Daily Papers

Motivation: The Genomic Data Commons (GDC) provides access to high quality, harmonized cancer genomics data through a unified curation and analysis platform centered around patient cohorts. While GDC users can interactively create complex cohorts through the graphical Cohort Builder, users (especially new ones) may struggle to find specific cohort descriptors across hundreds of possible fields and properties. However, users may be better able to describe their desired cohort in free-text natural language. Results: We introduce GDC Cohort Copilot, an open-source copilot tool for curating cohorts from the GDC. GDC Cohort Copilot automatically generates the GDC cohort filter corresponding to a user-input natural language description of their desired cohort, before exporting the cohort back to the GDC for further analysis. An interactive user interface allows users to further refine the generated cohort. We develop and evaluate multiple large language models (LLMs) for GDC Cohort Copilot and demonstrate that our locally-served, open-source GDC Cohort LLM achieves better results than GPT-4o prompting in generating GDC cohorts. Availability and implementation: The standalone docker image for GDC Cohort Copilot is available at https://quay.io/repository/cdis/gdc-cohort-copilot. Source code is available at https://github.com/uc-cdis/gdc-cohort-copilot. GDC Cohort LLM weights are available at https://huggingface.co/uc-ctds.

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

Reproducibility remains a significant challenge in machine learning (ML) for healthcare. In this field, datasets, model pipelines, and even task/cohort definitions are often private, leading to a significant barrier in sharing, iterating, and understanding ML results on electronic health record (EHR) datasets. In this paper, we address a significant part of this problem by introducing the Automatic Cohort Extraction System for Event-Stream Datasets (ACES). This tool is designed to simultaneously simplify the development of task/cohorts for ML in healthcare and enable the reproduction of these cohorts, both at an exact level for single datasets and at a conceptual level across datasets. To accomplish this, ACES provides (1) a highly intuitive and expressive configuration language for defining both dataset-specific concepts and dataset-agnostic inclusion/exclusion criteria, and (2) a pipeline to automatically extract patient records that meet these defined criteria from real-world data. ACES can be automatically applied to any dataset in either the Medical Event Data Standard (MEDS) or EventStreamGPT (ESGPT) formats, or to *any* dataset for which the necessary task-specific predicates can be extracted in an event-stream form. ACES has the potential to significantly lower the barrier to entry for defining ML tasks, redefine the way researchers interact with EHR datasets, and significantly improve the state of reproducibility for ML studies in this modality. ACES is available at https://github.com/justin13601/aces.

Ensuring equitable treatment (fairness) across protected attributes (such as gender or ethnicity) is a critical issue in machine learning. Most existing literature focuses on binary classification, but achieving fairness in regression tasks-such as insurance pricing or hiring score assessments-is equally important. Moreover, anti-discrimination laws also apply to continuous attributes, such as age, for which many existing methods are not applicable. In practice, multiple protected attributes can exist simultaneously; however, methods targeting fairness across several attributes often overlook so-called "fairness gerrymandering", thereby ignoring disparities among intersectional subgroups (e.g., African-American women or Hispanic men). In this paper, we propose a distance covariance regularisation framework that mitigates the association between model predictions and protected attributes, in line with the fairness definition of demographic parity, and that captures both linear and nonlinear dependencies. To enhance applicability in the presence of multiple protected attributes, we extend our framework by incorporating two multivariate dependence measures based on distance covariance: the previously proposed joint distance covariance (JdCov) and our novel concatenated distance covariance (CCdCov), which effectively address fairness gerrymandering in both regression and classification tasks involving protected attributes of various types. We discuss and illustrate how to calibrate regularisation strength, including a method based on Jensen-Shannon divergence, which quantifies dissimilarities in prediction distributions across groups. We apply our framework to the COMPAS recidivism dataset and a large motor insurance claims dataset.

Score-based generative models, commonly referred to as diffusion models, have proven to be successful at generating text and image data. However, their adaptation to mixed-type tabular data remains underexplored. In this work, we propose CDTD, a Continuous Diffusion model for mixed-type Tabular Data. CDTD is based on a novel combination of score matching and score interpolation to enforce a unified continuous noise distribution for both continuous and categorical features. We explicitly acknowledge the necessity of homogenizing distinct data types by relying on model-specific loss calibration and initialization schemes.To further address the high heterogeneity in mixed-type tabular data, we introduce adaptive feature- or type-specific noise schedules. These ensure balanced generative performance across features and optimize the allocation of model capacity across features and diffusion time. Our experimental results show that CDTD consistently outperforms state-of-the-art benchmark models, captures feature correlations exceptionally well, and that heterogeneity in the noise schedule design boosts sample quality. Replication code is available at https://github.com/muellermarkus/cdtd.

Glaucoma is the number one cause of irreversible blindness globally. A major challenge for accurate glaucoma detection and progression forecasting is the bottleneck of limited labeled patients with the state-of-the-art (SOTA) 3D retinal imaging data of optical coherence tomography (OCT). To address the data scarcity issue, this paper proposes two solutions. First, we develop a novel generalization-reinforced semi-supervised learning (SSL) model called pseudo supervisor to optimally utilize unlabeled data. Compared with SOTA models, the proposed pseudo supervisor optimizes the policy of predicting pseudo labels with unlabeled samples to improve empirical generalization. Our pseudo supervisor model is evaluated with two clinical tasks consisting of glaucoma detection and progression forecasting. The progression forecasting task is evaluated both unimodally and multimodally. Our pseudo supervisor model demonstrates superior performance than SOTA SSL comparison models. Moreover, our model also achieves the best results on the publicly available LAG fundus dataset. Second, we introduce the Harvard Glaucoma Detection and Progression (Harvard-GDP) Dataset, a multimodal multitask dataset that includes data from 1,000 patients with OCT imaging data, as well as labels for glaucoma detection and progression. This is the largest glaucoma detection dataset with 3D OCT imaging data and the first glaucoma progression forecasting dataset that is publicly available. Detailed sex and racial analysis are provided, which can be used by interested researchers for fairness learning studies. Our released dataset is benchmarked with several SOTA supervised CNN and transformer deep learning models. The dataset and code are made publicly available via https://ophai.hms.harvard.edu/datasets/harvard-gdp1000.

Selecting high-quality data for pre-training is crucial in shaping the downstream task performance of language models. A major challenge lies in identifying this optimal subset, a problem generally considered intractable, thus necessitating scalable and effective heuristics. In this work, we propose a data selection method, CoLoR-Filter (Conditional Loss Reduction Filtering), which leverages an empirical Bayes-inspired approach to derive a simple and computationally efficient selection criterion based on the relative loss values of two auxiliary models. In addition to the modeling rationale, we evaluate CoLoR-Filter empirically on two language modeling tasks: (1) selecting data from C4 for domain adaptation to evaluation on Books and (2) selecting data from C4 for a suite of downstream multiple-choice question answering tasks. We demonstrate favorable scaling both as we subselect more aggressively and using small auxiliary models to select data for large target models. As one headline result, CoLoR-Filter data selected using a pair of 150m parameter auxiliary models can train a 1.2b parameter target model to match a 1.2b parameter model trained on 25b randomly selected tokens with 25x less data for Books and 11x less data for the downstream tasks. Code: https://github.com/davidbrandfonbrener/color-filter-olmo Filtered data: https://huggingface.co/datasets/davidbrandfonbrener/color-filtered-c4

Gait is one of the most promising biometrics that aims to identify pedestrians from their walking patterns. However, prevailing methods are susceptible to confounders, resulting in the networks hardly focusing on the regions that reflect effective walking patterns. To address this fundamental problem in gait recognition, we propose a Generative Counterfactual Intervention framework, dubbed GaitGCI, consisting of Counterfactual Intervention Learning (CIL) and Diversity-Constrained Dynamic Convolution (DCDC). CIL eliminates the impacts of confounders by maximizing the likelihood difference between factual/counterfactual attention while DCDC adaptively generates sample-wise factual/counterfactual attention to efficiently perceive the sample-wise properties. With matrix decomposition and diversity constraint, DCDC guarantees the model to be efficient and effective. Extensive experiments indicate that proposed GaitGCI: 1) could effectively focus on the discriminative and interpretable regions that reflect gait pattern; 2) is model-agnostic and could be plugged into existing models to improve performance with nearly no extra cost; 3) efficiently achieves state-of-the-art performance on arbitrary scenarios (in-the-lab and in-the-wild).

Recently, Masked Diffusion Models (MDMs) have shown promising potential across vision, language, and cross-modal generation. However, a notable discrepancy exists between their training and inference procedures. In particular, MDM inference is a multi-step, iterative process governed not only by the model itself but also by various schedules that dictate the token-decoding trajectory (e.g., how many tokens to decode at each step). In contrast, MDMs are typically trained using a simplified, single-step BERT-style objective that masks a subset of tokens and predicts all of them simultaneously. This step-level simplification fundamentally disconnects the training paradigm from the trajectory-level nature of inference, leaving the inference schedules never optimized during training. In this paper, we introduce Co-GRPO, which reformulates MDM generation as a unified Markov Decision Process (MDP) that jointly incorporates both the model and the inference schedule. By applying Group Relative Policy Optimization at the trajectory level, Co-GRPO cooperatively optimizes model parameters and schedule parameters under a shared reward, without requiring costly backpropagation through the multi-step generation process. This holistic optimization aligns training with inference more thoroughly and substantially improves generation quality. Empirical results across four benchmarks-ImageReward, HPS, GenEval, and DPG-Bench-demonstrate the effectiveness of our approach. For more details, please refer to our project page: https://co-grpo.github.io/ .

Large language models' (LLMs) abilities are drawn from their pretraining data, and model development begins with data curation. However, decisions around what data is retained or removed during this initial stage is under-scrutinized. In our work, we ground web text, which is a popular pretraining data source, to its social and geographic contexts. We create a new dataset of 10.3 million self-descriptions of website creators, and extract information about who they are and where they are from: their topical interests, social roles, and geographic affiliations. Then, we conduct the first study investigating how ten "quality" and English language identification (langID) filters affect webpages that vary along these social dimensions. Our experiments illuminate a range of implicit preferences in data curation: we show that some quality classifiers act like topical domain filters, and langID can overlook English content from some regions of the world. Overall, we hope that our work will encourage a new line of research on pretraining data curation practices and its social implications.

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

Addressing fairness in artificial intelligence (AI), particularly in medical AI, is crucial for ensuring equitable healthcare outcomes. Recent efforts to enhance fairness have introduced new methodologies and datasets in medical AI. However, the fairness issue under the setting of domain transfer is almost unexplored, while it is common that clinics rely on different imaging technologies (e.g., different retinal imaging modalities) for patient diagnosis. This paper presents FairDomain, a pioneering systemic study into algorithmic fairness under domain shifts, employing state-of-the-art domain adaptation (DA) and generalization (DG) algorithms for both medical segmentation and classification tasks to understand how biases are transferred between different domains. We also introduce a novel plug-and-play fair identity attention (FIA) module that adapts to various DA and DG algorithms to improve fairness by using self-attention to adjust feature importance based on demographic attributes. Additionally, we curate the first fairness-focused dataset with two paired imaging modalities for the same patient cohort on medical segmentation and classification tasks, to rigorously assess fairness in domain-shift scenarios. Excluding the confounding impact of demographic distribution variation between source and target domains will allow clearer quantification of the performance of domain transfer models. Our extensive evaluations reveal that the proposed FIA significantly enhances both model performance accounted for fairness across all domain shift settings (i.e., DA and DG) with respect to different demographics, which outperforms existing methods on both segmentation and classification. The code and data can be accessed at https://ophai.hms.harvard.edu/datasets/harvard-fairdomain20k.

Recently diffusion models have shown improvement in synthetic image quality as well as better control in generation. We motivate and present Gen2Det, a simple modular pipeline to create synthetic training data for object detection for free by leveraging state-of-the-art grounded image generation methods. Unlike existing works which generate individual object instances, require identifying foreground followed by pasting on other images, we simplify to directly generating scene-centric images. In addition to the synthetic data, Gen2Det also proposes a suite of techniques to best utilize the generated data, including image-level filtering, instance-level filtering, and better training recipe to account for imperfections in the generation. Using Gen2Det, we show healthy improvements on object detection and segmentation tasks under various settings and agnostic to detection methods. In the long-tailed detection setting on LVIS, Gen2Det improves the performance on rare categories by a large margin while also significantly improving the performance on other categories, e.g. we see an improvement of 2.13 Box AP and 1.84 Mask AP over just training on real data on LVIS with Mask R-CNN. In the low-data regime setting on COCO, Gen2Det consistently improves both Box and Mask AP by 2.27 and 1.85 points. In the most general detection setting, Gen2Det still demonstrates robust performance gains, e.g. it improves the Box and Mask AP on COCO by 0.45 and 0.32 points.

Generative models have recently made remarkable progress in the field of 3D objects. However, their practical application in fields like engineering remains limited since they fail to deliver the accuracy, quality, and controllability needed for domain-specific tasks. Fine-tuning large generative models is a promising perspective for making these models available in these fields. Creating high-quality, domain-specific 3D datasets is crucial for fine-tuning large generative models, yet the data filtering and annotation process remains a significant bottleneck. We present MeshFleet, a filtered and annotated 3D vehicle dataset extracted from Objaverse-XL, the most extensive publicly available collection of 3D objects. Our approach proposes a pipeline for automated data filtering based on a quality classifier. This classifier is trained on a manually labeled subset of Objaverse, incorporating DINOv2 and SigLIP embeddings, refined through caption-based analysis and uncertainty estimation. We demonstrate the efficacy of our filtering method through a comparative analysis against caption and image aesthetic score-based techniques and fine-tuning experiments with SV3D, highlighting the importance of targeted data selection for domain-specific 3D generative modeling.

With the increasing availability of wearable devices, photoplethysmography (PPG) has emerged as a promising non-invasive tool for monitoring human hemodynamics. We propose a deep learning framework to estimate vascular age (AI-vascular age) from PPG signals, incorporating a distribution-aware loss to address biases caused by imbalanced data. The model was developed using data from the UK Biobank (UKB), with 98,672 participants in the development cohort and 113,559 participants (144,683 data pairs) for clinical evaluation. After adjusting for key confounders, individuals with a vascular age gap (AI-vascular age minus calendar age) exceeding 9 years had a significantly higher risk of major adverse cardiovascular and cerebrovascular events (MACCE) (HR = 2.37, p < 0.005) and secondary outcomes, including diabetes (HR = 2.69, p < 0.005), hypertension (HR = 2.88, p < 0.005), coronary heart disease (HR = 2.20, p < 0.005), heart failure (HR = 2.15, p < 0.005), myocardial infarction (HR = 2.51, p < 0.005), stroke (HR = 2.55, p < 0.005), and all-cause mortality (HR = 2.51, p < 0.005). Conversely, participants with a vascular age gap below -9 years exhibited a significantly lower incidence of these outcomes. We further evaluated the longitudinal applicability of AI-vascular age using serial PPG data from the UKB, demonstrating its value in risk stratification by leveraging AI-vascular age at two distinct time points to predict future MACCE incidence. External validation was performed on a MIMIC-III-derived cohort (n = 2,343), where each one-year increase in vascular age gap was significantly associated with elevated in-hospital mortality risk (OR = 1.02, p < 0.005). In conclusion, our study establishes AI-vascular age as a novel, non-invasive digital biomarker for cardiovascular health assessment.

We introduce a novel contextual embedding model med-gte-hybrid that was derived from the gte-large sentence transformer to extract information from unstructured clinical narratives. Our model tuning strategy for med-gte-hybrid combines contrastive learning and a denoising autoencoder. To evaluate the performance of med-gte-hybrid, we investigate several clinical prediction tasks in large patient cohorts extracted from the MIMIC-IV dataset, including Chronic Kidney Disease (CKD) patient prognosis, estimated glomerular filtration rate (eGFR) prediction, and patient mortality prediction. Furthermore, we demonstrate that the med-gte-hybrid model improves patient stratification, clustering, and text retrieval, thus outperforms current state-of-the-art models on the Massive Text Embedding Benchmark (MTEB). While some of our evaluations focus on CKD, our hybrid tuning of sentence transformers could be transferred to other medical domains and has the potential to improve clinical decision-making and personalised treatment pathways in various healthcare applications.

We introduce CCI4.0, a large-scale bilingual pre-training dataset engineered for superior data quality and diverse human-like reasoning trajectory. CCI4.0 occupies roughly 35 TB of disk space and comprises two sub-datasets: CCI4.0-M2-Base and CCI4.0-M2-CoT. CCI4.0-M2-Base combines a 5.2 TB carefully curated Chinese web corpus, a 22.5 TB English subset from Nemotron-CC, and diverse sources from math, wiki, arxiv, and code. Although these data are mostly sourced from well-processed datasets, the quality standards of various domains are dynamic and require extensive expert experience and labor to process. So, we propose a novel pipeline justifying data quality mainly based on models through two-stage deduplication, multiclassifier quality scoring, and domain-aware fluency filtering. We extract 4.5 billion pieces of CoT(Chain-of-Thought) templates, named CCI4.0-M2-CoT. Differing from the distillation of CoT from larger models, our proposed staged CoT extraction exemplifies diverse reasoning patterns and significantly decreases the possibility of hallucination. Empirical evaluations demonstrate that LLMs pre-trained in CCI4.0 benefit from cleaner, more reliable training signals, yielding consistent improvements in downstream tasks, especially in math and code reflection tasks. Our results underscore the critical role of rigorous data curation and human thinking templates in advancing LLM performance, shedding some light on automatically processing pretraining corpora.

Fine-tuning text-to-image diffusion models with human feedback is an effective method for aligning model behavior with human intentions. However, this alignment process often suffers from slow convergence due to the large size and noise present in human feedback datasets. In this work, we propose FiFA, a novel automated data filtering algorithm designed to enhance the fine-tuning of diffusion models using human feedback datasets with direct preference optimization (DPO). Specifically, our approach selects data by solving an optimization problem to maximize three components: preference margin, text quality, and text diversity. The concept of preference margin is used to identify samples that are highly informative in addressing the noisy nature of feedback dataset, which is calculated using a proxy reward model. Additionally, we incorporate text quality, assessed by large language models to prevent harmful contents, and consider text diversity through a k-nearest neighbor entropy estimator to improve generalization. Finally, we integrate all these components into an optimization process, with approximating the solution by assigning importance score to each data pair and selecting the most important ones. As a result, our method efficiently filters data automatically, without the need for manual intervention, and can be applied to any large-scale dataset. Experimental results show that FiFA significantly enhances training stability and achieves better performance, being preferred by humans 17% more, while using less than 0.5% of the full data and thus 1% of the GPU hours compared to utilizing full human feedback datasets.

Graph Convolution Network (GCN) has become new state-of-the-art for collaborative filtering. Nevertheless, the reasons of its effectiveness for recommendation are not well understood. Existing work that adapts GCN to recommendation lacks thorough ablation analyses on GCN, which is originally designed for graph classification tasks and equipped with many neural network operations. However, we empirically find that the two most common designs in GCNs -- feature transformation and nonlinear activation -- contribute little to the performance of collaborative filtering. Even worse, including them adds to the difficulty of training and degrades recommendation performance. In this work, we aim to simplify the design of GCN to make it more concise and appropriate for recommendation. We propose a new model named LightGCN, including only the most essential component in GCN -- neighborhood aggregation -- for collaborative filtering. Specifically, LightGCN learns user and item embeddings by linearly propagating them on the user-item interaction graph, and uses the weighted sum of the embeddings learned at all layers as the final embedding. Such simple, linear, and neat model is much easier to implement and train, exhibiting substantial improvements (about 16.0\% relative improvement on average) over Neural Graph Collaborative Filtering (NGCF) -- a state-of-the-art GCN-based recommender model -- under exactly the same experimental setting. Further analyses are provided towards the rationality of the simple LightGCN from both analytical and empirical perspectives.