arXiv subjects

John Guttag

Publications and source records attributed to John Guttag.

At least 19 recordsLinked to original sources

arXiv2026

A Removal Based Approach to Improve LLM Faithfulness at Test-Time

Large language models (LLMs) are increasingly used for consequential decisions, making their explanations an important tool for auditing model behavior. Unfortunately, these explanations can be unfaithful, failing to reflect the actual reasoning underlying the model's decisions. We consider a setting in which an LLM provides both an answer and an explanation in response to a question. We identify two distinct dimensions of unfaithful explanations: incompleteness, meaning that the explanation omits factors that influence the answer, and unsoundness, meaning that the explanation cites factors that did not influence the model's answer. Existing approaches to improving LLM faithfulness include training-time methods, which require access to model weights and extensive computational resources, and test-time methods that largely focus on addressing unsoundness. We introduce a test-time approach that directly targets incompleteness. We remove from the input the concepts not credited in the model's explanation and re-query the model on the reduced input. This eliminates unmentioned influences while preserving the influence of mentioned concepts. Across two datasets, multiple model families, and two independent faithfulness metrics, our approach improves explanation faithfulness compared to both standard prompting and prompting to encourage faithfulness. Our method is model-agnostic and can be applied at inference time without modifying model parameters, providing a flexible mechanism for reducing hidden influences and improving the reliability and safety of LLM-assisted decision making.

cs.AI↗

arXiv2026

Position: Evaluation of ECG Representations Must Be Fixed

This position paper argues that current benchmarking practice in 12-lead ECG representation learning must be fixed to ensure progress is reliable and aligned with clinically meaningful objectives. The field has largely converged on three public multi-label benchmarks (PTB-XL, CPSC2018, CSN) dominated by arrhythmia and waveform-morphology labels, even though the ECG is known to encode substantially broader clinical information. We argue that downstream evaluation should expand to include an assessment of structural heart disease and patient-level forecasting, in addition to other evolving ECG-related endpoints, as relevant clinical targets. Next, we outline evaluation best practices for multi-label, imbalanced settings, and show that when they are applied, the literature's current conclusion about which representations perform best is altered. Furthermore, we demonstrate the surprising result that a randomly initialized encoder with linear evaluation matches state-of-the-art pre-training on many tasks. This motivates the use of a random encoder as a reasonable baseline model. We substantiate our observations with an empirical evaluation of five representative ECG pre-training approaches across six evaluation settings: the three standard benchmarks, a structural disease dataset, hemodynamic inference, and patient forecasting.

cs.LG↗

arXiv2026

The 802.11 MAC protocol leads to inefficient equilibria

Wireless local area networks (WLANs) based on the family of 802.11 technologies are becoming ubiquitous. These technologies support multiple data transmission rates. Transmitting at a lower data rate (by using a more resilient modulation scheme) increases the frame transmission time but reduces the bit error rate. In non-cooperative environments such as public hot-spots or WLANs operated by different enterprises that are physically close to each other, individual nodes attempt to maximize their achieved throughput by adjusting the data rate or frame size used, irrespective of the impact of this on overall system performance. In this paper, we show both analytically using a game theoretic model and through simulation that the existing 802.11 distributed MAC protocol, DCF (for Distributed Coordination Function), as well as its enhanced version, which is being standardized as part of 802.11e, can lead non-cooperative nodes to undesirable Nash equilibriums in which the wireless channel is inefficiently used. We show that by establishing independence between the allocation of the shared channel resource and the transmission strategies used by individual nodes, an ideal MAC protocol can lead rational nodes to arrive at equilibriums in which all competing nodes achieve higher throughputs than with DCF.

cs.NI↗

arXiv2026

Role Classification of Hosts within Enterprise Networks Based on Connection Patterns

Role classification involves grouping hosts into related roles. It exposes the logical structure of a network, simplifies network management tasks such as policy checking and network segmentation, and can be used to improve the accuracy of network monitoring and analysis algorithms such as intrusion detection. This paper defines the role classification problem and introduces two practical algorithms that group hosts based on observed connection patterns while dealing with changes in these patterns over time. The algorithms have been implemented in a commercial network monitoring and analysis product for enterprise networks. Results from grouping two enterprise networks show that the number of groups identified by our algorithms can be two orders of magnitude smaller than the number of hosts and that the way our algorithms group hosts highly reflects the logical structure of the networks.

cs.NI↗

arXiv2026

Time-based Fairness Improves Performance in Multi-rate WLANs

The performance seen by individual clients on a wireless local area network (WLAN) is heavily influenced by the manner in which wireless channel capacity is allocated. The popular MAC protocol DCF (Distributed Coordination Function) used in 802.11 networks provides equal long-term transmission opportunities to competing nodes when all nodes experience similar channel conditions. When similar-sized packets are also used, DCF leads to equal achieved throughputs (throughput-based fairness) among contending nodes. Because of varying indoor channel conditions, the 802.11 standard supports multiple data transmission rates to exploit the trade-off between data rate and bit error rate. This leads to considerable rate diversity, particularly when the network is congested. Under such conditions, throughput-based fairness can lead to drastically reduced aggregate throughput. In this paper, we argue the advantages of time-based fairness, in which each competing node receives an equal share of the wireless channel occupancy time. We demonstrate that this notion of fairness can lead to significant improvements in aggregate performance while still guaranteeing that no node receives worse channel access than it would in a single-rate WLAN. We also describe our algorithm, TBR (Time-based Regulator), which runs on the AP and works with any MAC protocol to provide time-based fairness by regulating packets. Through experiments, we show that our practical and backward compatible implementation of TBR in conjunction with an existing implementation of DCF achieves time-based fairness.

cs.NI↗

arXiv2026

Improving Domain Generalization in Contrastive Learning using Adaptive Temperature Control

Self-supervised pre-training with contrastive learning is a powerful method for learning from sparsely labeled data. However, performance can drop considerably when there is a shift in the distribution of data from training to test time. We study this phenomenon in a setting in which the training data come from multiple domains, and the test data come from a domain not seen at training that is subject to significant covariate shift. We present a new method for contrastive learning that incorporates domain labels to increase the domain invariance of learned representations, leading to improved out-of-distribution generalization. Our method adjusts the temperature parameter in the InfoNCE loss -- which controls the relative weighting of negative pairs -- using the probability that a negative sample comes from the same domain as the anchor. This upweights pairs from more similar domains, encouraging the model to discriminate samples based on domain-invariant attributes. Through experiments on a variant of the MNIST dataset, we demonstrate that our method yields better out-of-distribution performance than domain generalization baselines. Furthermore, our method maintains strong in-distribution task performance, substantially outperforming baselines on this measure.

cs.LG↗

arXiv2025

Unified Brain Surface and Volume Registration

Accurate registration of brain MRI scans is fundamental for cross-subject analysis in neuroscientific studies. This involves aligning both the cortical surface of the brain and the interior volume. Traditional methods treat volumetric and surface-based registration separately, which often leads to inconsistencies that limit downstream analyses. We propose a deep learning framework, NeurAlign, that registers $3$D brain MRI images by jointly aligning both cortical and subcortical regions through a unified volume-and-surface-based representation. Our approach leverages an intermediate spherical coordinate space to bridge anatomical surface topology with volumetric anatomy, enabling consistent and anatomically accurate alignment. By integrating spherical registration into the learning, our method ensures geometric coherence between volume and surface domains. In a series of experiments on both in-domain and out-of-domain datasets, our method consistently outperforms both classical and machine learning-based registration methods -- improving the Dice score by up to 7 points while maintaining regular deformation fields. Additionally, it is orders of magnitude faster than the standard method for this task, and is simpler to use because it requires no additional inputs beyond an MRI scan. With its superior accuracy, fast inference, and ease of use, NeurAlign sets a new standard for joint cortical and subcortical registration.

cs.CV↗

arXiv2025

Classifying Phonotrauma Severity from Vocal Fold Images with Soft Ordinal Regression

Phonotrauma refers to vocal fold tissue damage resulting from exposure to forces during voicing. It occurs on a continuum from mild to severe, and treatment options can vary based on severity. Assessment of severity involves a clinician's expert judgment, which is costly and can vary widely in reliability. In this work, we present the first method for automatically classifying phonotrauma severity from vocal fold images. To account for the ordinal nature of the labels, we adopt a widely used ordinal regression framework. To account for label uncertainty, we propose a novel modification to ordinal regression loss functions that enables them to operate on soft labels reflecting annotator rating distributions. Our proposed soft ordinal regression method achieves predictive performance approaching that of clinical experts, while producing well-calibrated uncertainty estimates. By providing an automated tool for phonotrauma severity assessment, our work can enable large-scale studies of phonotrauma, ultimately leading to improved clinical understanding and patient care.

cs.CV↗

arXiv2025

Tyche: Stochastic In-Context Learning for Medical Image Segmentation

Existing learning-based solutions to medical image segmentation have two important shortcomings. First, for most new segmentation task, a new model has to be trained or fine-tuned. This requires extensive resources and machine learning expertise, and is therefore often infeasible for medical researchers and clinicians. Second, most existing segmentation methods produce a single deterministic segmentation mask for a given image. In practice however, there is often considerable uncertainty about what constitutes the correct segmentation, and different expert annotators will often segment the same image differently. We tackle both of these problems with Tyche, a model that uses a context set to generate stochastic predictions for previously unseen tasks without the need to retrain. Tyche differs from other in-context segmentation methods in two important ways. (1) We introduce a novel convolution block architecture that enables interactions among predictions. (2) We introduce in-context test-time augmentation, a new mechanism to provide prediction stochasticity. When combined with appropriate model design and loss functions, Tyche can predict a set of plausible diverse segmentation candidates for new or unseen medical images and segmentation tasks without the need to retrain.

eess.IV↗

arXiv2025

Evaluating multiple models using labeled and unlabeled data

It remains difficult to evaluate machine learning classifiers in the absence of a large, labeled dataset. While labeled data can be prohibitively expensive or impossible to obtain, unlabeled data is plentiful. Here, we introduce Semi-Supervised Model Evaluation (SSME), a method that uses both labeled and unlabeled data to evaluate machine learning classifiers. SSME is the first evaluation method to take advantage of the fact that: (i) there are frequently multiple classifiers for the same task, (ii) continuous classifier scores are often available for all classes, and (iii) unlabeled data is often far more plentiful than labeled data. The key idea is to use a semi-supervised mixture model to estimate the joint distribution of ground truth labels and classifier predictions. We can then use this model to estimate any metric that is a function of classifier scores and ground truth labels (e.g., accuracy or expected calibration error). We present experiments in four domains where obtaining large labeled datasets is often impractical: (1) healthcare, (2) content moderation, (3) molecular property prediction, and (4) image annotation. Our results demonstrate that SSME estimates performance more accurately than do competing methods, reducing error by 5.1x relative to using labeled data alone and 2.4x relative to the next best competing method. SSME also improves accuracy when evaluating performance across subsets of the test distribution (e.g., specific demographic subgroups) and when evaluating the performance of language models.

cs.LG↗

arXiv2025

MultiverSeg: Scalable Interactive Segmentation of Biomedical Imaging Datasets with In-Context Guidance

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

cs.CV↗

arXiv2025

Test-time augmentation improves efficiency in conformal prediction

A conformal classifier produces a set of predicted classes and provides a probabilistic guarantee that the set includes the true class. Unfortunately, it is often the case that conformal classifiers produce uninformatively large sets. In this work, we show that test-time augmentation (TTA)--a technique that introduces inductive biases during inference--reduces the size of the sets produced by conformal classifiers. Our approach is flexible, computationally efficient, and effective. It can be combined with any conformal score, requires no model retraining, and reduces prediction set sizes by 10%-14% on average. We conduct an evaluation of the approach spanning three datasets, three models, two established conformal scoring methods, different guarantee strengths, and several distribution shifts to show when and why test-time augmentation is a useful addition to the conformal pipeline.

cs.LG↗

arXiv2025

Walk the Talk? Measuring the Faithfulness of Large Language Model Explanations

Large language models (LLMs) are capable of generating plausible explanations of how they arrived at an answer to a question. However, these explanations can misrepresent the model's "reasoning" process, i.e., they can be unfaithful. This, in turn, can lead to over-trust and misuse. We introduce a new approach for measuring the faithfulness of LLM explanations. First, we provide a rigorous definition of faithfulness. Since LLM explanations mimic human explanations, they often reference high-level concepts in the input question that purportedly influenced the model. We define faithfulness in terms of the difference between the set of concepts that LLM explanations imply are influential and the set that truly are. Second, we present a novel method for estimating faithfulness that is based on: (1) using an auxiliary LLM to modify the values of concepts within model inputs to create realistic counterfactuals, and (2) using a Bayesian hierarchical model to quantify the causal effects of concepts at both the example- and dataset-level. Our experiments show that our method can be used to quantify and discover interpretable patterns of unfaithfulness. On a social bias task, we uncover cases where LLM explanations hide the influence of social bias. On a medical question answering task, we uncover cases where LLM explanations provide misleading claims about which pieces of evidence influenced the model's decisions.

cs.CL↗

arXiv2025

MultiMorph: On-demand Atlas Construction

We present MultiMorph, a fast and efficient method for constructing anatomical atlases on the fly. Atlases capture the canonical structure of a collection of images and are essential for quantifying anatomical variability across populations. However, current atlas construction methods often require days to weeks of computation, thereby discouraging rapid experimentation. As a result, many scientific studies rely on suboptimal, precomputed atlases from mismatched populations, negatively impacting downstream analyses. MultiMorph addresses these challenges with a feedforward model that rapidly produces high-quality, population-specific atlases in a single forward pass for any 3D brain dataset, without any fine-tuning or optimization. MultiMorph is based on a linear group-interaction layer that aggregates and shares features within the group of input images. Further, by leveraging auxiliary synthetic data, MultiMorph generalizes to new imaging modalities and population groups at test-time. Experimentally, MultiMorph outperforms state-of-the-art optimization-based and learning-based atlas construction methods in both small and large population settings, with a 100-fold reduction in time. This makes MultiMorph an accessible framework for biomedical researchers without machine learning expertise, enabling rapid, high-quality atlas generation for diverse studies.

cs.CV↗

arXiv2024

ScribblePrompt: Fast and Flexible Interactive Segmentation for Any Biomedical Image

Biomedical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific biomedical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive and requires domain expertise. We present \emph{ScribblePrompt}, a flexible neural network based interactive segmentation tool for biomedical imaging that enables human annotators to segment previously unseen structures using scribbles, clicks, and bounding boxes. Through rigorous quantitative experiments, we demonstrate that given comparable amounts of interaction, ScribblePrompt produces more accurate segmentations than previous methods on datasets unseen during training. In a user study with domain experts, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to the next best method. ScribblePrompt's success rests on a set of careful design decisions. These include a training strategy that incorporates both a highly diverse set of images and tasks, novel algorithms for simulated user interactions and labels, and a network that enables fast inference. We showcase ScribblePrompt in an interactive demo, provide code, and release a dataset of scribble annotations at https://scribbleprompt.csail.mit.edu

cs.CV↗

arXiv2023

Coarse race data conceals disparities in clinical risk score performance

Healthcare data in the United States often records only a patient's coarse race group: for example, both Indian and Chinese patients are typically coded as "Asian." It is unknown, however, whether this coarse coding conceals meaningful disparities in the performance of clinical risk scores across granular race groups. Here we show that it does. Using data from 418K emergency department visits, we assess clinical risk score performance disparities across 26 granular groups for three outcomes, five risk scores, and four performance metrics. Across outcomes and metrics, we show that the risk scores exhibit significant granular performance disparities within coarse race groups. In fact, variation in performance within coarse groups often *exceeds* the variation between coarse groups. We explore why these disparities arise, finding that outcome rates, feature distributions, and the relationships between features and outcomes all vary significantly across granular groups. Our results suggest that healthcare providers, hospital systems, and machine learning researchers should strive to collect, release, and use granular race data in place of coarse race data, and that existing analyses may significantly underestimate racial disparities in performance.

cs.CY↗

arXiv2023

GIST: Generating Image-Specific Text for Fine-grained Object Classification

Recent vision-language models outperform vision-only models on many image classification tasks. However, because of the absence of paired text/image descriptions, it remains difficult to fine-tune these models for fine-grained image classification. In this work, we propose a method, GIST, for generating image-specific fine-grained text descriptions from image-only datasets, and show that these text descriptions can be used to improve classification. Key parts of our method include 1. prompting a pretrained large language model with domain-specific prompts to generate diverse fine-grained text descriptions for each class and 2. using a pretrained vision-language model to match each image to label-preserving text descriptions that capture relevant visual features in the image. We demonstrate the utility of GIST by fine-tuning vision-language models on the image-and-generated-text pairs to learn an aligned vision-language representation space for improved classification. We evaluate our learned representation space in full-shot and few-shot scenarios across four diverse fine-grained classification datasets, each from a different domain. Our method achieves an average improvement of $4.1\%$ in accuracy over CLIP linear probes and an average of $1.1\%$ improvement in accuracy over the previous state-of-the-art image-text classification method on the full-shot datasets. Our method achieves similar improvements across few-shot regimes. Code is available at https://github.com/emu1729/GIST.

cs.CV↗

arXiv2023

Sequential Multi-Dimensional Self-Supervised Learning for Clinical Time Series

Self-supervised learning (SSL) for clinical time series data has received significant attention in recent literature, since these data are highly rich and provide important information about a patient's physiological state. However, most existing SSL methods for clinical time series are limited in that they are designed for unimodal time series, such as a sequence of structured features (e.g., lab values and vitals signs) or an individual high-dimensional physiological signal (e.g., an electrocardiogram). These existing methods cannot be readily extended to model time series that exhibit multimodality, with structured features and high-dimensional data being recorded at each timestep in the sequence. In this work, we address this gap and propose a new SSL method -- Sequential Multi-Dimensional SSL -- where a SSL loss is applied both at the level of the entire sequence and at the level of the individual high-dimensional data points in the sequence in order to better capture information at both scales. Our strategy is agnostic to the specific form of loss function used at each level -- it can be contrastive, as in SimCLR, or non-contrastive, as in VICReg. We evaluate our method on two real-world clinical datasets, where the time series contains sequences of (1) high-frequency electrocardiograms and (2) structured data from lab values and vitals signs. Our experimental results indicate that pre-training with our method and then fine-tuning on downstream tasks improves performance over baselines on both datasets, and in several settings, can lead to improvements across different self-supervised loss functions.

cs.LG↗