In this work, we propose a novel fine-grained reward maximization (FGRM) framework, to address uncertainty estimation by directly utilizing an uncertainty metric related reward function with a reinforcement learning based model tuning algorithm. This would benefit the model uncertainty estimation with direct optimization guidance for model calibration. Specifically, our method designs a new uncertainty estimation reward function using the calibration metric, which is maximized to fine-tune an evidential learning pre-trained segmentation model for calibrating prediction risk. Importantly, we innovate an effective fine-grained parameter update scheme, which imposes fine-grained reward-weighting of each network parameter according to the parameter importance quantified by the fisher information matrix. To the best of our knowledge, this is the first work exploring reward optimization for model uncertainty estimation in safety-critical vision tasks. The effectiveness of our method is demonstrated on two large safety-critical surgical scene segmentation datasets under two different uncertainty estimation settings. With real-time one forward pass at inference, our method outperforms state-of-the-art methods by a clear margin on all the calibration metrics of uncertainty estimation, while maintaining a high task accuracy for the segmentation results. Code is available at https://github.com/med-air/FGRM.

Applications/Health

Yuchao Qin, Mihaela van der Schaar, Changhee Lee

Timely outcome prediction is essential in healthcare to enable early detection and intervention of adverse events. However, in longitudinal follow-ups to patients' health status, cost-efficient acquisition of patient covariates is usually necessary due to the significant expense involved in screening and lab tests. To balance the timely and accurate outcome predictions with acquisition costs, an effective active sensing strategy is crucial. In this paper, we propose a novel risk-averse active sensing approach RAS that addresses the composite decision problem of when to conduct the acquisition and which measurements to make. Our approach decomposes the policy into two sub-policies: acquisition scheduler and feature selector, respectively. Moreover, we introduce a novel risk-aversion training strategy to focus on the underrepresented subgroup of high-risk patients for whom timely and accurate prediction of disease progression is of greater value. Our method outperforms baseline active sensing approaches in experiments with both synthetic and real-world datasets, and we illustrate the significance of our policy decomposition and the necessity of a risk-averse sensing policy through case studies.

Applications/Health

Matthew Lyon, Paul Armitage, Mauricio A Álvarez

Diffusion MRI (dMRI) is a widely used imaging modality, but requires long scanning times to acquire high resolution datasets. By leveraging the unique geometry present within this domain, we present a novel approach to dMRI angular super-resolution that extends upon the parametric continuous convolution (PCConv) framework. We introduce several additions to the operation including a Fourier feature mapping, 'global' co-ordinates, and domain specific context. Using this framework, we build a fully parametric continuous convolution network (PCCNN) and compare against existing models. We demonstrate the PCCNN performs competitively while using significantly fewer parameters. Moreover, we show that this formulation generalises well to clinically relevant downstream analyses such as fixel-based analysis, and neurite orientation dispersion and density imaging.

Applications/Health

Andre Vauvelle, Benjamin Wild, Roland Eils, Spiros Denaxas

Survival analysis is a crucial semi-supervised task in machine learning with significant real-world applications, especially in healthcare. The most common approach to survival analysis, Cox’s partial likelihood, can be interpreted as a ranking model optimized on a lower bound of the concordance index. We follow these connections further, with listwise ranking losses that allow for a relaxation of the pairwise independence assumption. Given the inherent transitivity of ranking, we explore differentiable sorting networks as a means to introduce a stronger transitive inductive bias during optimization. Despite their potential, current differentiable sorting methods cannot account for censoring, a crucial aspect of many real-world datasets. We propose a novel method, Diffsurv, to overcome this limitation by extending differentiable sorting methods to handle censored tasks. Diffsurv predicts matrices of possible permutations that accommodate the label uncertainty introduced by censored samples. Our experiments reveal that Diffsurv outperforms established baselines in various simulated and real-world risk prediction scenarios. Furthermore, we demonstrate the algorithmic advantages of Diffsurv by presenting a novel method for top-k risk prediction that surpasses current methods.