NeurIPS 2024 论文列表

The practical utility of machine learning models in the sciences often hinges on their interpretability. It is common to assess a model's merit for scientific discovery, and thus novel insights, by how well it aligns with already available domain knowledge - a dimension that is currently largely disregarded in the comparison of neural network models. While pruning can simplify deep neural network architectures and excels in identifying sparse models, as we show in the context of gene regulatory network inference, state-of-the-art techniques struggle with biologically meaningful structure learning. To address this issue, we propose DASH, a generalizable framework that guides network pruning by using domain-specific structural information in model fitting and leads to sparser, better interpretable models that are more robust to noise. Using both synthetic data with ground truth information, as well as real-world gene expression data, we show that DASH, using knowledge about gene interaction partners within the putative regulatory network, outperforms general pruning methods by a large margin and yields deeper insights into the biological systems being studied.

Electrocardiogram (ECG) signals provide essential information about the heart's condition and are widely used for diagnosing cardiovascular diseases. The morphology of a single heartbeat over the available leads is a primary biosignal for monitoring cardiac conditions. However, analyzing heartbeat morphology can be challenging due to noise and artifacts, missing leads, and a lack of annotated data. Generative models, such as denoising diffusion generative models (DDMs), have proven successful in generating complex data. We introduce $\texttt{BeatDiff}$, a light-weight DDM tailored for the morphology of multiple leads heartbeats. We then show that many important ECG downstream tasks can be formulated as conditional generation methods in a Bayesian inverse problem framework using $\texttt{BeatDiff}$ as priors. We propose $\texttt{EM-BeatDiff}$, an Expectation-Maximization algorithm, to solve this conditional generation tasks without fine-tuning. We illustrate our results with several tasks, such as removal of ECG noise and artifacts (baseline wander, electrode motion), reconstruction of a 12-lead ECG from a single lead (useful for ECG reconstruction of smartwatch experiments), and unsupervised explainable anomaly detection. Numerical experiments show that the combination of $\texttt{BeatDiff}$ and $\texttt{EM-BeatDiff}$ outperforms SOTA methods for the problems considered in this work.

Foundation models are becoming valuable tools in medicine. Yet despite their promise, the best way to leverage Large Language Models (LLMs) in complex medical tasks remains an open question. We introduce a novel multi-agent framework, named **M**edical **D**ecision-making **Agents** (**MDAgents**) that helps to address this gap by automatically assigning a collaboration structure to a team of LLMs. The assigned solo or group collaboration structure is tailored to the medical task at hand, a simple emulation inspired by the way real-world medical decision-making processes are adapted to tasks of different complexities. We evaluate our framework and baseline methods using state-of-the-art LLMs across a suite of real-world medical knowledge and clinical diagnosis benchmarks, including a comparison of LLMs’ medical complexity classification against human physicians. MDAgents achieved the **best performance in seven out of ten** benchmarks on tasks requiring an understanding of medical knowledge and multi-modal reasoning, showing a significant **improvement of up to 4.2\%** ($p$ < 0.05) compared to previous methods' best performances. Ablation studies reveal that MDAgents effectively determines medical complexity to optimize for efficiency and accuracy across diverse medical tasks. Notably, the combination of moderator review and external medical knowledge in group collaboration resulted in an average accuracy **improvement of 11.8\%**. Our code can be found at https://github.com/mitmedialab/MDAgents.

Motion time series collected from low-power, always-on mobile and wearable devices such as smartphones and smartwatches offer significant insights into human behavioral patterns, with wide applications in healthcare, automation, IoT, and AR/XR. However, given security and privacy concerns, building large-scale motion time series datasets remains difficult, hindering the development of pre-trained models for human activity analysis. Typically, existing models are trained and tested on the same dataset, leading to poor generalizability across variations in device location, device mounting orientation, and human activity type. In this paper, we introduce UniMTS, the first unified pre-training procedure for motion time series that generalizes across diverse device latent factors and activities. Specifically, we employ a contrastive learning framework that aligns motion time series with text descriptions enriched by large language models. This helps the model learn the semantics of time series to generalize across activities. Given the absence of large-scale motion time series data, we derive and synthesize time series from existing motion skeleton data with all-joint coverage. We use spatio-temporal graph networks to capture the relationships across joints for generalization across different device locations. We further design rotation-invariant augmentation to make the model agnostic to changes in device mounting orientations. Our model shows exceptional generalizability across 18 motion time series classification benchmark datasets, outperforming the best baselines by 340% in the zero-shot setting, 16.3% in the few-shot setting, and 9.2% in the full-shot setting.

Large language models (LLMs) have shown impressive capabilities in solving a wide range of tasks based on human instructions. However, developing a conversational AI assistant for electronic health record (EHR) data remains challenging due to (1) the lack of large-scale instruction-following datasets and (2) the limitations of existing model architectures in handling complex and heterogeneous EHR data. In this paper, we introduce MIMIC-Instr, a dataset comprising over 400K open-ended instruction-following examples derived from the MIMIC-IV EHR database. This dataset covers various topics and is suitable for instruction-tuning general-purpose LLMs for diverse clinical use cases. Additionally, we propose Llemr, a general framework that enables LLMs to process and interpret EHRs with complex data structures. Llemr demonstrates competitive performance in answering a wide range of patient-related questions based on EHR data. Furthermore, our evaluations on clinical predictive modeling benchmarks reveal that the fine-tuned Llemr achieves performance comparable to state-of-the-art (SOTA) baselines using curated features. The dataset and code are available at \url{https://github.com/zzachw/llemr}.

Quantitative analysis of cardiac motion is crucial for assessing cardiac function. This analysis typically uses imaging modalities such as MRI and Echocardiograms that capture detailed image sequences throughout the heartbeat cycle. Previous methods predominantly focused on the analysis of image pairs lacking consideration of the motion dynamics and spatial variability. Consequently, these methods often overlook the long-term relationships and regional motion characteristic of cardiac. To overcome these limitations, we introduce the GPTrack, a novel unsupervised framework crafted to fully explore the temporal and spatial dynamics of cardiac motion. The GPTrack enhances motion tracking by employing the sequential Gaussian Process in the latent space and encoding statistics by spatial information at each time stamp, which robustly promotes temporal consistency and spatial variability of cardiac dynamics. Also, we innovatively aggregate sequential information in a bidirectional recursive manner, mimicking the behavior of diffeomorphic registration to better capture consistent long-term relationships of motions across cardiac regions such as the ventricles and atria. Our GPTrack significantly improves the precision of motion tracking in both 3D and 4D medical images while maintaining computational efficiency. The code is available at: https://github.com/xmed-lab/GPTrack.

The study of cells and their responses to genetic or chemical perturbations promises to accelerate the discovery of therapeutics targets. However, designing adequate and insightful models for such data is difficult because the response of a cell to perturbations essentially depends on contextual covariates (e.g., genetic background or type of the cell). There is therefore a need for models that can identify interactions between drugs and contextual covariates. This is crucial for discovering therapeutics targets, as such interactions may reveal drugs that affect certain cell types but not others. We tackle this problem with a novel Factorized Causal Representation (FCR) learning method, an identifiable deep generative model that reveals causal structure in single-cell perturbation data from several cell lines. FCR learns multiple cellular representations that are disentangled, comprised of covariate-specific (Z_x), treatment-specific (Z_t) and interaction-specific (Z_tx) representations. Based on recent advances of non-linear ICA theory, we prove the component-wise identifiability of Z_tx and block-wise identifiability of Z_t and Z_x. Then, we present our implementation of FCR, and empirically demonstrate that FCR outperforms state-of-the-art baselines in various tasks across four single-cell datasets.

The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring the incorporation of prior knowledge and decomposition of data into multiple subspaces. Traditional linear methods fall short in modeling more than one space, while more expressive deep learning approaches lack interpretability. Here, we introduce Supervised Independent Subspace Principal Component Analysis ($\texttt{sisPCA}$), a PCA extension designed for multi-subspace learning. Leveraging the Hilbert-Schmidt Independence Criterion (HSIC), $\texttt{sisPCA}$ incorporates supervision and simultaneously ensures subspace disentanglement. We demonstrate $\texttt{sisPCA}$'s connections with autoencoders and regularized linear regression and showcase its ability to identify and separate hidden data structures through extensive applications, including breast cancer diagnosis from image features, learning aging-associated DNA methylation changes, and single-cell analysis of malaria infection. Our results reveal distinct functional pathways associated with malaria colonization, underscoring the essentiality of explainable representation in high-dimensional data analysis.

Different from classical one-model-fits-all strategy, individualized models allow parameters to vary across samples and are gaining popularity in various fields, particularly in personalized medicine. Motivated by medical imaging analysis, this paper introduces a novel individualized modeling framework for matrix-valued data that does not require additional information on sample similarity for the individualized coefficients. Under our framework, the model individualization stems from an optimal internal relation map within the samples themselves. We refer to the proposed method as Attention boosted Individualized Regression, due to its close connections with the self-attention mechanism. Therefore, our approach provides a new interpretation for attention from the perspective of individualized modeling. Comprehensive numerical experiments and real brain MRI analysis using an ADNI dataset demonstrated the superior performance of our model.

We introduce a new representation for 3D molecules based on their continuous atomic density fields. Using this representation, we propose a new model based on walk-jump sampling for unconditional 3D molecule generation in the continuous space using neural fields. Our model, FuncMol, encodes molecular fields into latent codes using a conditional neural field, samples noisy codes from a Gaussian-smoothed distribution with Langevin MCMC (walk), denoises these samples in a single step (jump), and finally decodes them into molecular fields. FuncMol performs all-atom generation of 3D molecules without assumptions on the molecular structure and scales well with the size of molecules, unlike most approaches. Our method achieves competitive results on drug-like molecules and easily scales to macro-cyclic peptides, with at least one order of magnitude faster sampling. The code is available at https://github.com/prescient-design/funcmol.

Irregularly Sampled Medical Time Series (ISMTS) are commonly found in the healthcare domain, where different variables exhibit unique temporal patterns while interrelated. However, many existing methods fail to efficiently consider the differences and correlations among medical variables together, leading to inadequate capture of fine-grained features at the variable level in ISMTS. We propose Knowledge-Empowered Dynamic Graph Network (KEDGN), a graph neural network empowered by variables' textual medical knowledge, aiming to model variable-specific temporal dependencies and inter-variable dependencies in ISMTS. Specifically, we leverage a pre-trained language model to extract semantic representations for each variable from their textual descriptions of medical properties, forming an overall semantic view among variables from a medical perspective. Based on this, we allocate variable-specific parameter spaces to capture variable-specific temporal patterns and generate a complete variable graph to measure medical correlations among variables. Additionally, we employ a density-aware mechanism to dynamically adjust the variable graph at different timestamps, adapting to the time-varying correlations among variables in ISMTS. The variable-specific parameter spaces and dynamic graphs are injected into the graph convolutional recurrent network to capture intra-variable and inter-variable dependencies in ISMTS together. Experiment results on four healthcare datasets demonstrate that KEDGN significantly outperforms existing methods.

Phenotype imputation plays a crucial role in improving comprehensive and accurate medical evaluation, which in turn can optimize patient treatment and bolster the reliability of clinical research. Despite the adoption of various techniques, multi-modal biological data, which can provide crucial insights into a patient's overall health, is often overlooked. With multi-modal biological data, patient characterization can be enriched from two distinct views: the biological view and the phenotype view. However, the heterogeneity and imprecise nature of the multimodal data still pose challenges in developing an effective method to model from two views. In this paper, we propose a novel framework to incorporate multi-modal biological data via view decoupling. Specifically, we segregate the modeling of biological data from phenotype data in a graph-based learning framework. From the biological view, the latent factors in biological data are discovered to model patient correlation. From the phenotype view, phenotype co-occurrence can be modeled to reveal patterns across patients. Then patients are encoded from these two distinct views. To mitigate the influence of noise and irrelevant information in biological data, we devise a cross-view contrastive knowledge distillation aimed at distilling insights from the biological view to enhance phenotype imputation. We show that phenotype imputation with the proposed model significantly outperforms the state-of-the-art models on the real-world biomedical database.

Electronic health record (EHR) data has emerged as a valuable resource for analyzing patient health status. However, the prevalence of missing data in EHR poses significant challenges to existing methods, leading to spurious correlations and suboptimal predictions. While various imputation techniques have been developed to address this issue, they often obsess difficult-to-interpolate details and may introduce additional noise when making clinical predictions. To tackle this problem, we propose SMART, a Self-Supervised Missing-Aware RepresenTation Learning approach for patient health status prediction, which encodes missing information via missing-aware temporal and variable attentions and learns to impute missing values through a novel self-supervised pre-training approach which reconstructs missing data representations in the latent space rather than in input space as usual. By adopting elaborated attentions and focusing on learning higher-order representations, SMART promotes better generalization and robustness to missing data. We validate the effectiveness of SMART through extensive experiments on six EHR tasks, demonstrating its superiority over state-of-the-art methods.

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining model remains unexplored. In this work, we present an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, examining the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale the model to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show the consistent improvement on the downstream tasks as the model size grows up. The model with 1.1 billion parameters also outperform over existing methods, achieving an average 27\% improvement on the QM9 and 14\% on COMPAS-1D dataset.

The lack of interpretability in the field of medical image analysis has significant ethical and legal implications. Existing interpretable methods in this domain encounter several challenges, including dependency on specific models, difficulties in understanding and visualization, and issues related to efficiency. To address these limitations, we propose a novel framework called Med-MICN (Medical Multi-dimensional Interpretable Concept Network). Med-MICN provides interpretability alignment for various angles, including neural symbolic reasoning, concept semantics, and saliency maps, which are superior to current interpretable methods. Its advantages include high prediction accuracy, interpretability across multiple dimensions, and automation through an end-to-end concept labeling process that reduces the need for extensive human training effort when working with new datasets. To demonstrate the effectiveness and interpretability of Med-MICN, we apply it to four benchmark datasets and compare it with baselines. The results clearly demonstrate the superior performance and interpretability of our Med-MICN.

Randomized trials are widely considered as the gold standard for evaluating the effects of decision policies. Trial data is, however, drawn from a population which may differ from the intended target population and this raises a problem of external validity (aka. generalizability). In this paper we seek to use trial data to draw valid inferences about the outcome of a policy on the target population. Additional covariate data from the target population is used to model the sampling of individuals in the trial study. We develop a method that yields certifiably valid trial-based policy evaluations under any specified range of model miscalibrations. The method is nonparametric and the validity is assured even with finite samples. The certified policy evaluations are illustrated using both simulated and real data.

Precise image segmentation provides clinical study with instructive information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence of a 3D foundation segmentation model that can segment a wide range of anatomical categories with easy user interaction. In this paper, we propose a 3D foundation segmentation model, named SegVol, supporting universal and interactive volumetric medical image segmentation. By scaling up training data to 90K unlabeled Computed Tomography (CT) volumes and 6K labeled CT volumes, this foundation model supports the segmentation of over 200 anatomical categories using semantic and spatial prompts. To facilitate efficient and precise inference on volumetric images, we design a zoom-out-zoom-in mechanism. Extensive experiments on 22 anatomical segmentation tasks verify that SegVol outperforms the competitors in 19 tasks, with improvements up to 37.24\% compared to the runner-up methods. We demonstrate the effectiveness and importance of specific designs by ablation study. We expect this foundation model can promote the development of volumetric medical image analysis. The model and code are publicly available at https://github.com/BAAI-DCAI/SegVol.