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Longitudinal 3D Foundation Modeling for Neoadjuvant Breast Cancer Response Prediction from Serial DCE-MRI
Authors:
Fidel Omar Tito Cruz,
Neda Ghafouri,
Zengyan Wang,
Pegah Khosravi,
Yu Tian,
Chen Chen
Abstract:
Pathologic complete response (pCR) is an important endpoint in neoadjuvant chemotherapy (NAC) for breast cancer, and predicting pCR from imaging during treatment could support treatment response assessment. Many existing imaging-based approaches rely on a single static timepoint, which fails to capture changes that occur during treatment. In this work, we present a longitudinal framework that comb…
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Pathologic complete response (pCR) is an important endpoint in neoadjuvant chemotherapy (NAC) for breast cancer, and predicting pCR from imaging during treatment could support treatment response assessment. Many existing imaging-based approaches rely on a single static timepoint, which fails to capture changes that occur during treatment. In this work, we present a longitudinal framework that combines a frozen 3D foundation encoder (Pillar-0) with our Temporal Dynamics Network (TDN) to predict treatment response from serial Dynamic Contrast-Enhanced (DCE) MRI acquired across four clinical timepoints from pre-treatment to pre-surgery. The TDN combines time-aware volumetric embeddings with clinical and treatment data to predict pCR. Evaluated on 982 patients from the combined I-SPY2 and ACRIN-6698 cohort, the proposed model achieves strong performance across all reported metrics when longitudinal 3D imaging is fused with clinical data (test AUROC: 73.6%, balanced accuracy: 69.1%). While clinical variables provide the strongest individual predictive signal, longitudinal 3D imaging contributes complementary information when fused with clinical data, improving pCR prediction. Our source code is available at: https://github.com/omarftt/longitudinal_temporal_pillar.
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Submitted 7 August, 2026;
originally announced August 2026.
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OncoTriad-QA: A Patient-Level Radiology-Pathology-Genomics Benchmark for Pan-Cancer Reasoning
Authors:
Ahnaf Munir,
Dannong Wang,
Michael W. McDonald,
Mubarak Shah,
Pegah Khosravi,
Yu Tian
Abstract:
Cancer diagnosis and characterization require integrating complementary evidence from radiology, pathology, genomics, and clinical metadata. However, most medical large language model (LLM) and vision-language model (VLM) benchmarks focus on isolated modalities or narrow image-text tasks, leaving patient-level oncology assessment across multiple evidence streams largely untested. We introduce Onco…
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Cancer diagnosis and characterization require integrating complementary evidence from radiology, pathology, genomics, and clinical metadata. However, most medical large language model (LLM) and vision-language model (VLM) benchmarks focus on isolated modalities or narrow image-text tasks, leaving patient-level oncology assessment across multiple evidence streams largely untested. We introduce OncoTriad-QA, a patient-level radiology-pathology-genomics benchmark for pan-cancer question answering. OncoTriad-QA contains 86.1k semantic questions across 9,281 TCGA patient cases from 32 cancer cohorts, aligning CT/MRI radiology, whole-slide histopathology, somatic mutations, copy-number alterations, DNA methylation, bulk RNA-seq, and clinical metadata. Case-specific annotations are constructed through a source-grounded LLM-assisted pipeline using curated labels, diagnostic reports, molecular profiles, and modality-derived evidence as primary sources of truth, with automated consistency checks and clinician review. We also introduce OncoVLM, a reference multimodal model that maps modality-native radiology, pathology, DNA methylation, and RNA-seq evidence into an LLM interface through learned projectors. Experiments show that existing general-purpose and medical LLMs remain limited on comprehensive pan-cancer QA, especially when questions require integrating imaging findings, tumor morphology, and molecular evidence. After fine-tuning on OncoTriad-QA, OncoVLM exceeds MedGemma-4B by an average of 10.7 points when using MCQ accuracy and BERTScore-F1, with consistent gains across multiple-choice and open-ended questions under radiology-only, pathology-only, and all-available settings. These results demonstrate the benchmark's value for training and evaluating models for integrated cancer question answering.
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Submitted 21 May, 2026;
originally announced August 2026.
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Rotation Equivariant Convolutions in Deformable Registration of Brain MRI
Authors:
Arghavan Rezvani,
Kun Han,
Anthony T. Wu,
Pooya Khosravi,
Xiaohui Xie
Abstract:
Image registration is a fundamental task that aligns anatomical structures between images. While CNNs perform well, they lack rotation equivariance - a rotated input does not produce a correspondingly rotated output. This hinders performance by failing to exploit the rotational symmetries inherent in anatomical structures, particularly in brain MRI. In this work, we integrate rotation-equivariant…
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Image registration is a fundamental task that aligns anatomical structures between images. While CNNs perform well, they lack rotation equivariance - a rotated input does not produce a correspondingly rotated output. This hinders performance by failing to exploit the rotational symmetries inherent in anatomical structures, particularly in brain MRI. In this work, we integrate rotation-equivariant convolutions into deformable brain MRI registration networks. We evaluate this approach by replacing standard encoders with equivariant ones in three baseline architectures, testing on multiple public brain MRI datasets.
Our experiments demonstrate that equivariant encoders have three key advantages: 1) They achieve higher registration accuracy while reducing network parameters, confirming the benefit of this anatomical inductive bias. 2) They outperform baselines on rotated input pairs, demonstrating robustness to orientation variations common in clinical practice. 3) They show improved performance with less training data, indicating greater sample efficiency. Our results demonstrate that incorporating geometric priors is a critical step toward building more robust, accurate, and efficient registration models.
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Submitted 9 April, 2026;
originally announced April 2026.
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Benchmarking Deep Learning for Future Liver Remnant Segmentation in Colorectal Liver Metastasis
Authors:
Anthony T. Wu,
Arghavan Rezvani,
Kela Liu,
Roozbeh Houshyar,
Pooya Khosravi,
Whitney Li,
Xiaohui Xie
Abstract:
Accurate segmentation of the future liver remnant (FLR) is critical for surgical planning in colorectal liver metastases (CRLM) to prevent fatal post-hepatectomy liver failure. However, this segmentation task is technically challenging due to complex resection boundaries, convoluted hepatic vasculature and diffuse metastatic lesions. A primary bottleneck in developing automated AI tools has been t…
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Accurate segmentation of the future liver remnant (FLR) is critical for surgical planning in colorectal liver metastases (CRLM) to prevent fatal post-hepatectomy liver failure. However, this segmentation task is technically challenging due to complex resection boundaries, convoluted hepatic vasculature and diffuse metastatic lesions. A primary bottleneck in developing automated AI tools has been the lack of high-fidelity, validated data. We address this gap by manually refining all 197 volumes from the public CRLM-CT-Seg dataset, creating the first open-source, validated benchmark for this task. We then establish the first segmentation baselines, comparing cascaded (Liver->CRLM->FLR) and end-to-end (E2E) strategies using nnU-Net, SwinUNETR, and STU-Net. We find a cascaded nnU-Net achieves the best final FLR segmentation Dice (0.767), while the pretrained STU-Net provides superior CRLM segmentation (0.620 Dice) and is significantly more robust to cascaded errors. This work provides the first validated benchmark and a reproducible framework to accelerate research in AI-assisted surgical planning.
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Submitted 9 April, 2026;
originally announced April 2026.
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Unlocking Multi-Site Clinical Data: A Federated Approach to Privacy-First Child Autism Behavior Analysis
Authors:
Guangyu Sun,
Wenhan Wu,
Zhishuai Guo,
Ziteng Wang,
Pegah Khosravi,
Chen Chen
Abstract:
Automated recognition of autistic behaviors in children is essential for early intervention and objective clinical assessment. However, the development of robust models is severely hindered by strict privacy regulations (e.g., HIPAA) and the sensitive nature of pediatric data, which prevents the centralized aggregation of clinical datasets. Furthermore, individual clinical sites often suffer from…
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Automated recognition of autistic behaviors in children is essential for early intervention and objective clinical assessment. However, the development of robust models is severely hindered by strict privacy regulations (e.g., HIPAA) and the sensitive nature of pediatric data, which prevents the centralized aggregation of clinical datasets. Furthermore, individual clinical sites often suffer from data scarcity, making it difficult to learn generalized behavior patterns or tailor models to site-specific patient distributions. To address these challenges, we observe that Federated Learning (FL) can decouple model training from raw data access, enabling multi-site collaboration while maintaining strict data residency. In this paper, we present the first study exploring Federated Learning for pose-based child autism behavior recognition. Our framework employs a two-layer privacy protection mechanism: utilizing human skeletal abstraction to remove identifiable visual information from the raw RGB videos and FL to ensure sensitive pose data remains within the clinic. This approach leverages distributed clinical data to learn generalized representations while providing the flexibility for site-specific personalization. Experimental results on the MMASD benchmark demonstrate that our framework achieves high recognition accuracy, outperforming traditional federated baselines and providing a robust, privacy-first solution for multi-site clinical analysis.
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Submitted 2 April, 2026;
originally announced April 2026.
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MoME: Mixture of Visual Language Medical Experts for Medical Imaging Segmentation
Authors:
Arghavan Rezvani,
Xiangyi Yan,
Anthony T. Wu,
Kun Han,
Pooya Khosravi,
Xiaohui Xie
Abstract:
In this study, we propose MoME, a Mixture of Visual Language Medical Experts, for Medical Image Segmentation. MoME adapts the successful Mixture of Experts (MoE) paradigm, widely used in Large Language Models (LLMs), for medical vision-language tasks. The architecture enables dynamic expert selection by effectively utilizing multi-scale visual features tailored to the intricacies of medical imager…
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In this study, we propose MoME, a Mixture of Visual Language Medical Experts, for Medical Image Segmentation. MoME adapts the successful Mixture of Experts (MoE) paradigm, widely used in Large Language Models (LLMs), for medical vision-language tasks. The architecture enables dynamic expert selection by effectively utilizing multi-scale visual features tailored to the intricacies of medical imagery, enriched with textual embeddings. This work explores a novel integration of vision-language models for this domain. Utilizing an assembly of 10 datasets, encompassing 3,410 CT scans, MoME demonstrates strong performance on a comprehensive medical imaging segmentation benchmark. Our approach explores the integration of foundation models for medical imaging, benefiting from the established efficacy of MoE in boosting model performance by incorporating textual information. Demonstrating competitive precision across multiple datasets, MoME explores a novel architecture for achieving robust results in medical image analysis.
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Submitted 30 October, 2025;
originally announced October 2025.
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XOCT: Enhancing OCT to OCTA Translation via Cross-Dimensional Supervised Multi-Scale Feature Learning
Authors:
Pooya Khosravi,
Kun Han,
Anthony T. Wu,
Arghavan Rezvani,
Zexin Feng,
Xiaohui Xie
Abstract:
Optical Coherence Tomography Angiography (OCTA) and its derived en-face projections provide high-resolution visualization of the retinal and choroidal vasculature, which is critical for the rapid and accurate diagnosis of retinal diseases. However, acquiring high-quality OCTA images is challenging due to motion sensitivity and the high costs associated with software modifications for conventional…
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Optical Coherence Tomography Angiography (OCTA) and its derived en-face projections provide high-resolution visualization of the retinal and choroidal vasculature, which is critical for the rapid and accurate diagnosis of retinal diseases. However, acquiring high-quality OCTA images is challenging due to motion sensitivity and the high costs associated with software modifications for conventional OCT devices. Moreover, current deep learning methods for OCT-to-OCTA translation often overlook the vascular differences across retinal layers and struggle to reconstruct the intricate, dense vascular details necessary for reliable diagnosis. To overcome these limitations, we propose XOCT, a novel deep learning framework that integrates Cross-Dimensional Supervision (CDS) with a Multi-Scale Feature Fusion (MSFF) network for layer-aware vascular reconstruction. Our CDS module leverages 2D layer-wise en-face projections, generated via segmentation-weighted z-axis averaging, as supervisory signals to compel the network to learn distinct representations for each retinal layer through fine-grained, targeted guidance. Meanwhile, the MSFF module enhances vessel delineation through multi-scale feature extraction combined with a channel reweighting strategy, effectively capturing vascular details at multiple spatial scales. Our experiments on the OCTA-500 dataset demonstrate XOCT's improvements, especially for the en-face projections which are significant for clinical evaluation of retinal pathologies, underscoring its potential to enhance OCTA accessibility, reliability, and diagnostic value for ophthalmic disease detection and monitoring. The code is available at https://github.com/uci-cbcl/XOCT.
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Submitted 9 September, 2025;
originally announced September 2025.
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MedGen3D: A Deep Generative Framework for Paired 3D Image and Mask Generation
Authors:
Kun Han,
Yifeng Xiong,
Chenyu You,
Pooya Khosravi,
Shanlin Sun,
Xiangyi Yan,
James Duncan,
Xiaohui Xie
Abstract:
Acquiring and annotating sufficient labeled data is crucial in developing accurate and robust learning-based models, but obtaining such data can be challenging in many medical image segmentation tasks. One promising solution is to synthesize realistic data with ground-truth mask annotations. However, no prior studies have explored generating complete 3D volumetric images with masks. In this paper,…
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Acquiring and annotating sufficient labeled data is crucial in developing accurate and robust learning-based models, but obtaining such data can be challenging in many medical image segmentation tasks. One promising solution is to synthesize realistic data with ground-truth mask annotations. However, no prior studies have explored generating complete 3D volumetric images with masks. In this paper, we present MedGen3D, a deep generative framework that can generate paired 3D medical images and masks. First, we represent the 3D medical data as 2D sequences and propose the Multi-Condition Diffusion Probabilistic Model (MC-DPM) to generate multi-label mask sequences adhering to anatomical geometry. Then, we use an image sequence generator and semantic diffusion refiner conditioned on the generated mask sequences to produce realistic 3D medical images that align with the generated masks. Our proposed framework guarantees accurate alignment between synthetic images and segmentation maps. Experiments on 3D thoracic CT and brain MRI datasets show that our synthetic data is both diverse and faithful to the original data, and demonstrate the benefits for downstream segmentation tasks. We anticipate that MedGen3D's ability to synthesize paired 3D medical images and masks will prove valuable in training deep learning models for medical imaging tasks.
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Submitted 4 July, 2023; v1 submitted 8 April, 2023;
originally announced April 2023.
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Generating High Fidelity Synthetic Data via Coreset selection and Entropic Regularization
Authors:
Omead Pooladzandi,
Pasha Khosravi,
Erik Nijkamp,
Baharan Mirzasoleiman
Abstract:
Generative models have the ability to synthesize data points drawn from the data distribution, however, not all generated samples are high quality. In this paper, we propose using a combination of coresets selection methods and ``entropic regularization'' to select the highest fidelity samples. We leverage an Energy-Based Model which resembles a variational auto-encoder with an inference and gener…
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Generative models have the ability to synthesize data points drawn from the data distribution, however, not all generated samples are high quality. In this paper, we propose using a combination of coresets selection methods and ``entropic regularization'' to select the highest fidelity samples. We leverage an Energy-Based Model which resembles a variational auto-encoder with an inference and generator model for which the latent prior is complexified by an energy-based model. In a semi-supervised learning scenario, we show that augmenting the labeled data-set, by adding our selected subset of samples, leads to better accuracy improvement rather than using all the synthetic samples.
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Submitted 31 January, 2023;
originally announced February 2023.
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Sales Channel Optimization via Simulations Based on Observational Data with Delayed Rewards: A Case Study at LinkedIn
Authors:
Diana M. Negoescu,
Pasha Khosravi,
Shadow Zhao,
Nanyu Chen,
Parvez Ahammad,
Humberto Gonzalez
Abstract:
Training models on data obtained from randomized experiments is ideal for making good decisions. However, randomized experiments are often time-consuming, expensive, risky, infeasible or unethical to perform, leaving decision makers little choice but to rely on observational data collected under historical policies when training models. This opens questions regarding not only which decision-making…
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Training models on data obtained from randomized experiments is ideal for making good decisions. However, randomized experiments are often time-consuming, expensive, risky, infeasible or unethical to perform, leaving decision makers little choice but to rely on observational data collected under historical policies when training models. This opens questions regarding not only which decision-making policies would perform best in practice, but also regarding the impact of different data collection protocols on the performance of various policies trained on the data, or the robustness of policy performance with respect to changes in problem characteristics such as action- or reward- specific delays in observing outcomes. We aim to answer such questions for the problem of optimizing sales channel allocations at LinkedIn, where sales accounts (leads) need to be allocated to one of three channels, with the goal of maximizing the number of successful conversions over a period of time. A key problem feature constitutes the presence of stochastic delays in observing allocation outcomes, whose distribution is both channel- and outcome- dependent. We built a discrete-time simulation that can handle our problem features and used it to evaluate: a) a historical rule-based policy; b) a supervised machine learning policy (XGBoost); and c) multi-armed bandit (MAB) policies, under different scenarios involving: i) data collection used for training (observational vs randomized); ii) lead conversion scenarios; iii) delay distributions. Our simulation results indicate that LinUCB, a simple MAB policy, consistently outperforms the other policies, achieving a 18-47% lift relative to a rule-based policy
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Submitted 16 September, 2022;
originally announced September 2022.
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Medical Image Registration via Neural Fields
Authors:
Shanlin Sun,
Kun Han,
Chenyu You,
Hao Tang,
Deying Kong,
Junayed Naushad,
Xiangyi Yan,
Haoyu Ma,
Pooya Khosravi,
James S. Duncan,
Xiaohui Xie
Abstract:
Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to mo…
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Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to model generalization and the inefficiency in handling individual image specific deformations. Here we present a new neural net based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural nets to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. Experiments on two 3D MR brain scan datasets demonstrate that NIR yields state-of-the-art performance in terms of both registration accuracy and regularity, while running significantly faster than traditional optimization-based methods.
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Submitted 10 October, 2024; v1 submitted 7 June, 2022;
originally announced June 2022.
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Probabilistic Sufficient Explanations
Authors:
Eric Wang,
Pasha Khosravi,
Guy Van den Broeck
Abstract:
Understanding the behavior of learned classifiers is an important task, and various black-box explanations, logical reasoning approaches, and model-specific methods have been proposed. In this paper, we introduce probabilistic sufficient explanations, which formulate explaining an instance of classification as choosing the "simplest" subset of features such that only observing those features is "s…
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Understanding the behavior of learned classifiers is an important task, and various black-box explanations, logical reasoning approaches, and model-specific methods have been proposed. In this paper, we introduce probabilistic sufficient explanations, which formulate explaining an instance of classification as choosing the "simplest" subset of features such that only observing those features is "sufficient" to explain the classification. That is, sufficient to give us strong probabilistic guarantees that the model will behave similarly when all features are observed under the data distribution. In addition, we leverage tractable probabilistic reasoning tools such as probabilistic circuits and expected predictions to design a scalable algorithm for finding the desired explanations while keeping the guarantees intact. Our experiments demonstrate the effectiveness of our algorithm in finding sufficient explanations, and showcase its advantages compared to Anchors and logical explanations.
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Submitted 21 May, 2021;
originally announced May 2021.
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Handling Missing Data in Decision Trees: A Probabilistic Approach
Authors:
Pasha Khosravi,
Antonio Vergari,
YooJung Choi,
Yitao Liang,
Guy Van den Broeck
Abstract:
Decision trees are a popular family of models due to their attractive properties such as interpretability and ability to handle heterogeneous data. Concurrently, missing data is a prevalent occurrence that hinders performance of machine learning models. As such, handling missing data in decision trees is a well studied problem. In this paper, we tackle this problem by taking a probabilistic approa…
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Decision trees are a popular family of models due to their attractive properties such as interpretability and ability to handle heterogeneous data. Concurrently, missing data is a prevalent occurrence that hinders performance of machine learning models. As such, handling missing data in decision trees is a well studied problem. In this paper, we tackle this problem by taking a probabilistic approach. At deployment time, we use tractable density estimators to compute the "expected prediction" of our models. At learning time, we fine-tune parameters of already learned trees by minimizing their "expected prediction loss" w.r.t.\ our density estimators. We provide brief experiments showcasing effectiveness of our methods compared to few baselines.
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Submitted 29 June, 2020;
originally announced June 2020.
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On Tractable Computation of Expected Predictions
Authors:
Pasha Khosravi,
YooJung Choi,
Yitao Liang,
Antonio Vergari,
Guy Van den Broeck
Abstract:
Computing expected predictions of discriminative models is a fundamental task in machine learning that appears in many interesting applications such as fairness, handling missing values, and data analysis. Unfortunately, computing expectations of a discriminative model with respect to a probability distribution defined by an arbitrary generative model has been proven to be hard in general. In fact…
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Computing expected predictions of discriminative models is a fundamental task in machine learning that appears in many interesting applications such as fairness, handling missing values, and data analysis. Unfortunately, computing expectations of a discriminative model with respect to a probability distribution defined by an arbitrary generative model has been proven to be hard in general. In fact, the task is intractable even for simple models such as logistic regression and a naive Bayes distribution. In this paper, we identify a pair of generative and discriminative models that enables tractable computation of expectations, as well as moments of any order, of the latter with respect to the former in case of regression. Specifically, we consider expressive probabilistic circuits with certain structural constraints that support tractable probabilistic inference. Moreover, we exploit the tractable computation of high-order moments to derive an algorithm to approximate the expectations for classification scenarios in which exact computations are intractable. Our framework to compute expected predictions allows for handling of missing data during prediction time in a principled and accurate way and enables reasoning about the behavior of discriminative models. We empirically show our algorithm to consistently outperform standard imputation techniques on a variety of datasets. Finally, we illustrate how our framework can be used for exploratory data analysis.
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Submitted 31 October, 2019; v1 submitted 4 October, 2019;
originally announced October 2019.
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What to Expect of Classifiers? Reasoning about Logistic Regression with Missing Features
Authors:
Pasha Khosravi,
Yitao Liang,
YooJung Choi,
Guy Van den Broeck
Abstract:
While discriminative classifiers often yield strong predictive performance, missing feature values at prediction time can still be a challenge. Classifiers may not behave as expected under certain ways of substituting the missing values, since they inherently make assumptions about the data distribution they were trained on. In this paper, we propose a novel framework that classifies examples with…
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While discriminative classifiers often yield strong predictive performance, missing feature values at prediction time can still be a challenge. Classifiers may not behave as expected under certain ways of substituting the missing values, since they inherently make assumptions about the data distribution they were trained on. In this paper, we propose a novel framework that classifies examples with missing features by computing the expected prediction with respect to a feature distribution. Moreover, we use geometric programming to learn a naive Bayes distribution that embeds a given logistic regression classifier and can efficiently take its expected predictions. Empirical evaluations show that our model achieves the same performance as the logistic regression with all features observed, and outperforms standard imputation techniques when features go missing during prediction time. Furthermore, we demonstrate that our method can be used to generate "sufficient explanations" of logistic regression classifications, by removing features that do not affect the classification.
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Submitted 1 June, 2019; v1 submitted 4 March, 2019;
originally announced March 2019.