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.

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.

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

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.

MultiZoo & MultiBench: A Standardized Toolkit for Multimodal Deep Learning

Learning multimodal representations involves integrating information from multiple heterogeneous sources of data. In order to accelerate progress towards understudied modalities and tasks while ensuring real-world robustness, we release MultiZoo, a public toolkit consisting of standardized implementations of > 20 core multimodal algorithms and MultiBench, a large-scale benchmark spanning 15 datasets, 10 modalities, 20 prediction tasks, and 6 research areas. Together, these provide an automated end-to-end machine learning pipeline that simplifies and standardizes data loading, experimental setup, and model evaluation. To enable holistic evaluation, we offer a comprehensive methodology to assess (1) generalization, (2) time and space complexity, and (3) modality robustness. MultiBench paves the way towards a better understanding of the capabilities and limitations of multimodal models, while ensuring ease of use, accessibility, and reproducibility. Our toolkits are publicly available, will be regularly updated, and welcome inputs from the community.

Fine-grained Text Style Transfer with Diffusion-Based Language Models

Diffusion probabilistic models have shown great success in generating high-quality images controllably, and researchers have tried to utilize this controllability into text generation domain. Previous works on diffusion-based language models have shown that they can be trained without external knowledge (such as pre-trained weights) and still achieve stable performance and controllability. In this paper, we trained a diffusion-based model on StylePTB dataset, the standard benchmark for fine-grained text style transfers. The tasks in StylePTB requires much more refined control over the output text compared to tasks evaluated in previous works, and our model was able to achieve state-of-the-art performance on StylePTB on both individual and compositional transfers. Moreover, our model, trained on limited data from StylePTB without external knowledge, outperforms previous works that utilized pretrained weights, embeddings, and external grammar parsers, and this may indicate that diffusion-based language models have great potential under low-resource settings.

Risk-aware Safe Control for Decentralized Multi-agent Systems via Dynamic Responsibility Allocation

Decentralized control schemes are increasingly favored in various domains that involve multi-agent systems due to the need for computational efficiency as well as general applicability to large-scale systems. However, in the absence of an explicit global coordinator, it is hard for distributed agents to determine how to efficiently interact with others. In this paper, we present a risk-aware decentralized control framework that provides guidance on how much relative responsibility share (a percentage) an individual agent should take to avoid collisions with others while moving efficiently without direct communications. We propose a novel Control Barrier Function (CBF)-inspired risk measurement to characterize the aggregate risk agents face from potential collisions under motion uncertainty. We use this measurement to allocate responsibility shares among agents dynamically and develop risk-aware decentralized safe controllers. In this way, we are able to leverage the flexibility of robots with lower risk to improve the motion flexibility for those with higher risk, thus achieving improved collective safety. We demonstrate the validity and efficiency of our proposed approach through two examples: ramp merging in autonomous driving and a multi-agent position-swapping game.

Active Probing and Influencing Human Behaviors Via Autonomous Agents

Autonomous agents (robots) face tremendous challenges while interacting with heterogeneous human agents in close proximity. One of these challenges is that the autonomous agent does not have an accurate model tailored to the specific human that the autonomous agent is interacting with, which could sometimes result in inefficient human-robot interaction and suboptimal system dynamics. Developing an online method to enable the autonomous agent to learn information about the human model is therefore an ongoing research goal. Existing approaches position the robot as a passive learner in the environment to observe the physical states and the associated human response. This passive design, however, only allows the robot to obtain information that the human chooses to exhibit, which sometimes doesn't capture the human's full intention. In this work, we present an online optimization-based probing procedure for the autonomous agent to clarify its belief about the human model in an active manner. By optimizing an information radius, the autonomous agent chooses the action that most challenges its current conviction. This procedure allows the autonomous agent to actively probe the human agents to reveal information that's previously unavailable to the autonomous agent. With this gathered information, the autonomous agent can interactively influence the human agent for some designated objectives. Our main contributions include a coherent theoretical framework that unifies the probing and influence procedures and two case studies in autonomous driving that show how active probing can help to create better participant experience during influence, like higher efficiency or less perturbations.