arXiv subjects

Michael C. Hughes

Publications and source records attributed to Michael C. Hughes.

At least 19 recordsLinked to original sources

arXiv2026

Normal Guidance is what Attention Needs

We consider training classifiers for 3D medical images using only one binary label for the entire volume rather than a label for each 2D slice. In such weakly supervised settings, can we learn accurate classifiers for slice-level predictions? Attention-based multiple instance learning (MIL) can produce an attention score for every slice. Yet recent work demonstrates that a simple center-focused baseline that ignores image content can outperform attention-based and transformer-based MIL at slice-level classification of 3D brain scans. We show this baseline also outperforms existing MIL at slice-level classification of thoracic and abdominal CT scans. Motivated by this baseline, we propose Normal Guidance, a regularization technique that encourages the learned attention distribution to follow a bell-shaped curve. Across three medical imaging datasets totaling over 4 million 2D slices, we show our Normal Guidance enables attention-based and transformer-based MIL methods to deliver significantly better slice-level localization than the state-of-the-art while remaining competitive at whole-scan classification.

cs.LG↗

arXiv2026

A Multi-Dataset Benchmark of Multiple Instance Learning for 3D Neuroimage Classification

Despite being resource-intensive to train, 3D convolutional neural networks (CNNs) have been the standard approach to classify CT and MRI scans. Recent work suggests that deep multiple instance learning (MIL) may be a more efficient alternative for 3D brain scans, especially when the pre-trained image encoder used to embed each 2D slice is frozen and only the pooling operation and classifier are trained. In this paper, we provide a systematic comparison of simple MIL, attention-based MIL, 3D CNNs, and 3D ViTs across three CT and four MRI datasets, including two large datasets of at least 10,000 scans. Our goal is to help resource-constrained practitioners understand which neural networks work well for 3D neuroimages and why. We further compare design choices for attention-based MIL, including different encoders, pooling operations, and architectural orderings. We find that simple mean pooling MIL, without any learnable attention, matches or outperforms recent MIL or 3D CNN alternatives on 4 of 6 moderate-sized tasks. This baseline remains competitive on two large datasets while being 25x faster to train. To explain mean pooling's success, we examine per-slice attention quality and a semi-synthetic dataset where we can derive the best possible classifier via a Bayes estimator. This analysis reveals the limits of existing MIL approaches and suggests routes for future improvements.

cs.LG↗

arXiv2026

Occam's Razor is Only as Sharp as Your ELBO

The marginal likelihood, also known as the evidence, is regarded as a mathematical embodiment of Occam's razor, enabling model selection that avoids overfitting. The evidence lower bound (ELBO) objective from variational inference has also been used for similar purposes. Prior work has shown that restricting the approximate posterior family via a mean-field approximation can lead the ELBO to underfit. In this paper, we show how ELBO-based hyperparameter learning in a simple over-parameterized regression model can also produce overfitting, depending on the assumed rank of the covariance matrix in a Gaussian approximate posterior. Surprisingly, among only the underfit and overfit options, Bayesian model selection via the evidence itself sometimes prefers the overfit version, while the ELBO does not. Bayesian practitioners hoping to scale to large models should be cautious about how reduced-rank assumptions needed for tractability may impact the potential for model selection.

stat.ML↗

arXiv2026

Locating acts of mechanistic reasoning in student team conversations with mechanistic machine learning

STEM education researchers are often interested in identifying moments of students' mechanistic reasoning for deeper analysis, but have limited capacity to search through many team conversation transcripts to find segments with a high concentration of such reasoning. We offer a solution in the form of an interpretable machine learning model that outputs time-varying probabilities that individual students are engaging in acts of mechanistic reasoning, leveraging evidence from their own utterances as well as contributions from the rest of the group. Using the toolkit of intentionally-designed probabilistic models, we introduce a specific inductive bias that steers the probabilistic dynamics toward desired, domain-aligned behavior. Experiments compare trained models with and without the inductive bias components, investigating whether their presence improves the desired model behavior on transcripts involving never-before-seen students and a novel discussion context. Our results show that the inductive bias improves generalization -- supporting the claim that interpretability is built into the model for this task rather than imposed post hoc. We conclude with practical recommendations for STEM education researchers seeking to adopt the tool and for ML researchers aiming to extend the model's design. Overall, we hope this work encourages the development of mechanistically interpretable models that are understandable and controllable for both end users and model designers in STEM education research.

physics.ed-ph↗

arXiv2026

Partial VOROS: A Cost-aware Performance Metric for Binary Classifiers with Precision and Capacity Constraints

The ROC curve is widely used to assess binary classifiers. Yet for some applications, such as alert systems for monitoring hospitalized patients, conventional ROC analysis cannot meet two key deployment needs: enforcing a constraint on precision to avoid false alarm fatigue and imposing an upper bound on the number of predicted positives to represent the capacity of hospital staff. The usual area under the curve metric also does not reflect asymmetric costs for false positives and false negatives. In this paper we address all three of these issues. First, we show how the subset of classifiers that meet precision and capacity constraints occupy a feasible region in ROC space. We establish the polygon-shaped geometry of this region. We then define the partial area of lesser classifiers, a performance metric that is monotonic with cost and only accounts for the feasible region. Averaging this area over a desired distribution for cost parameters results in the partial volume over the ROC surface, or partial VOROS. In experiments predicting mortality risk from vital sign history on several datasets, we show this cost-aware metric can outperform alternatives at ranking classifiers for in-hospital alerts.

cs.LG↗

arXiv2026

Learning Hyperparameters via a Data-Emphasized Variational Objective

When training large models on limited data, avoiding overfitting is paramount. Common grid search or smarter search methods rely on expensive separate runs for each candidate hyperparameter, while carving out a validation set that reduces available training data. In this paper, we study gradient-based learning of hyperparameters via the evidence lower bound (ELBO) objective from Bayesian variational methods. This avoids the need for any validation set. We focus on scenarios where the model is over-parameterized for flexibility and the approximate posterior is chosen to be Gaussian with isotropic covariance for tractability, even though it cannot match the true posterior. In such scenarios, we find the ELBO prioritizes posteriors that match the prior, leading to severe underfitting. Instead, we recommend a data-emphasized ELBO that upweights the likelihood but not the prior. In Bayesian transfer learning of image and text classifiers, our method reduces the 88+ hour grid search of past work to under 3 hours while delivering comparable accuracy. We further demonstrate how our approach enables efficient yet accurate approximations of Gaussian processes with learnable lengthscale kernels.

cs.LG↗

arXiv2025

Subgroup Validity in Machine Learning for Echocardiogram Data

Echocardiogram datasets enable training deep learning models to automate interpretation of cardiac ultrasound, thereby expanding access to accurate readings of diagnostically-useful images. However, the gender, sex, race, and ethnicity of the patients in these datasets are underreported and subgroup-specific predictive performance is unevaluated. These reporting deficiencies raise concerns about subgroup validity that must be studied and addressed before model deployment. In this paper, we show that current open echocardiogram datasets are unable to assuage subgroup validity concerns. We improve sociodemographic reporting for two datasets: TMED-2 and MIMIC-IV-ECHO. Analysis of six open datasets reveals no consideration of gender-diverse patients and insufficient patient counts for many racial and ethnic groups. We further perform an exploratory subgroup analysis of two published aortic stenosis detection models on TMED-2. We find insufficient evidence for subgroup validity for sex, racial, and ethnic subgroups. Our findings highlight that more data for underrepresented subgroups, improved demographic reporting, and subgroup-focused analyses are needed to prove subgroup validity in future work.

cs.LG↗

arXiv2025

Synthetic Data Reveals Generalization Gaps in Correlated Multiple Instance Learning

Multiple instance learning (MIL) is often used in medical imaging to classify high-resolution 2D images by processing patches or classify 3D volumes by processing slices. However, conventional MIL approaches treat instances separately, ignoring contextual relationships such as the appearance of nearby patches or slices that can be essential in real applications. We design a synthetic classification task where accounting for adjacent instance features is crucial for accurate prediction. We demonstrate the limitations of off-the-shelf MIL approaches by quantifying their performance compared to the optimal Bayes estimator for this task, which is available in closed-form. We empirically show that newer correlated MIL methods still do not achieve the best possible performance when trained with ten thousand training samples, each containing many instances.

cs.LG↗

arXiv2025

Decision-aware training of spatiotemporal forecasting models to select a top K subset of sites for intervention

Optimal allocation of scarce resources is a common problem for decision makers faced with choosing a limited number of locations for intervention. Spatiotemporal prediction models could make such decisions data-driven. A recent performance metric called fraction of best possible reach (BPR) measures the impact of using a model's recommended size K subset of sites compared to the best possible top-K in hindsight. We tackle two open problems related to BPR. First, we explore how to rank all sites numerically given a probabilistic model that predicts event counts jointly across sites. Ranking via the per-site mean is suboptimal for BPR. Instead, we offer a better ranking for BPR backed by decision theory. Second, we explore how to train a probabilistic model's parameters to maximize BPR. Discrete selection of K sites implies all-zero parameter gradients which prevent standard gradient training. We overcome this barrier via advances in perturbed optimizers. We further suggest a training objective that combines likelihood with a decision-aware BPR constraint to deliver high-quality top-K rankings as well as good forecasts for all sites. We demonstrate our approach on two where-to-intervene applications: mitigating opioid-related fatal overdoses for public health and monitoring endangered wildlife.

cs.LG↗

arXiv2025

Combining physics education and machine learning research to measure evidence of students' mechanistic sensemaking

Advances in machine learning (ML) offer new possibilities for science education research. We report on early progress in the design of an ML-based tool to analyze students' mechanistic sensemaking, working from a coding scheme that is aligned with previous work in physics education research (PER) and amenable to recently developed ML classification strategies using language encoders. We describe pilot tests of the tool, in three versions with different language encoders, to analyze sensemaking evident in college students' written responses to brief conceptual questions. The results show, first, that the tool's measurements of sensemaking can achieve useful agreement with a human coder, and, second, that encoder design choices entail a tradeoff between accuracy and computational expense. We discuss the promise and limitations of this approach, providing examples as to how this measurement scheme may serve PER in the future. We conclude with reflections on the use of ML to support PER research, with cautious optimism for strategies of co-design between PER and ML.

physics.ed-ph↗

arXiv2025

Discovering group dynamics in coordinated time series via hierarchical recurrent switching-state models

We seek a computationally efficient model for a collection of time series arising from multiple interacting entities (a.k.a. "agents"). Recent models of temporal patterns across individuals fail to incorporate explicit system-level collective behavior that can influence the trajectories of individual entities. To address this gap in the literature, we present a new hierarchical switching-state model that can be trained in an unsupervised fashion to simultaneously learn both system-level and individual-level dynamics. We employ a latent system-level discrete state Markov chain that provides top-down influence on latent entity-level chains which in turn govern the emission of each observed time series. Recurrent feedback from the observations to the latent chains at both entity and system levels allows recent situational context to inform how dynamics unfold at all levels in bottom-up fashion. We hypothesize that including both top-down and bottom-up influences on group dynamics will improve interpretability of the learned dynamics and reduce error when forecasting. Our hierarchical switching recurrent dynamical model can be learned via closed-form variational coordinate ascent updates to all latent chains that scale linearly in the number of entities. This is asymptotically no more costly than fitting a separate model for each entity. Analysis of both synthetic data and real basketball team movements suggests our lean parametric model can achieve competitive forecasts compared to larger neural network models that require far more computational resources. Further experiments on soldier data as well as a synthetic task with 64 cooperating entities show how our approach can yield interpretable insights about team dynamics over time.

stat.ML↗

arXiv2025

Learning the Regularization Strength for Deep Fine-Tuning via a Data-Emphasized Variational Objective

A number of popular transfer learning methods rely on grid search to select regularization hyperparameters that control over-fitting. This grid search requirement has several key disadvantages: the search is computationally expensive, requires carving out a validation set that reduces the size of available data for model training, and requires practitioners to specify candidate values. In this paper, we propose an alternative to grid search: directly learning regularization hyperparameters on the full training set via model selection techniques based on the evidence lower bound ("ELBo") objective from variational methods. For deep neural networks with millions of parameters, we specifically recommend a modified ELBo that upweights the influence of the data likelihood relative to the prior while remaining a valid bound on the evidence for Bayesian model selection. Our proposed technique overcomes all three disadvantages of grid search. We demonstrate effectiveness on image classification tasks on several datasets, yielding heldout accuracy comparable to existing approaches with far less compute time.

cs.LG↗

arXiv2024

SINCERE: Supervised Information Noise-Contrastive Estimation REvisited

The information noise-contrastive estimation (InfoNCE) loss function provides the basis of many self-supervised deep learning methods due to its strong empirical results and theoretic motivation. Previous work suggests a supervised contrastive (SupCon) loss to extend InfoNCE to learn from available class labels. This SupCon loss has been widely-used due to reports of good empirical performance. However, in this work we find that the prior SupCon loss formulation has questionable justification because it can encourage some images from the same class to repel one another in the learned embedding space. This problematic intra-class repulsion gets worse as the number of images sharing one class label increases. We propose the Supervised InfoNCE REvisited (SINCERE) loss as a theoretically-justified supervised extension of InfoNCE that eliminates intra-class repulsion. Experiments show that SINCERE leads to better separation of embeddings from different classes and improves transfer learning classification accuracy. We additionally utilize probabilistic modeling to derive an information-theoretic bound that relates SINCERE loss to the symmeterized KL divergence between data-generating distributions for a target class and all other classes.

cs.CV↗

arXiv2024

Transfer Learning with Informative Priors: Simple Baselines Better than Previously Reported

We pursue transfer learning to improve classifier accuracy on a target task with few labeled examples available for training. Recent work suggests that using a source task to learn a prior distribution over neural net weights, not just an initialization, can boost target task performance. In this study, we carefully compare transfer learning with and without source task informed priors across 5 datasets. We find that standard transfer learning informed by an initialization only performs far better than reported in previous comparisons. The relative gains of methods using informative priors over standard transfer learning vary in magnitude across datasets. For the scenario of 5-300 examples per class, we find negative or negligible gains on 2 datasets, modest gains (between 1.5-3 points of accuracy) on 2 other datasets, and substantial gains (>8 points) on one dataset. Among methods using informative priors, we find that an isotropic covariance appears competitive with learned low-rank covariance matrix while being substantially simpler to understand and tune. Further analysis suggests that the mechanistic justification for informed priors -- hypothesized improved alignment between train and test loss landscapes -- is not consistently supported due to high variability in empirical landscapes. We release code to allow independent reproduction of all experiments.

cs.LG↗

arXiv2024

Detecting Heart Disease from Multi-View Ultrasound Images via Supervised Attention Multiple Instance Learning

Aortic stenosis (AS) is a degenerative valve condition that causes substantial morbidity and mortality. This condition is under-diagnosed and under-treated. In clinical practice, AS is diagnosed with expert review of transthoracic echocardiography, which produces dozens of ultrasound images of the heart. Only some of these views show the aortic valve. To automate screening for AS, deep networks must learn to mimic a human expert's ability to identify views of the aortic valve then aggregate across these relevant images to produce a study-level diagnosis. We find previous approaches to AS detection yield insufficient accuracy due to relying on inflexible averages across images. We further find that off-the-shelf attention-based multiple instance learning (MIL) performs poorly. We contribute a new end-to-end MIL approach with two key methodological innovations. First, a supervised attention technique guides the learned attention mechanism to favor relevant views. Second, a novel self-supervised pretraining strategy applies contrastive learning on the representation of the whole study instead of individual images as commonly done in prior literature. Experiments on an open-access dataset and an external validation set show that our approach yields higher accuracy while reducing model size.

eess.IV↗

arXiv2024

Systematic comparison of semi-supervised and self-supervised learning for medical image classification

In typical medical image classification problems, labeled data is scarce while unlabeled data is more available. Semi-supervised learning and self-supervised learning are two different research directions that can improve accuracy by learning from extra unlabeled data. Recent methods from both directions have reported significant gains on traditional benchmarks. Yet past benchmarks do not focus on medical tasks and rarely compare self- and semi- methods together on an equal footing. Furthermore, past benchmarks often handle hyperparameter tuning suboptimally. First, they may not tune hyperparameters at all, leading to underfitting. Second, when tuning does occur, it often unrealistically uses a labeled validation set that is much larger than the training set. Therefore currently published rankings might not always corroborate with their practical utility This study contributes a systematic evaluation of self- and semi- methods with a unified experimental protocol intended to guide a practitioner with scarce overall labeled data and a limited compute budget. We answer two key questions: Can hyperparameter tuning be effective with realistic-sized validation sets? If so, when all methods are tuned well, which self- or semi-supervised methods achieve the best accuracy? Our study compares 13 representative semi- and self-supervised methods to strong labeled-set-only baselines on 4 medical datasets. From 20000+ GPU hours of computation, we provide valuable best practices to resource-constrained practitioners: hyperparameter tuning is effective, and the semi-supervised method known as MixMatch delivers the most reliable gains across 4 datasets.

cs.CV↗

arXiv2024

InterLUDE: Interactions between Labeled and Unlabeled Data to Enhance Semi-Supervised Learning

Semi-supervised learning (SSL) seeks to enhance task performance by training on both labeled and unlabeled data. Mainstream SSL image classification methods mostly optimize a loss that additively combines a supervised classification objective with a regularization term derived solely from unlabeled data. This formulation neglects the potential for interaction between labeled and unlabeled images. In this paper, we introduce InterLUDE, a new approach to enhance SSL made of two parts that each benefit from labeled-unlabeled interaction. The first part, embedding fusion, interpolates between labeled and unlabeled embeddings to improve representation learning. The second part is a new loss, grounded in the principle of consistency regularization, that aims to minimize discrepancies in the model's predictions between labeled versus unlabeled inputs. Experiments on standard closed-set SSL benchmarks and a medical SSL task with an uncurated unlabeled set show clear benefits to our approach. On the STL-10 dataset with only 40 labels, InterLUDE achieves 3.2% error rate, while the best previous method reports 14.9%.

cs.CV↗

arXiv2024

Semi-Supervised Multimodal Multi-Instance Learning for Aortic Stenosis Diagnosis

Automated interpretation of ultrasound imaging of the heart (echocardiograms) could improve the detection and treatment of aortic stenosis (AS), a deadly heart disease. However, existing deep learning pipelines for assessing AS from echocardiograms have two key limitations. First, most methods rely on limited 2D cineloops, thereby ignoring widely available Doppler imaging that contains important complementary information about pressure gradients and blood flow abnormalities associated with AS. Second, obtaining labeled data is difficult. There are often far more unlabeled echocardiogram recordings available, but these remain underutilized by existing methods. To overcome these limitations, we introduce Semi-supervised Multimodal Multiple-Instance Learning (SMMIL), a new deep learning framework for automatic interpretation for structural heart diseases like AS. When deployed, SMMIL can combine information from two input modalities, spectral Dopplers and 2D cineloops, to produce a study-level AS diagnosis. During training, SMMIL can combine a smaller labeled set and an abundant unlabeled set of both modalities to improve its classifier. Experiments demonstrate that SMMIL outperforms recent alternatives at 3-level AS severity classification as well as several clinically relevant AS detection tasks.

cs.CV↗