Super-resolution of biomedical volumes with 2D supervision

Volumetric biomedical microscopy has the potential to increase the diagnostic information extracted from clinical tissue specimens and improve the diagnostic accuracy of both human pathologists and computational pathology models. Unfortunately, barriers to integrating 3-dimensional (3D) volumetric microscopy into clinical medicine include long imaging times, poor depth / z-axis resolution, and an insufficient amount of high-quality volumetric data. Leveraging the abundance of high-resolution 2D microscopy data, we introduce masked slice diffusion for super-resolution (MSDSR), which exploits the inherent equivalence in the data-generating distribution across all spatial dimensions of biological specimens. This intrinsic characteristic allows for super-resolution models trained on high-resolution images from one plane (e.g., XY) to effectively generalize to others (XZ, YZ), overcoming the traditional dependency on orientation. We focus on the application of MSDSR to stimulated Raman histology (SRH), an optical imaging modality for biological specimen analysis and intraoperative diagnosis, characterized by its rapid acquisition of high-resolution 2D images but slow and costly optical z-sectioning. To evaluate MSDSR's efficacy, we introduce a new performance metric, SliceFID, and demonstrate MSDSR's superior performance over baseline models through extensive evaluations. Our findings reveal that MSDSR not only significantly enhances the quality and resolution of 3D volumetric data, but also addresses major obstacles hindering the broader application of 3D volumetric microscopy in clinical diagnostics and biomedical research.

View Selection for 3D Captioning via Diffusion Ranking

Scalable annotation approaches are crucial for constructing extensive 3D-text datasets, facilitating a broader range of applications. However, existing methods sometimes lead to the generation of hallucinated captions, compromising caption quality. This paper explores the issue of hallucination in 3D object captioning, with a focus on Cap3D method, which renders 3D objects into 2D views for captioning using pre-trained models. We pinpoint a major challenge: certain rendered views of 3D objects are atypical, deviating from the training data of standard image captioning models and causing hallucinations. To tackle this, we present DiffuRank, a method that leverages a pre-trained text-to-3D model to assess the alignment between 3D objects and their 2D rendered views, where the view with high alignment closely represent the object's characteristics. By ranking all rendered views and feeding the top-ranked ones into GPT4-Vision, we enhance the accuracy and detail of captions, enabling the correction of 200k captions in the Cap3D dataset and extending it to 1 million captions across Objaverse and Objaverse-XL datasets. Additionally, we showcase the adaptability of DiffuRank by applying it to pre-trained text-to-image models for a Visual Question Answering task, where it outperforms the CLIP model.

Source-Aware Training Enables Knowledge Attribution in Language Models

Large language models (LLMs) learn a vast amount of knowledge during pretraining, but they are often oblivious to the source(s) of such knowledge. We investigate the problem of intrinsic source citation, where LLMs are required to cite the pretraining source supporting a generated response. Intrinsic source citation can enhance LLM transparency, interpretability, and verifiability. To give LLMs such ability, we explore source-aware training -- a post pretraining recipe that involves (i) training the LLM to associate unique source document identifiers with the knowledge in each document, followed by (ii) an instruction-tuning to teach the LLM to cite a supporting pretraining source when prompted. Source-aware training can easily be applied to pretrained LLMs off the shelf, and diverges minimally from existing pretraining/fine-tuning frameworks. Through experiments on carefully curated data, we demonstrate that our training recipe can enable faithful attribution to the pretraining data without a substantial impact on the model's quality compared to standard pretraining. Our results also highlight the importance of data augmentation in achieving attribution. Code and data available here: \url{https://github.com/mukhal/intrinsic-source-citation}

Step-Calibrated Diffusion for Biomedical Optical Image Restoration

High-quality, high-resolution medical imaging is essential for clinical care. Raman-based biomedical optical imaging uses non-ionizing infrared radiation to evaluate human tissues in real time and is used for early cancer detection, brain tumor diagnosis, and intraoperative tissue analysis. Unfortunately, optical imaging is vulnerable to image degradation due to laser scattering and absorption, which can result in diagnostic errors and misguided treatment. Restoration of optical images is a challenging computer vision task because the sources of image degradation are multi-factorial, stochastic, and tissue-dependent, preventing a straightforward method to obtain paired low-quality/high-quality data. Here, we present Restorative Step-Calibrated Diffusion (RSCD), an unpaired image restoration method that views the image restoration problem as completing the finishing steps of a diffusion-based image generation task. RSCD uses a step calibrator model to dynamically determine the severity of image degradation and the number of steps required to complete the reverse diffusion process for image restoration. RSCD outperforms other widely used unpaired image restoration methods on both image quality and perceptual evaluation metrics for restoring optical images. Medical imaging experts consistently prefer images restored using RSCD in blinded comparison experiments and report minimal to no hallucinations. Finally, we show that RSCD improves performance on downstream clinical imaging tasks, including automated brain tumor diagnosis and deep tissue imaging. Our code is available at https://github.com/MLNeurosurg/restorative_step-calibrated_diffusion.

AutoGuide: Automated Generation and Selection of State-Aware Guidelines for Large Language Model Agents

The primary limitation of large language models (LLMs) is their restricted understanding of the world. This poses significant difficulties for LLM-based agents, particularly in domains where pre-trained LLMs lack sufficient knowledge. In this paper, we introduce a novel framework, called AutoGuide, that bridges the knowledge gap in pre-trained LLMs by leveraging implicit knowledge in offline experiences. Specifically, AutoGuide effectively extracts knowledge embedded in offline data by extracting a set of state-aware guidelines. Importantly, each state-aware guideline is expressed in concise natural language and follows a conditional structure, clearly describing the state where it is applicable. As such, the resulting guidelines enable a principled way to provide helpful knowledge pertinent to an agent's current decision-making process. We show that our approach outperforms competitive LLM-based baselines by a large margin in sequential decision-making benchmarks.

A self-supervised framework for learning whole slide representations

Whole slide imaging is fundamental to biomedical microscopy and computational pathology. However, whole slide images (WSIs) present a complex computer vision challenge due to their gigapixel size, diverse histopathologic features, spatial heterogeneity, and limited/absent data annotations. These challenges highlight that supervised training alone can result in suboptimal whole slide representations. Self-supervised representation learning can achieve high-quality WSI visual feature learning for downstream diagnostic tasks, such as cancer diagnosis or molecular genetic prediction. Here, we present a general self-supervised whole slide learning (S3L) framework for gigapixel-scale self-supervision of WSIs. S3L combines data transformation strategies from transformer-based vision and language modeling into a single unified framework to generate paired views for self-supervision. S3L leverages the inherent regional heterogeneity, histologic feature variability, and information redundancy within WSIs to learn high-quality whole-slide representations. We benchmark S3L visual representations on two diagnostic tasks for two biomedical microscopy modalities. S3L significantly outperforms WSI baselines for cancer diagnosis and genetic mutation prediction. Additionally, S3L achieves good performance using both in-domain and out-of-distribution patch encoders, demonstrating good flexibility and generalizability.

TOD-Flow: Modeling the Structure of Task-Oriented Dialogues

Task-Oriented Dialogue (TOD) systems have become crucial components in interactive artificial intelligence applications. While recent advances have capitalized on pre-trained language models (PLMs), they exhibit limitations regarding transparency and controllability. To address these challenges, we propose a novel approach focusing on inferring the TOD-Flow graph from dialogue data annotated with dialog acts, uncovering the underlying task structure in the form of a graph. The inferred TOD-Flow graph can be easily integrated with any dialogue model to improve its prediction performance, transparency, and controllability. Our TOD-Flow graph learns what a model can, should, and should not predict, effectively reducing the search space and providing a rationale for the model's prediction. We show that the proposed TOD-Flow graph better resembles human-annotated graphs compared to prior approaches. Furthermore, when combined with several dialogue policies and end-to-end dialogue models, we demonstrate that our approach significantly improves dialog act classification and end-to-end response generation performance in the MultiWOZ and SGD benchmarks. Code available at: https://github.com/srsohn/TOD-Flow

Projection Regret: Reducing Background Bias for Novelty Detection via Diffusion Models

Novelty detection is a fundamental task of machine learning which aims to detect abnormal ($\textit{i.e.}$ out-of-distribution (OOD)) samples. Since diffusion models have recently emerged as the de facto standard generative framework with surprising generation results, novelty detection via diffusion models has also gained much attention. Recent methods have mainly utilized the reconstruction property of in-distribution samples. However, they often suffer from detecting OOD samples that share similar background information to the in-distribution data. Based on our observation that diffusion models can \emph{project} any sample to an in-distribution sample with similar background information, we propose \emph{Projection Regret (PR)}, an efficient novelty detection method that mitigates the bias of non-semantic information. To be specific, PR computes the perceptual distance between the test image and its diffusion-based projection to detect abnormality. Since the perceptual distance often fails to capture semantic changes when the background information is dominant, we cancel out the background bias by comparing it against recursive projections. Extensive experiments demonstrate that PR outperforms the prior art of generative-model-based novelty detection methods by a significant margin.

Code Models are Zero-shot Precondition Reasoners

One of the fundamental skills required for an agent acting in an environment to complete tasks is the ability to understand what actions are plausible at any given point. This work explores a novel use of code representations to reason about action preconditions for sequential decision making tasks. Code representations offer the flexibility to model procedural activities and associated constraints as well as the ability to execute and verify constraint satisfaction. Leveraging code representations, we extract action preconditions from demonstration trajectories in a zero-shot manner using pre-trained code models. Given these extracted preconditions, we propose a precondition-aware action sampling strategy that ensures actions predicted by a policy are consistent with preconditions. We demonstrate that the proposed approach enhances the performance of few-shot policy learning approaches across task-oriented dialog and embodied textworld benchmarks.