arXiv subjects

Anna Goldenberg

Publications and source records attributed to Anna Goldenberg.

At least 19 recordsLinked to original sources

arXiv2026

LiNC: Lightweight Noise Correction via Per-Sample Trust and Gaussian Mixture Modeling

Label noise is common in medical imaging datasets due to factors such as inter-rater variability, annotation errors, and ambiguous cases. This can severely undermine the reliability and clinical effectiveness of machine learning models trained using those datasets. To address this challenge, we introduce Lightweight Noise Correction (LiNC), which adds a single trainable trust parameter per training sample and learns when to use the observed label and when to defer to the model during a standard training loop. The key idea is to train using a convex combination of the observed label and the model's own predictive distribution, controlled by a per-sample trust parameter. We show that the gradient of this objective drives trust values in opposite directions for clean versus noisy samples in the early training phase, yielding separable trust distributions. We use a 3-component Gaussian Mixture Model over the trust values to separate them into clean, ambiguous, and noisy cases and then execute a short soft-correction phase on the noisy cases and a final hard correction phase. Experiments on ten 2D datasets from MedMNISTv2 under label noise of up to 50% show consistent gains in accuracy and strong mislabel detection. LiNC adds negligible asymptotic overhead: the training-time complexity remains dominated by the base network, with additional memory growing linearly with the size of the training set.

cs.LG↗

arXiv2026

LiBaGS: Lightweight Boundary Gap Synthesis for Targeted Synthetic Data Selection

Synthetic data is useful only when the added samples fill missing parts of the training distribution that matter for the downstream task. We introduce LiBaGS, a lightweight, generator-agnostic method for targeted synthetic training data selection. LiBaGS scores candidate synthetic samples by combining decision-boundary proximity, predictive uncertainty, real-data density, and support validity, so that selected samples are both informative and likely to remain on the real data manifold. We then use a boundary-gap allocation rule that targets sparse but realistic decision-boundary neighborhoods, rather than simply adding more data or selecting only the most uncertain candidates. LiBaGS also learns when enough synthetic samples have been added through a marginal-value stopping rule, assigns softer labels near ambiguous boundaries, and uses a diversity objective to avoid redundant near-duplicate selections. Experiments show that LiBaGS improves accuracy over classical oversampling, hard augmentation, uncertainty and density ablations, and targeted-generation selection criteria.

cs.LG↗

arXiv2026

Dialogue to Question Generation for Evidence-based Medical Guideline Agent Development

Evidence-based medicine (EBM) is central to high-quality care, but remains difficult to implement in fast-paced primary care settings. Physicians face short consultations, increasing patient loads, and lengthy guideline documents that are impractical to consult in real time. To address this gap, we investigate the feasibility of using large language models (LLMs) as ambient assistants that surface targeted, evidence-based questions during physician-patient encounters. Our study focuses on question generation rather than question answering, with the aim of scaffolding physician reasoning and integrating guideline-based practice into brief consultations. We implemented two prompting strategies, a zero-shot baseline and a multi-stage reasoning variant, using Gemini 2.5 as the backbone model. We evaluated on a benchmark of 80 de-identified transcripts from real clinical encounters, with six experienced physicians contributing over 90 hours of structured review. Results indicate that while general-purpose LLMs are not yet fully reliable, they can produce clinically meaningful and guideline-relevant questions, suggesting significant potential to reduce cognitive burden and make EBM more actionable at the point of care.

cs.CL↗

arXiv2026

Can we generate portable representations for clinical time series data using LLMs?

Deploying clinical ML is slow and brittle: models that work at one hospital often degrade under distribution shifts at the next. In this work, we study a simple question -- can large language models (LLMs) create portable patient embeddings i.e. representations of patients enable a downstream predictor built on one hospital to be used elsewhere with minimal-to-no retraining and fine-tuning. To do so, we map from irregular ICU time series onto concise natural language summaries using a frozen LLM, then embed each summary with a frozen text embedding model to obtain a fixed length vector capable of serving as input to a variety of downstream predictors. Across three cohorts (MIMIC-IV, HIRID, PPICU), on multiple clinically grounded forecasting and classification tasks, we find that our approach is simple, easy to use and competitive with in-distribution with grid imputation, self-supervised representation learning, and time series foundation models, while exhibiting smaller relative performance drops when transferring to new hospitals. We study the variation in performance across prompt design, with structured prompts being crucial to reducing the variance of the predictive models without altering mean accuracy. We find that using these portable representations improves few-shot learning and does not increase demographic recoverability of age or sex relative to baselines, suggesting little additional privacy risk. Our work points to the potential that LLMs hold as tools to enable the scalable deployment of production grade predictive models by reducing the engineering overhead.

cs.LG↗

arXiv2025

LiLAW: Lightweight Learnable Adaptive Weighting to Learn Sample Difficulty & Improve Noisy Training

Training deep neural networks with noise and data heterogeneity is a major challenge. We introduce Lightweight Learnable Adaptive Weighting (LiLAW), a method that dynamically adjusts the loss weight of each training sample based on its evolving difficulty, categorized as easy, moderate, and hard, using only three global learnable scalar parameters. LiLAW learns to adaptively prioritize samples by updating these parameters with a single gradient descent step on a validation mini-batch after each training mini-batch, without requiring a clean, unbiased validation set. Experiments across general and medical imaging datasets, several noise types and levels, loss functions, and architectures with and without pretraining, including linear probing and full fine-tuning, show that LiLAW consistently improves accuracy and AUROC, especially in higher-noise settings, without requiring excessive tuning. We also obtain state-of-the-art results incorporating synthetic and augmented data from SynPAIN, GAITGen, ECG5000, and improved fairness on the Adult dataset. LiLAW is lightweight, practical, and computationally efficient, making it an effective, scalable approach to boost generalization and robustness across diverse deep learning training setups, especially in resource-constrained settings.

cs.LG↗

arXiv2025

Impute With Confidence: A Framework for Uncertainty Aware Multivariate Time Series Imputation

Time series data with missing values is common across many domains. Healthcare presents special challenges due to prolonged periods of sensor disconnection. In such cases, having a confidence measure for imputed values is critical. Most existing methods either overlook model uncertainty or lack mechanisms to estimate it. To address this gap, we introduce a general framework that quantifies and leverages uncertainty for selective imputation. By focusing on values the model is most confident in, highly unreliable imputations are avoided. Our experiments on multiple EHR datasets, covering diverse types of missingness, demonstrate that selectively imputing less-uncertain values not only reduces imputation errors but also improves downstream tasks. Specifically, we show performance gains in a 24-hour mortality prediction task, underscoring the practical benefit of incorporating uncertainty into time series imputation.

cs.LG↗

arXiv2025

DynaSubVAE: Adaptive Subgrouping for Scalable and Robust OOD Detection

Real-world observational data often contain existing or emerging heterogeneous subpopulations that deviate from global patterns. The majority of models tend to overlook these underrepresented groups, leading to inaccurate or even harmful predictions. Existing solutions often rely on detecting these samples as Out-of-domain (OOD) rather than adapting the model to new emerging patterns. We introduce DynaSubVAE, a Dynamic Subgrouping Variational Autoencoder framework that jointly performs representation learning and adaptive OOD detection. Unlike conventional approaches, DynaSubVAE evolves with the data by dynamically updating its latent structure to capture new trends. It leverages a novel non-parametric clustering mechanism, inspired by Gaussian Mixture Models, to discover and model latent subgroups based on embedding similarity. Extensive experiments show that DynaSubVAE achieves competitive performance in both near-OOD and far-OOD detection, and excels in class-OOD scenarios where an entire class is missing during training. We further illustrate that our dynamic subgrouping mechanism outperforms standalone clustering methods such as GMM and KMeans++ in terms of both OOD accuracy and regret precision.

cs.LG↗

arXiv2025

ExOSITO: Explainable Off-Policy Learning with Side Information for Intensive Care Unit Blood Test Orders

Ordering a minimal subset of lab tests for patients in the intensive care unit (ICU) can be challenging. Care teams must balance between ensuring the availability of the right information and reducing the clinical burden and costs associated with each lab test order. Most in-patient settings experience frequent over-ordering of lab tests, but are now aiming to reduce this burden on both hospital resources and the environment. This paper develops a novel method that combines off-policy learning with privileged information to identify the optimal set of ICU lab tests to order. Our approach, EXplainable Off-policy learning with Side Information for ICU blood Test Orders (ExOSITO) creates an interpretable assistive tool for clinicians to order lab tests by considering both the observed and predicted future status of each patient. We pose this problem as a causal bandit trained using offline data and a reward function derived from clinically-approved rules; we introduce a novel learning framework that integrates clinical knowledge with observational data to bridge the gap between the optimal and logging policies. The learned policy function provides interpretable clinical information and reduces costs without omitting any vital lab orders, outperforming both a physician's policy and prior approaches to this practical problem.

cs.LG↗

arXiv2024

Needles in Needle Stacks: Meaningful Clinical Information Buried in Noisy Waveform Data

Central Venous Lines (C-Lines) and Arterial Lines (A-Lines) are routinely used in the Critical Care Unit (CCU) for blood sampling, medication administration, and high-frequency blood pressure measurement. Judiciously accessing these lines is important, as over-utilization is associated with significant in-hospital morbidity and mortality. Documenting the frequency of line-access is an important step in reducing these adverse outcomes. Unfortunately, the current gold-standard for documentation is manual and subject to error, omission, and bias. The high-frequency blood pressure waveform data from sensors in these lines are often noisy and full of artifacts. Standard approaches in signal processing remove noise artifacts before meaningful analysis. However, from bedside observations, we characterized a distinct artifact that occurs during each instance of C-Line or A-Line use. These artifacts are buried amongst physiological waveform and extraneous noise. We focus on Machine Learning (ML) models that can detect these artifacts from waveform data in real-time - finding needles in needle stacks, in order to automate the documentation of line-access. We built and evaluated ML classifiers running in real-time at a major children's hospital to achieve this goal. We demonstrate the utility of these tools for reducing documentation burden, increasing available information for bedside clinicians, and informing unit-level initiatives to improve patient safety.

eess.SP↗

arXiv2024

Measurement Scheduling for ICU Patients with Offline Reinforcement Learning

Scheduling laboratory tests for ICU patients presents a significant challenge. Studies show that 20-40% of lab tests ordered in the ICU are redundant and could be eliminated without compromising patient safety. Prior work has leveraged offline reinforcement learning (Offline-RL) to find optimal policies for ordering lab tests based on patient information. However, new ICU patient datasets have since been released, and various advancements have been made in Offline-RL methods. In this study, we first introduce a preprocessing pipeline for the newly-released MIMIC-IV dataset geared toward time-series tasks. We then explore the efficacy of state-of-the-art Offline-RL methods in identifying better policies for ICU patient lab test scheduling. Besides assessing methodological performance, we also discuss the overall suitability and practicality of using Offline-RL frameworks for scheduling laboratory tests in ICU settings.

cs.LG↗

arXiv2024

Learning under Temporal Label Noise

Many time series classification tasks, where labels vary over time, are affected by label noise that also varies over time. Such noise can cause label quality to improve, worsen, or periodically change over time. We first propose and formalize temporal label noise, an unstudied problem for sequential classification of time series. In this setting, multiple labels are recorded over time while being corrupted by a time-dependent noise function. We first demonstrate the importance of modeling the temporal nature of the label noise function and how existing methods will consistently underperform. We then propose methods to train noise-tolerant classifiers by estimating the temporal label noise function directly from data. We show that our methods lead to state-of-the-art performance under diverse types of temporal label noise on real-world datasets

cs.LG↗

arXiv2024

Integrate Any Omics: Towards genome-wide data integration for patient stratification

High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or imputation often compromise biological diversity and dependencies. Furthermore, the critical task of accurately classifying new patients with partial omics data into existing subtypes is commonly overlooked. To address these issues, we introduce IntegrAO (Integrate Any Omics), an unsupervised framework for integrating incomplete multi-omics data and classifying new samples. IntegrAO first combines partially overlapping patient graphs from diverse omics sources and utilizes graph neural networks to produce unified patient embeddings. Our systematic evaluation across five cancer cohorts involving six omics modalities demonstrates IntegrAO's robustness to missing data and its accuracy in classifying new samples with partial profiles. An acute myeloid leukemia case study further validates its capability to uncover biological and clinical heterogeneity in incomplete datasets. IntegrAO's ability to handle heterogeneous and incomplete data makes it an essential tool for precision oncology, offering a holistic approach to patient characterization.

q-bio.GN↗

arXiv2023

CongFu: Conditional Graph Fusion for Drug Synergy Prediction

Drug synergy, characterized by the amplified combined effect of multiple drugs, is critically important for optimizing therapeutic outcomes. Limited data on drug synergy, arising from the vast number of possible drug combinations and testing costs, motivate the need for predictive methods. In this work, we introduce CongFu, a novel Conditional Graph Fusion Layer, designed to predict drug synergy. CongFu employs an attention mechanism and a bottleneck to extract local graph contexts and conditionally fuse graph data within a global context. Its modular architecture enables flexible replacement of layer modules, including readouts and graph encoders, facilitating customization for diverse applications. To evaluate the performance of CongFu, we conduct comprehensive experiments on four datasets, encompassing three distinct setups for drug synergy prediction. CongFu achieves state-of-the-art results on 11 out of 12 benchmark datasets, demonstrating its ability to capture intricate patterns of drug synergy. Through ablation studies, we validate the significance of individual layer components, affirming their contributions to overall predictive performance. Finally, we propose an explainability strategy for elucidating the effect of drugs on genes. By addressing the challenge of predicting drug synergy in untested drug pairs and utilizing our proposed explainability approach, CongFu opens new avenues for optimizing drug combinations and advancing personalized medicine.

cs.LG↗

arXiv2023

Maintaining Stability and Plasticity for Predictive Churn Reduction

Deployed machine learning models should be updated to take advantage of a larger sample size to improve performance, as more data is gathered over time. Unfortunately, even when model updates improve aggregate metrics such as accuracy, they can lead to errors on samples that were correctly predicted by the previous model causing per-sample regression in performance known as predictive churn. Such prediction flips erode user trust thereby reducing the effectiveness of the human-AI team as a whole. We propose a solution called Accumulated Model Combination (AMC) based keeping the previous and current model version, and generating a meta-output using the prediction of the two models. AMC is a general technique and we propose several instances of it, each having their own advantages depending on the model and data properties. AMC requires minimal additional computation and changes to training procedures. We motivate the need for AMC by showing the difficulty of making a single model consistent with its own predictions throughout training thereby revealing an implicit stability-plasticity tradeoff when training a single model. We demonstrate the effectiveness of AMC on a variety of modalities including computer vision, text, and tabular datasets comparing against state-of-the-art churn reduction methods, and showing superior churn reduction ability compared to all existing methods while being more efficient than ensembles.

cs.LG↗

arXiv2022

From Single-Visit to Multi-Visit Image-Based Models: Single-Visit Models are Enough to Predict Obstructive Hydronephrosis

Previous work has shown the potential of deep learning to predict renal obstruction using kidney ultrasound images. However, these image-based classifiers have been trained with the goal of single-visit inference in mind. We compare methods from video action recognition (i.e. convolutional pooling, LSTM, TSM) to adapt single-visit convolutional models to handle multiple visit inference. We demonstrate that incorporating images from a patient's past hospital visits provides only a small benefit for the prediction of obstructive hydronephrosis. Therefore, inclusion of prior ultrasounds is beneficial, but prediction based on the latest ultrasound is sufficient for patient risk stratification.

cs.CV↗

arXiv2022

Dynamic Interpretable Change Point Detection

Identifying change points (CPs) in a time series is crucial to guide better decision making across various fields like finance and healthcare and facilitating timely responses to potential risks or opportunities. Existing Change Point Detection (CPD) methods have a limitation in tracking changes in the joint distribution of multidimensional features. In addition, they fail to generalize effectively within the same time series as different types of CPs may require different detection methods. As the volume of multidimensional time series continues to grow, capturing various types of complex CPs such as changes in the correlation structure of the time-series features has become essential. To overcome the limitations of existing methods, we propose TiVaCPD, an approach that uses a Time-Varying Graphical Lasso (TVGL) to identify changes in correlation patterns between multidimensional features over time, and combines that with an aggregate Kernel Maximum Mean Discrepancy (MMD) test to identify changes in the underlying statistical distributions of dynamic time windows with varying length. The MMD and TVGL scores are combined using a novel ensemble method based on similarity measures leveraging the power of both statistical tests. We evaluate the performance of TiVaCPD in identifying and characterizing various types of CPs and show that our method outperforms current state-of-the-art methods in real-world CPD datasets. We further demonstrate that TiVaCPD scores characterize the type of CPs and facilitate interpretation of change dynamics, offering insights into real-life applications.

cs.LG↗

arXiv2022

Considerations for Visualizing Uncertainty in Clinical Machine Learning Models

Clinician-facing predictive models are increasingly present in the healthcare setting. Regardless of their success with respect to performance metrics, all models have uncertainty. We investigate how to visually communicate uncertainty in this setting in an actionable, trustworthy way. To this end, we conduct a qualitative study with cardiac critical care clinicians. Our results reveal that clinician trust may be impacted most not by the degree of uncertainty, but rather by how transparent the visualization of what the sources of uncertainty are. Our results show a clear connection between feature interpretability and clinical actionability.

cs.HC↗

arXiv2022

Decoupling Local and Global Representations of Time Series

Real-world time series data are often generated from several sources of variation. Learning representations that capture the factors contributing to this variability enables a better understanding of the data via its underlying generative process and improves performance on downstream machine learning tasks. This paper proposes a novel generative approach for learning representations for the global and local factors of variation in time series. The local representation of each sample models non-stationarity over time with a stochastic process prior, and the global representation of the sample encodes the time-independent characteristics. To encourage decoupling between the representations, we introduce counterfactual regularization that minimizes the mutual information between the two variables. In experiments, we demonstrate successful recovery of the true local and global variability factors on simulated data, and show that representations learned using our method yield superior performance on downstream tasks on real-world datasets. We believe that the proposed way of defining representations is beneficial for data modelling and yields better insights into the complexity of real-world data.

cs.LG↗