Effectively Fine-tune to Improve Large Multimodal Models for Radiology Report Generation

Writing radiology reports from medical images requires a high level of domain expertise. It is time-consuming even for trained radiologists and can be error-prone for inexperienced radiologists. It would be appealing to automate this task by leveraging generative AI, which has shown drastic progress in vision and language understanding. In particular, Large Language Models (LLM) have demonstrated impressive capabilities recently and continued to set new state-of-the-art performance on almost all natural language tasks. While many have proposed architectures to combine vision models with LLMs for multimodal tasks, few have explored practical fine-tuning strategies. In this work, we proposed a simple yet effective two-stage fine-tuning protocol to align visual features to LLM's text embedding space as soft visual prompts. Our framework with OpenLLaMA-7B achieved state-of-the-art level performance without domain-specific pretraining. Moreover, we provide detailed analyses of soft visual prompts and attention mechanisms, shedding light on future research directions.

Characterizing Out-of-Distribution Error via Optimal Transport

Out-of-distribution (OOD) data poses serious challenges in deployed machine learning models, so methods of predicting a model's performance on OOD data without labels are important for machine learning safety. While a number of methods have been proposed by prior work, they often underestimate the actual error, sometimes by a large margin, which greatly impacts their applicability to real tasks. In this work, we identify pseudo-label shift, or the difference between the predicted and true OOD label distributions, as a key indicator to this underestimation. Based on this observation, we introduce a novel method for estimating model performance by leveraging optimal transport theory, Confidence Optimal Transport (COT), and show that it provably provides more robust error estimates in the presence of pseudo-label shift. Additionally, we introduce an empirically-motivated variant of COT, Confidence Optimal Transport with Thresholding (COTT), which applies thresholding to the individual transport costs and further improves the accuracy of COT's error estimates. We evaluate COT and COTT on a variety of standard benchmarks that induce various types of distribution shift -- synthetic, novel subpopulation, and natural -- and show that our approaches significantly outperform existing state-of-the-art methods with an up to 3x lower prediction error.

Predicting Out-of-Distribution Error with Confidence Optimal Transport

Out-of-distribution (OOD) data poses serious challenges in deployed machine learning models as even subtle changes could incur significant performance drops. Being able to estimate a model's performance on test data is important in practice as it indicates when to trust to model's decisions. We present a simple yet effective method to predict a model's performance on an unknown distribution without any addition annotation. Our approach is rooted in the Optimal Transport theory, viewing test samples' output softmax scores from deep neural networks as empirical samples from an unknown distribution. We show that our method, Confidence Optimal Transport (COT), provides robust estimates of a model's performance on a target domain. Despite its simplicity, our method achieves state-of-the-art results on three benchmark datasets and outperforms existing methods by a large margin.

On-the-fly Object Detection using StyleGAN with CLIP Guidance

We present a fully automated framework for building object detectors on satellite imagery without requiring any human annotation or intervention. We achieve this by leveraging the combined power of modern generative models (e.g., StyleGAN) and recent advances in multi-modal learning (e.g., CLIP). While deep generative models effectively encode the key semantics pertinent to a data distribution, this information is not immediately accessible for downstream tasks, such as object detection. In this work, we exploit CLIP's ability to associate image features with text descriptions to identify neurons in the generator network, which are subsequently used to build detectors on-the-fly.

Wasserstein Task Embedding for Measuring Task Similarities

Measuring similarities between different tasks is critical in a broad spectrum of machine learning problems, including transfer, multi-task, continual, and meta-learning. Most current approaches to measuring task similarities are architecture-dependent: 1) relying on pre-trained models, or 2) training networks on tasks and using forward transfer as a proxy for task similarity. In this paper, we leverage the optimal transport theory and define a novel task embedding for supervised classification that is model-agnostic, training-free, and capable of handling (partially) disjoint label sets. In short, given a dataset with ground-truth labels, we perform a label embedding through multi-dimensional scaling and concatenate dataset samples with their corresponding label embeddings. Then, we define the distance between two datasets as the 2-Wasserstein distance between their updated samples. Lastly, we leverage the 2-Wasserstein embedding framework to embed tasks into a vector space in which the Euclidean distance between the embedded points approximates the proposed 2-Wasserstein distance between tasks. We show that the proposed embedding leads to a significantly faster comparison of tasks compared to related approaches like the Optimal Transport Dataset Distance (OTDD). Furthermore, we demonstrate the effectiveness of our proposed embedding through various numerical experiments and show statistically significant correlations between our proposed distance and the forward and backward transfer between tasks.

Glo-In-One: Holistic Glomerular Detection, Segmentation, and Lesion Characterization with Large-scale Web Image Mining

The quantitative detection, segmentation, and characterization of glomeruli from high-resolution whole slide imaging (WSI) play essential roles in the computer-assisted diagnosis and scientific research in digital renal pathology. Historically, such comprehensive quantification requires extensive programming skills in order to be able to handle heterogeneous and customized computational tools. To bridge the gap of performing glomerular quantification for non-technical users, we develop the Glo-In-One toolkit to achieve holistic glomerular detection, segmentation, and characterization via a single line of command. Additionally, we release a large-scale collection of 30,000 unlabeled glomerular images to further facilitate the algorithmic development of self-supervised deep learning. The inputs of the Glo-In-One toolkit are WSIs, while the outputs are (1) WSI-level multi-class circle glomerular detection results (which can be directly manipulated with ImageScope), (2) glomerular image patches with segmentation masks, and (3) different lesion types. To leverage the performance of the Glo-In-One toolkit, we introduce self-supervised deep learning to glomerular quantification via large-scale web image mining. The GGS fine-grained classification model achieved a decent performance compared with baseline supervised methods while only using 10% of the annotated data. The glomerular detection achieved an average precision of 0.627 with circle representations, while the glomerular segmentation achieved a 0.955 patch-wise Dice Similarity Coefficient (DSC).

Teaching Networks to Solve Optimization Problems

Leveraging machine learning to optimize the optimization process is an emerging field which holds the promise to bypass the fundamental computational bottleneck caused by traditional iterative solvers in critical applications requiring near-real-time optimization. The majority of existing approaches focus on learning data-driven optimizers that lead to fewer iterations in solving an optimization. In this paper, we take a different approach and propose to replace the iterative solvers altogether with a trainable parametric set function that outputs the optimal arguments/parameters of an optimization problem in a single feed-forward. We denote our method as, Learning to Optimize the Optimization Process (LOOP). We show the feasibility of learning such parametric (set) functions to solve various classic optimization problems, including linear/nonlinear regression, principal component analysis, transport-based core-set, and quadratic programming in supply management applications. In addition, we propose two alternative approaches for learning such parametric functions, with and without a solver in the-LOOP. Finally, we demonstrate the effectiveness of our proposed approach through various numerical experiments.

Holistic Fine-grained GGS Characterization: From Detection to Unbalanced Classification

Recent studies have demonstrated the diagnostic and prognostic values of global glomerulosclerosis (GGS) in IgA nephropathy, aging, and end-stage renal disease. However, the fine-grained quantitative analysis of multiple GGS subtypes (e.g., obsolescent, solidified, and disappearing glomerulosclerosis) is typically a resource extensive manual process. Very few automatic methods, if any, have been developed to bridge this gap for such analytics. In this paper, we present a holistic pipeline to quantify GGS (with both detection and classification) from a whole slide image in a fully automatic manner. In addition, we conduct the fine-grained classification for the sub-types of GGS. Our study releases the open-source quantitative analytical tool for fine-grained GGS characterization while tackling the technical challenges in unbalanced classification and integrating detection and classification.

SLOSH: Set LOcality Sensitive Hashing via Sliced-Wasserstein Embeddings

Learning from set-structured data is an essential problem with many applications in machine learning and computer vision. This paper focuses on non-parametric and data-independent learning from set-structured data using approximate nearest neighbor (ANN) solutions, particularly locality-sensitive hashing. We consider the problem of set retrieval from an input set query. Such retrieval problem requires: 1) an efficient mechanism to calculate the distances/dissimilarities between sets, and 2) an appropriate data structure for fast nearest neighbor search. To that end, we propose Sliced-Wasserstein set embedding as a computationally efficient "set-2-vector" mechanism that enables downstream ANN, with theoretical guarantees. The set elements are treated as samples from an unknown underlying distribution, and the Sliced-Wasserstein distance is used to compare sets. We demonstrate the effectiveness of our algorithm, denoted as Set-LOcality Sensitive Hashing (SLOSH), on various set retrieval datasets and compare our proposed embedding with standard set embedding approaches, including Generalized Mean (GeM) embedding/pooling, Featurewise Sort Pooling (FSPool), and Covariance Pooling and show consistent improvement in retrieval results. The code for replicating our results is available here: \href{https://github.com/mint-vu/SLOSH}{https://github.com/mint-vu/SLOSH}.

Circle Representation for Medical Object Detection

Box representation has been extensively used for object detection in computer vision. Such representation is efficacious but not necessarily optimized for biomedical objects (e.g., glomeruli), which play an essential role in renal pathology. In this paper, we propose a simple circle representation for medical object detection and introduce CircleNet, an anchor-free detection framework. Compared with the conventional bounding box representation, the proposed bounding circle representation innovates in three-fold: (1) it is optimized for ball-shaped biomedical objects; (2) The circle representation reduced the degree of freedom compared with box representation; (3) It is naturally more rotation invariant. When detecting glomeruli and nuclei on pathological images, the proposed circle representation achieved superior detection performance and be more rotation-invariant, compared with the bounding box. The code has been made publicly available: https://github.com/hrlblab/CircleNet