ProtoSAM -- One Shot Medical Image Segmentation With Foundational Models

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model.

X-ray2CTPA: Generating 3D CTPA scans from 2D X-ray conditioning

Chest X-rays or chest radiography (CXR), commonly used for medical diagnostics, typically enables limited imaging compared to computed tomography (CT) scans, which offer more detailed and accurate three-dimensional data, particularly contrast-enhanced scans like CT Pulmonary Angiography (CTPA). However, CT scans entail higher costs, greater radiation exposure, and are less accessible than CXRs. In this work we explore cross-modal translation from a 2D low contrast-resolution X-ray input to a 3D high contrast and spatial-resolution CTPA scan. Driven by recent advances in generative AI, we introduce a novel diffusion-based approach to this task. We evaluate the models performance using both quantitative metrics and qualitative feedback from radiologists, ensuring diagnostic relevance of the generated images. Furthermore, we employ the synthesized 3D images in a classification framework and show improved AUC in a PE categorization task, using the initial CXR input. The proposed method is generalizable and capable of performing additional cross-modality translations in medical imaging. It may pave the way for more accessible and cost-effective advanced diagnostic tools. The code for this project is available: https://github.com/NoaCahan/X-ray2CTPA .

DeciMamba: Exploring the Length Extrapolation Potential of Mamba

Long-range sequence processing poses a significant challenge for Transformers due to their quadratic complexity in input length. A promising alternative is Mamba, which demonstrates high performance and achieves Transformer-level capabilities while requiring substantially fewer computational resources. In this paper we explore the length-generalization capabilities of Mamba, which we find to be relatively limited. Through a series of visualizations and analyses we identify that the limitations arise from a restricted effective receptive field, dictated by the sequence length used during training. To address this constraint, we introduce DeciMamba, a context-extension method specifically designed for Mamba. This mechanism, built on top of a hidden filtering mechanism embedded within the S6 layer, enables the trained model to extrapolate well even without additional training. Empirical experiments over real-world long-range NLP tasks show that DeciMamba can extrapolate to context lengths that are 25x times longer than the ones seen during training, and does so without utilizing additional computational resources. We will release our code and models.

Comparison Visual Instruction Tuning

Comparing two images in terms of Commonalities and Differences (CaD) is a fundamental human capability that forms the basis of advanced visual reasoning and interpretation. It is essential for the generation of detailed and contextually relevant descriptions, performing comparative analysis, novelty detection, and making informed decisions based on visual data. However, surprisingly, little attention has been given to these fundamental concepts in the best current mimic of human visual intelligence - Large Multimodal Models (LMMs). We develop and contribute a new two-phase approach CaD-VI for collecting synthetic visual instructions, together with an instruction-following dataset CaD-Inst containing 349K image pairs with CaD instructions collected using CaD-VI. Our approach significantly improves the CaD spotting capabilities in LMMs, advancing the SOTA on a diverse set of related tasks by up to 17.5%. It is also complementary to existing difference-only instruction datasets, allowing automatic targeted refinement of those resources increasing their effectiveness for CaD tuning by up to 10%. Additionally, we propose an evaluation benchmark with 7.5K open-ended QAs to assess the CaD understanding abilities of LMMs.

Effective Subset Selection Through The Lens of Neural Network Pruning

Having large amounts of annotated data significantly impacts the effectiveness of deep neural networks. However, the annotation task can be very expensive in some domains, such as medical data. Thus, it is important to select the data to be annotated wisely, which is known as the subset selection problem. We investigate the relationship between subset selection and neural network pruning, which is more widely studied, and establish a correspondence between them. Leveraging insights from network pruning, we propose utilizing the norm criterion of neural network features to improve subset selection methods. We empirically validate our proposed strategy on various networks and datasets, demonstrating enhanced accuracy. This shows the potential of employing pruning tools for subset selection.

Deep Phase Coded Image Prior

Phase-coded imaging is a computational imaging method designed to tackle tasks such as passive depth estimation and extended depth of field (EDOF) using depth cues inserted during image capture. Most of the current deep learning-based methods for depth estimation or all-in-focus imaging require a training dataset with high-quality depth maps and an optimal focus point at infinity for all-in-focus images. Such datasets are difficult to create, usually synthetic, and require external graphic programs. We propose a new method named "Deep Phase Coded Image Prior" (DPCIP) for jointly recovering the depth map and all-in-focus image from a coded-phase image using solely the captured image and the optical information of the imaging system. Our approach does not depend on any specific dataset and surpasses prior supervised techniques utilizing the same imaging system. This improvement is achieved through the utilization of a problem formulation based on implicit neural representation (INR) and deep image prior (DIP). Due to our zero-shot method, we overcome the barrier of acquiring accurate ground-truth data of depth maps and all-in-focus images for each new phase-coded system introduced. This allows focusing mainly on developing the imaging system, and not on ground-truth data collection.

DINOv2 based Self Supervised Learning For Few Shot Medical Image Segmentation

Deep learning models have emerged as the cornerstone of medical image segmentation, but their efficacy hinges on the availability of extensive manually labeled datasets and their adaptability to unforeseen categories remains a challenge. Few-shot segmentation (FSS) offers a promising solution by endowing models with the capacity to learn novel classes from limited labeled examples. A leading method for FSS is ALPNet, which compares features between the query image and the few available support segmented images. A key question about using ALPNet is how to design its features. In this work, we delve into the potential of using features from DINOv2, which is a foundational self-supervised learning model in computer vision. Leveraging the strengths of ALPNet and harnessing the feature extraction capabilities of DINOv2, we present a novel approach to few-shot segmentation that not only enhances performance but also paves the way for more robust and adaptable medical image analysis.

ICC: Quantifying Image Caption Concreteness for Multimodal Dataset Curation

Web-scale training on paired text-image data is becoming increasingly central to multimodal learning, but is challenged by the highly noisy nature of datasets in the wild. Standard data filtering approaches succeed in removing mismatched text-image pairs, but permit semantically related but highly abstract or subjective text. These approaches lack the fine-grained ability to isolate the most concrete samples that provide the strongest signal for learning in a noisy dataset. In this work, we propose a new metric, image caption concreteness, that evaluates caption text without an image reference to measure its concreteness and relevancy for use in multimodal learning. Our approach leverages strong foundation models for measuring visual-semantic information loss in multimodal representations. We demonstrate that this strongly correlates with human evaluation of concreteness in both single-word and sentence-level texts. Moreover, we show that curation using ICC complements existing approaches: It succeeds in selecting the highest quality samples from multimodal web-scale datasets to allow for efficient training in resource-constrained settings.

Implicit Bias of Policy Gradient in Linear Quadratic Control: Extrapolation to Unseen Initial States

In modern machine learning, models can often fit training data in numerous ways, some of which perform well on unseen (test) data, while others do not. Remarkably, in such cases gradient descent frequently exhibits an implicit bias that leads to excellent performance on unseen data. This implicit bias was extensively studied in supervised learning, but is far less understood in optimal control (reinforcement learning). There, learning a controller applied to a system via gradient descent is known as policy gradient, and a question of prime importance is the extent to which a learned controller extrapolates to unseen initial states. This paper theoretically studies the implicit bias of policy gradient in terms of extrapolation to unseen initial states. Focusing on the fundamental Linear Quadratic Regulator (LQR) problem, we establish that the extent of extrapolation depends on the degree of exploration induced by the system when commencing from initial states included in training. Experiments corroborate our theory, and demonstrate its conclusions on problems beyond LQR, where systems are non-linear and controllers are neural networks. We hypothesize that real-world optimal control may be greatly improved by developing methods for informed selection of initial states to train on.

How do Transformers perform In-Context Autoregressive Learning?

Transformers have achieved state-of-the-art performance in language modeling tasks. However, the reasons behind their tremendous success are still unclear. In this paper, towards a better understanding, we train a Transformer model on a simple next token prediction task, where sequences are generated as a first-order autoregressive process $s_{t+1} = W s_t$. We show how a trained Transformer predicts the next token by first learning $W$ in-context, then applying a prediction mapping. We call the resulting procedure in-context autoregressive learning. More precisely, focusing on commuting orthogonal matrices $W$, we first show that a trained one-layer linear Transformer implements one step of gradient descent for the minimization of an inner objective function, when considering augmented tokens. When the tokens are not augmented, we characterize the global minima of a one-layer diagonal linear multi-head Transformer. Importantly, we exhibit orthogonality between heads and show that positional encoding captures trigonometric relations in the data. On the experimental side, we consider the general case of non-commuting orthogonal matrices and generalize our theoretical findings.