Showing 1–10 of 10 results for author: Teneggi, J

Parameter-Free and Group Conditional Online Conformal Prediction

Authors: Beepul Bharti, Ambar Pal, Jacopo Teneggi, Jeremias Sulam

Abstract: Uncertainty quantification (UQ) is critical for the deployment of machine learning predictors in real-world scenarios where the data distribution may shift over time (i.e., data may not be exchangeable). Online conformal prediction (OCP) methods address this issue at the expense of either (i) group-wise error control or (ii) learning-rate independent implementation. Group-conditional coverage is e… ▽ More Uncertainty quantification (UQ) is critical for the deployment of machine learning predictors in real-world scenarios where the data distribution may shift over time (i.e., data may not be exchangeable). Online conformal prediction (OCP) methods address this issue at the expense of either (i) group-wise error control or (ii) learning-rate independent implementation. Group-conditional coverage is essential for fairness across different collections of data points and for providing finer UQ guarantees. Parameter-free optimization is crucial for robustness to adversarial and unknown data shifts. We propose a parameter-free algorithm for group-conditional OCP and demonstrate that it achieves the best group-conditional coverage guarantees. We evaluate our algorithm on synthetic and real-world data, demonstrating that our method not only improves the reliability of existing parameter-free OCP methods but also provides prediction intervals that are comparable in size to well-tuned group-conditional approaches. By unifying group-conditional coverage with parameter-free online algorithms, our work lays a foundation for fair and robust uncertainty quantification in shifting environments. △ Less

Submitted 7 July, 2026; v1 submitted 29 May, 2026; originally announced June 2026.

Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents

Authors: Jacopo Teneggi, S. M. Bargeen A. Turzo, Tanya Marwah, Alberto Bietti, P. Douglas Renfrew, Vikram Khipple Mulligan, Siavash Golkar

Abstract: Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broa… ▽ More Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broad design pipelines. We introduce Agent Rosetta, an LLM agent paired with a structured environment for operating Rosetta, the leading physics-based heteropolymer design software, capable of modeling non-canonical building blocks and geometries. Agent Rosetta iteratively refines designs to achieve user-defined objectives, combining LLM reasoning with Rosetta's generality. We evaluate Agent Rosetta on design with canonical amino acids, matching specialized models and expert baselines, and with non-canonical residues -- where ML approaches fail -- achieving comparable performance. Critically, prompt engineering alone often fails to generate Rosetta actions, demonstrating that environment design is essential for integrating LLM agents with specialized software. Our results show that properly designed environments enable LLM agents to make scientific software accessible while matching specialized tools and human experts. △ Less

Submitted 15 June, 2026; v1 submitted 16 March, 2026; originally announced March 2026.

Direct Preference Optimization for Adaptive Concept-based Explanations

Authors: Jacopo Teneggi, Zhenzhen Wang, Paul H. Yi, Tianmin Shu, Jeremias Sulam

Abstract: Concept-based explanation methods aim at making machine learning models more transparent by finding the most important semantic features of an input (e.g., colors, patterns, shapes) for a given prediction task. However, these methods generally ignore the communicative context of explanations, such as the preferences of a listener. For example, medical doctors understand explanations in terms of cl… ▽ More Concept-based explanation methods aim at making machine learning models more transparent by finding the most important semantic features of an input (e.g., colors, patterns, shapes) for a given prediction task. However, these methods generally ignore the communicative context of explanations, such as the preferences of a listener. For example, medical doctors understand explanations in terms of clinical markers, but patients may not, needing a different vocabulary to rationalize the same diagnosis. We address this gap with listener-adaptive explanations grounded in principles of pragmatic reasoning and the rational speech act. We introduce an iterative training procedure based on direct preference optimization where a speaker learns to compose explanations that maximize communicative utility for a listener. Our approach only needs access to pairwise preferences, which can be collected from human feedback, making it particularly relevant in real-world scenarios where a model of the listener may not be available. We demonstrate that our method is able to align speakers with the preferences of simulated listeners on image classification across three datasets, and further validate that pragmatic explanations generated with our method improve the classification accuracy of participants in a user study. △ Less

Submitted 1 October, 2025; v1 submitted 21 May, 2025; originally announced May 2025.

Conformal Risk Control for Semantic Uncertainty Quantification in Computed Tomography

Authors: Jacopo Teneggi, J Webster Stayman, Jeremias Sulam

Abstract: Uncertainty quantification is necessary for developers, physicians, and regulatory agencies to build trust in machine learning predictors and improve patient care. Beyond measuring uncertainty, it is crucial to express it in clinically meaningful terms that provide actionable insights. This work introduces a conformal risk control (CRC) procedure for organ-dependent uncertainty estimation, ensurin… ▽ More Uncertainty quantification is necessary for developers, physicians, and regulatory agencies to build trust in machine learning predictors and improve patient care. Beyond measuring uncertainty, it is crucial to express it in clinically meaningful terms that provide actionable insights. This work introduces a conformal risk control (CRC) procedure for organ-dependent uncertainty estimation, ensuring high-probability coverage of the ground-truth image. We first present a high-dimensional CRC procedure that leverages recent ideas of length minimization. We make this procedure semantically adaptive to each patient's anatomy and positioning of organs. Our method, sem-CRC, provides tighter uncertainty intervals with valid coverage on real-world computed tomography (CT) data while communicating uncertainty with clinically relevant features. △ Less

Submitted 28 February, 2025; originally announced March 2025.

I Bet You Did Not Mean That: Testing Semantic Importance via Betting

Authors: Jacopo Teneggi, Jeremias Sulam

Abstract: Recent works have extended notions of feature importance to semantic concepts that are inherently interpretable to the users interacting with a black-box predictive model. Yet, precise statistical guarantees, such as false positive rate and false discovery rate control, are needed to communicate findings transparently and to avoid unintended consequences in real-world scenarios. In this paper, we… ▽ More Recent works have extended notions of feature importance to semantic concepts that are inherently interpretable to the users interacting with a black-box predictive model. Yet, precise statistical guarantees, such as false positive rate and false discovery rate control, are needed to communicate findings transparently and to avoid unintended consequences in real-world scenarios. In this paper, we formalize the global (i.e., over a population) and local (i.e., for a sample) statistical importance of semantic concepts for the predictions of opaque models by means of conditional independence, which allows for rigorous testing. We use recent ideas of sequential kernelized independence testing (SKIT) to induce a rank of importance across concepts, and showcase the effectiveness and flexibility of our framework on synthetic datasets as well as on image classification tasks using several and diverse vision-language models. △ Less

Submitted 7 October, 2024; v1 submitted 29 May, 2024; originally announced May 2024.

How to Trust Your Diffusion Model: A Convex Optimization Approach to Conformal Risk Control

Authors: Jacopo Teneggi, Matthew Tivnan, J. Webster Stayman, Jeremias Sulam

Abstract: Score-based generative modeling, informally referred to as diffusion models, continue to grow in popularity across several important domains and tasks. While they provide high-quality and diverse samples from empirical distributions, important questions remain on the reliability and trustworthiness of these sampling procedures for their responsible use in critical scenarios. Conformal prediction i… ▽ More Score-based generative modeling, informally referred to as diffusion models, continue to grow in popularity across several important domains and tasks. While they provide high-quality and diverse samples from empirical distributions, important questions remain on the reliability and trustworthiness of these sampling procedures for their responsible use in critical scenarios. Conformal prediction is a modern tool to construct finite-sample, distribution-free uncertainty guarantees for any black-box predictor. In this work, we focus on image-to-image regression tasks and we present a generalization of the Risk-Controlling Prediction Sets (RCPS) procedure, that we term $K$-RCPS, which allows to $(i)$ provide entrywise calibrated intervals for future samples of any diffusion model, and $(ii)$ control a certain notion of risk with respect to a ground truth image with minimal mean interval length. Differently from existing conformal risk control procedures, ours relies on a novel convex optimization approach that allows for multidimensional risk control while provably minimizing the mean interval length. We illustrate our approach on two real-world image denoising problems: on natural images of faces as well as on computed tomography (CT) scans of the abdomen, demonstrating state of the art performance. △ Less

Submitted 27 December, 2023; v1 submitted 7 February, 2023; originally announced February 2023.

Journal ref: International Conference on Machine Learning (2023)

Weakly Supervised Learning Significantly Reduces the Number of Labels Required for Intracranial Hemorrhage Detection on Head CT

Authors: Jacopo Teneggi, Paul H. Yi, Jeremias Sulam

Abstract: Modern machine learning pipelines, in particular those based on deep learning (DL) models, require large amounts of labeled data. For classification problems, the most common learning paradigm consists of presenting labeled examples during training, thus providing strong supervision on what constitutes positive and negative samples. This constitutes a major obstacle for the development of DL model… ▽ More Modern machine learning pipelines, in particular those based on deep learning (DL) models, require large amounts of labeled data. For classification problems, the most common learning paradigm consists of presenting labeled examples during training, thus providing strong supervision on what constitutes positive and negative samples. This constitutes a major obstacle for the development of DL models in radiology--in particular for cross-sectional imaging (e.g., computed tomography [CT] scans)--where labels must come from manual annotations by expert radiologists at the image or slice-level. These differ from examination-level annotations, which are coarser but cheaper, and could be extracted from radiology reports using natural language processing techniques. This work studies the question of what kind of labels should be collected for the problem of intracranial hemorrhage detection in brain CT. We investigate whether image-level annotations should be preferred to examination-level ones. By framing this task as a multiple instance learning problem, and employing modern attention-based DL architectures, we analyze the degree to which different levels of supervision improve detection performance. We find that strong supervision (i.e., learning with local image-level annotations) and weak supervision (i.e., learning with only global examination-level labels) achieve comparable performance in examination-level hemorrhage detection (the task of selecting the images in an examination that show signs of hemorrhage) as well as in image-level hemorrhage detection (highlighting those signs within the selected images). Furthermore, we study this behavior as a function of the number of labels available during training. Our results suggest that local labels may not be necessary at all for these tasks, drastically reducing the time and cost involved in collecting and curating datasets. △ Less

Submitted 28 November, 2022; originally announced November 2022.

SHAP-XRT: The Shapley Value Meets Conditional Independence Testing

Authors: Jacopo Teneggi, Beepul Bharti, Yaniv Romano, Jeremias Sulam

Abstract: The complex nature of artificial neural networks raises concerns on their reliability, trustworthiness, and fairness in real-world scenarios. The Shapley value -- a solution concept from game theory -- is one of the most popular explanation methods for machine learning models. More traditionally, from a statistical perspective, feature importance is defined in terms of conditional independence. So… ▽ More The complex nature of artificial neural networks raises concerns on their reliability, trustworthiness, and fairness in real-world scenarios. The Shapley value -- a solution concept from game theory -- is one of the most popular explanation methods for machine learning models. More traditionally, from a statistical perspective, feature importance is defined in terms of conditional independence. So far, these two approaches to interpretability and feature importance have been considered separate and distinct. In this work, we show that Shapley-based explanation methods and conditional independence testing are closely related. We introduce the SHAPley EXplanation Randomization Test (SHAP-XRT), a testing procedure inspired by the Conditional Randomization Test (CRT) for a specific notion of local (i.e., on a sample) conditional independence. With it, we prove that for binary classification problems, the marginal contributions in the Shapley value provide lower and upper bounds to the expected $p$-values of their respective tests. Furthermore, we show that the Shapley value itself provides an upper bound to the expected $p$-value of a global (i.e., overall) null hypothesis. As a result, we further our understanding of Shapley-based explanation methods from a novel perspective and characterize the conditions under which one can make statistically valid claims about feature importance via the Shapley value. △ Less

Submitted 27 December, 2023; v1 submitted 14 July, 2022; originally announced July 2022.

Journal ref: Transactions on Machine Learning Research (2023)

Fast Hierarchical Games for Image Explanations

Authors: Jacopo Teneggi, Alexandre Luster, Jeremias Sulam

Abstract: As modern complex neural networks keep breaking records and solving harder problems, their predictions also become less and less intelligible. The current lack of interpretability often undermines the deployment of accurate machine learning tools in sensitive settings. In this work, we present a model-agnostic explanation method for image classification based on a hierarchical extension of Shapley… ▽ More As modern complex neural networks keep breaking records and solving harder problems, their predictions also become less and less intelligible. The current lack of interpretability often undermines the deployment of accurate machine learning tools in sensitive settings. In this work, we present a model-agnostic explanation method for image classification based on a hierarchical extension of Shapley coefficients--Hierarchical Shap (h-Shap)--that resolves some of the limitations of current approaches. Unlike other Shapley-based explanation methods, h-Shap is scalable and can be computed without the need of approximation. Under certain distributional assumptions, such as those common in multiple instance learning, h-Shap retrieves the exact Shapley coefficients with an exponential improvement in computational complexity. We compare our hierarchical approach with popular Shapley-based and non-Shapley-based methods on a synthetic dataset, a medical imaging scenario, and a general computer vision problem, showing that h-Shap outperforms the state of the art in both accuracy and runtime. Code and experiments are made publicly available. △ Less

Submitted 9 June, 2022; v1 submitted 13 April, 2021; originally announced April 2021.

Comments: 20 pages, 8 figures

Fitting Splines to Axonal Arbors Quantifies Relationship between Branch Order and Geometry

Authors: Thomas L. Athey, Jacopo Teneggi, Joshua T. Vogelstein, Daniel Tward, Ulrich Mueller, Michael I. Miller

Abstract: Neuromorphology is crucial to identifying neuronal subtypes and understanding learning. It is also implicated in neurological disease. However, standard morphological analysis focuses on macroscopic features such as branching frequency and connectivity between regions, and often neglects the internal geometry of neurons. In this work, we treat neuron trace points as a sampling of differentiable cu… ▽ More Neuromorphology is crucial to identifying neuronal subtypes and understanding learning. It is also implicated in neurological disease. However, standard morphological analysis focuses on macroscopic features such as branching frequency and connectivity between regions, and often neglects the internal geometry of neurons. In this work, we treat neuron trace points as a sampling of differentiable curves and fit them with a set of branching B-splines. We designed our representation with the Frenet-Serret formulas from differential geometry in mind. The Frenet-Serret formulas completely characterize smooth curves, and involve two parameters, curvature and torsion. Our representation makes it possible to compute these parameters from neuron traces in closed form. These parameters are defined continuously along the curve, in contrast to other parameters like tortuosity which depend on start and end points. We applied our method to a dataset of cortical projection neurons traced in two mouse brains, and found that the parameters are distributed differently between primary, collateral, and terminal axon branches, thus quantifying geometric differences between different components of an axonal arbor. The results agreed in both brains, further validating our representation. The code used in this work can be readily applied to neuron traces in SWC format and is available in our open-source Python package brainlit: http://brainlit.neurodata.io/. △ Less

Submitted 5 June, 2021; v1 submitted 3 April, 2021; originally announced April 2021.

Journal ref: Front. Neuroinform. 15 (2021)