Random Token Fusion for Multi-View Medical Diagnosis

In multi-view medical diagnosis, deep learning-based models often fuse information from different imaging perspectives to improve diagnostic performance. However, existing approaches are prone to overfitting and rely heavily on view-specific features, which can lead to trivial solutions. In this work, we introduce Random Token Fusion (RTF), a novel technique designed to enhance multi-view medical image analysis using vision transformers. By integrating randomness into the feature fusion process during training, RTF addresses the issue of overfitting and enhances the robustness and accuracy of diagnostic models without incurring any additional cost at inference. We validate our approach on standard mammography and chest X-ray benchmark datasets. Through extensive experiments, we demonstrate that RTF consistently improves the performance of existing fusion methods, paving the way for a new generation of multi-view medical foundation models.

Learning from Offline Foundation Features with Tensor Augmentations

We introduce Learning from Offline Foundation Features with Tensor Augmentations (LOFF-TA), an efficient training scheme designed to harness the capabilities of foundation models in limited resource settings where their direct development is not feasible. LOFF-TA involves training a compact classifier on cached feature embeddings from a frozen foundation model, resulting in up to $37\times$ faster training and up to $26\times$ reduced GPU memory usage. Because the embeddings of augmented images would be too numerous to store, yet the augmentation process is essential for training, we propose to apply tensor augmentations to the cached embeddings of the original non-augmented images. LOFF-TA makes it possible to leverage the power of foundation models, regardless of their size, in settings with limited computational capacity. Moreover, LOFF-TA can be used to apply foundation models to high-resolution images without increasing compute. In certain scenarios, we find that training with LOFF-TA yields better results than directly fine-tuning the foundation model.

Evaluating Large Vision-and-Language Models on Children's Mathematical Olympiads

Recent years have seen a significant progress in the general-purpose problem solving abilities of large vision and language models (LVLMs), such as ChatGPT, Gemini, etc.; some of these breakthroughs even seem to enable AI models to outperform human abilities in varied tasks that demand higher-order cognitive skills. Are the current large AI models indeed capable of generalized problem solving as humans do? A systematic analysis of AI capabilities for joint vision and text reasoning, however, is missing in the current scientific literature. In this paper, we make an effort towards filling this gap, by evaluating state-of-the-art LVLMs on their mathematical and algorithmic reasoning abilities using visuo-linguistic problems from children's Olympiads. Specifically, we consider problems from the Mathematical Kangaroo (MK) Olympiad, which is a popular international competition targeted at children from grades 1-12, that tests children's deeper mathematical abilities using puzzles that are appropriately gauged to their age and skills. Using the puzzles from MK, we created a dataset, dubbed SMART-840, consisting of 840 problems from years 2020-2024. With our dataset, we analyze LVLMs power on mathematical reasoning; their responses on our puzzles offer a direct way to compare against that of children. Our results show that modern LVLMs do demonstrate increasingly powerful reasoning skills in solving problems for higher grades, but lack the foundations to correctly answer problems designed for younger children. Further analysis shows that there is no significant correlation between the reasoning capabilities of AI models and that of young children, and their capabilities appear to be based on a different type of reasoning than the cumulative knowledge that underlies children's mathematics and logic skills.

MAMOC: MRI Motion Correction via Masked Autoencoding

The presence of motion artifacts in magnetic resonance imaging (MRI) scans poses a significant challenge, where even minor patient movements can lead to artifacts that may compromise the scan's utility. This paper introduces Masked Motion Correction (MAMOC), a novel method designed to address the issue of Retrospective Artifact Correction (RAC) in motion-affected MRI brain scans. MAMOC uses masked autoencoding self-supervision and test-time prediction to efficiently remove motion artifacts, producing state-of-the-art, native resolution scans. Until recently, realistic data to evaluate retrospective motion correction methods did not exist, motion artifacts had to be simulated. Leveraging the MR-ART dataset, this work is the first to evaluate motion correction in MRI scans using real motion data, showing the superiority of MAMOC to existing motion correction (MC) methods.

Bridging Generalization Gaps in High Content Imaging Through Online Self-Supervised Domain Adaptation

High Content Imaging (HCI) plays a vital role in modern drug discovery and development pipelines, facilitating various stages from hit identification to candidate drug characterization. Applying machine learning models to these datasets can prove challenging as they typically consist of multiple batches, affected by experimental variation, especially if different imaging equipment have been used. Moreover, as new data arrive, it is preferable that they are analyzed in an online fashion. To overcome this, we propose CODA, an online self-supervised domain adaptation approach. CODA divides the classifier's role into a generic feature extractor and a task-specific model. We adapt the feature extractor's weights to the new domain using cross-batch self-supervision while keeping the task-specific model unchanged. Our results demonstrate that this strategy significantly reduces the generalization gap, achieving up to a 300% improvement when applied to data from different labs utilizing different microscopes. CODA can be applied to new, unlabeled out-of-domain data sources of different sizes, from a single plate to multiple experimental batches.

Are Natural Domain Foundation Models Useful for Medical Image Classification?

The deep learning field is converging towards the use of general foundation models that can be easily adapted for diverse tasks. While this paradigm shift has become common practice within the field of natural language processing, progress has been slower in computer vision. In this paper we attempt to address this issue by investigating the transferability of various state-of-the-art foundation models to medical image classification tasks. Specifically, we evaluate the performance of five foundation models, namely SAM, SEEM, DINOv2, BLIP, and OpenCLIP across four well-established medical imaging datasets. We explore different training settings to fully harness the potential of these models. Our study shows mixed results. DINOv2 in particular, consistently outperforms the standard practice of ImageNet pretraining. However, other foundation models failed to consistently beat this established baseline indicating limitations in their transferability to medical image classification tasks.

3D Masked Autoencoders for Enhanced Privacy in MRI Scans

MRI scans provide valuable medical information, however they also contain sensitive and personally identifiable information (PII) that needs to be protected. Whereas MRI metadata is easily sanitized, MRI image data is a privacy risk because it contains information to render highly-realistic 3D visualizations of a patient's head, enabling malicious actors to possibly identify the subject by cross-referencing a database. Data anonymization and de-identification is concerned with ensuring the privacy and confidentiality of individuals' personal information. Traditional MRI de-identification methods remove privacy-sensitive parts (e.g. eyes, nose etc.) from a given scan. This comes at the expense of introducing a domain shift that can throw off downstream analyses. Recently, a GAN-based approach was proposed to de-identify a patient's scan by remodeling it (e.g. changing the face) rather than by removing parts. In this work, we propose CP-MAE, a model that de-identifies the face using masked autoencoders and that outperforms all previous approaches in terms of downstream task performance as well as de-identification. With our method we are able to synthesize scans of resolution up to $256^3$ (previously 128 cubic) which constitutes an eight-fold increase in the number of voxels. Using our construction we were able to design a system that exhibits a highly robust training stage, making it easy to fit the network on novel data.

STAMP: Differentiable Task and Motion Planning via Stein Variational Gradient Descent

Planning for many manipulation tasks, such as using tools or assembling parts, often requires both symbolic and geometric reasoning. Task and Motion Planning (TAMP) algorithms typically solve these problems by conducting a tree search over high-level task sequences while checking for kinematic and dynamic feasibility. While performant, most existing algorithms are highly inefficient as their time complexity grows exponentially with the number of possible actions and objects. Additionally, they only find a single solution to problems in which many feasible plans may exist. To address these limitations, we propose a novel algorithm called Stein Task and Motion Planning (STAMP) that leverages parallelization and differentiable simulation to efficiently search for multiple diverse plans. STAMP relaxes discrete-and-continuous TAMP problems into continuous optimization problems that can be solved using variational inference. Our algorithm builds upon Stein Variational Gradient Descent, a gradient-based variational inference algorithm, and parallelized differentiable physics simulators on the GPU to efficiently obtain gradients for inference. Further, we employ imitation learning to introduce action abstractions that reduce the inference problem to lower dimensions. We demonstrate our method on two TAMP problems and empirically show that STAMP is able to: 1) produce multiple diverse plans in parallel; and 2) search for plans more efficiently compared to existing TAMP baselines.

Pretrained ViTs Yield Versatile Representations For Medical Images

Convolutional Neural Networks (CNNs) have reigned for a decade as the de facto approach to automated medical image diagnosis, pushing the state-of-the-art in classification, detection and segmentation tasks. Over the last years, vision transformers (ViTs) have appeared as a competitive alternative to CNNs, yielding impressive levels of performance in the natural image domain, while possessing several interesting properties that could prove beneficial for medical imaging tasks. In this work, we explore the benefits and drawbacks of transformer-based models for medical image classification. We conduct a series of experiments on several standard 2D medical image benchmark datasets and tasks. Our findings show that, while CNNs perform better if trained from scratch, off-the-shelf vision transformers can perform on par with CNNs when pretrained on ImageNet, both in a supervised and self-supervised setting, rendering them as a viable alternative to CNNs.

Are Deep Neural Networks SMARTer than Second Graders?

Recent times have witnessed an increasing number of applications of deep neural networks towards solving tasks that require superior cognitive abilities, e.g., playing Go, generating art, question answering (such as ChatGPT), etc. Such a dramatic progress raises the question: how generalizable are neural networks in solving problems that demand broad skills? To answer this question, we propose SMART: a Simple Multimodal Algorithmic Reasoning Task and the associated SMART-101 dataset, for evaluating the abstraction, deduction, and generalization abilities of neural networks in solving visuo-linguistic puzzles designed specifically for children in the 6-8 age group. Our dataset consists of 101 unique puzzles; each puzzle comprises a picture and a question, and their solution needs a mix of several elementary skills, including arithmetic, algebra, and spatial reasoning, among others. To scale our dataset towards training deep neural networks, we programmatically generate entirely new instances for each puzzle while retaining their solution algorithm. To benchmark the performance on the SMART-101 dataset, we propose a vision and language meta-learning model using varied state-of-the-art backbone neural networks. Our experiments reveal that while powerful deep models offer reasonable performances on puzzles that they are trained on, they are not better than random accuracy when analyzed for generalization. We also evaluate the recent ChatGPT large language model on a subset of our dataset and find that while ChatGPT produces convincing reasoning abilities, the answers are often incorrect.