Theodore Zhao

Theodore Zhao, Mu Wei, J. Samuel Preston et al.

Large Language Models (LLMs) have shown impressive abilities in many applications. When a concrete and precise answer is desired, it is important to have a quantitative estimation of the potential error rate. However, this can be challenging due to the text-in-text-out nature of generative models. We present a method based on Pareto optimization that generates a risk score to estimate the probability of error in an LLM response by integrating multiple sources of information. We prove theoretically that the error estimator optimized in our framework aligns with the LLM and the information sources in an Pareto optimal manner. Experimental results show that the risk scores estimated by our method are well correlated with the true LLM error rate, thus facilitating error correction. By dynamically combining with prompting strategies such as self-verification and information retrieval, we demonstrate the proposed method can be utilized to increase the performance of an LLM, surpassing state-of-the-art task specific models.

Reuben Tan, Baolin Peng, Zhengyuan Yang et al.

Agentic reasoning models trained with multimodal reinforcement learning (MMRL) have become increasingly capable, yet they are almost universally optimized using sparse, outcome-based rewards computed based on the final answers. Richer rewards computed from the reasoning tokens can improve learning significantly by providing more fine-grained guidance. However, it is challenging to compute more informative rewards in MMRL beyond those based on outcomes since different samples may require different scoring functions and teacher models may provide noisy reward signals too. In this paper, we introduce the Argos (Agentic Reward for Grounded & Objective Scoring), a principled reward agent to train multimodal reasoning models for agentic tasks. For each sample, Argos selects from a pool of teacher-model derived and rule-based scoring functions to simultaneously evaluate: (i) final response accuracy, (ii) spatiotemporal localization of referred entities and actions, and (iii) the quality of the reasoning process. We find that by leveraging our agentic verifier across both SFT data curation and RL training, our model achieves state-of-the-art results across multiple agentic tasks such as spatial reasoning, visual hallucination as well as robotics and embodied AI benchmarks. Critically, we demonstrate that just relying on SFT post-training on highly curated reasoning data is insufficient, as agents invariably collapse to ungrounded solutions during RL without our online verification. We also show that our agentic verifier can help to reduce reward-hacking in MMRL. Finally, we also provide a theoretical justification for the effectiveness of Argos through the concept of pareto-optimality.

Theodore Zhao, Yu Gu, Jianwei Yang et al.

Biomedical image analysis is fundamental for biomedical discovery in cell biology, pathology, radiology, and many other biomedical domains. Holistic image analysis comprises interdependent subtasks such as segmentation, detection, and recognition of relevant objects. Here, we propose BiomedParse, a biomedical foundation model for imaging parsing that can jointly conduct segmentation, detection, and recognition for 82 object types across 9 imaging modalities. Through joint learning, we can improve accuracy for individual tasks and enable novel applications such as segmenting all relevant objects in an image through a text prompt, rather than requiring users to laboriously specify the bounding box for each object. We leveraged readily available natural-language labels or descriptions accompanying those datasets and use GPT-4 to harmonize the noisy, unstructured text information with established biomedical object ontologies. We created a large dataset comprising over six million triples of image, segmentation mask, and textual description. On image segmentation, we showed that BiomedParse is broadly applicable, outperforming state-of-the-art methods on 102,855 test image-mask-label triples across 9 imaging modalities (everything). On object detection, which aims to locate a specific object of interest, BiomedParse again attained state-of-the-art performance, especially on objects with irregular shapes (everywhere). On object recognition, which aims to identify all objects in a given image along with their semantic types, we showed that BiomedParse can simultaneously segment and label all biomedical objects in an image (all at once). In summary, BiomedParse is an all-in-one tool for biomedical image analysis by jointly solving segmentation, detection, and recognition for all major biomedical image modalities, paving the path for efficient and accurate image-based biomedical discovery.

Ho Hin Lee, Yu Gu, Theodore Zhao et al.

Recent advancements in biomedical image analysis have been significantly driven by the Segment Anything Model (SAM). This transformative technology, originally developed for general-purpose computer vision, has found rapid application in medical image processing. Within the last year, marked by over 100 publications, SAM has demonstrated its prowess in zero-shot learning adaptations for medical imaging. The fundamental premise of SAM lies in its capability to segment or identify objects in images without prior knowledge of the object type or imaging modality. This approach aligns well with tasks achievable by the human visual system, though its application in non-biological vision contexts remains more theoretically challenging. A notable feature of SAM is its ability to adjust segmentation according to a specified resolution scale or area of interest, akin to semantic priming. This adaptability has spurred a wave of creativity and innovation in applying SAM to medical imaging. Our review focuses on the period from April 1, 2023, to September 30, 2023, a critical first six months post-initial publication. We examine the adaptations and integrations of SAM necessary to address longstanding clinical challenges, particularly in the context of 33 open datasets covered in our analysis. While SAM approaches or achieves state-of-the-art performance in numerous applications, it falls short in certain areas, such as segmentation of the carotid artery, adrenal glands, optic nerve, and mandible bone. Our survey delves into the innovative techniques where SAM's foundational approach excels and explores the core concepts in translating and applying these models effectively in diverse medical imaging scenarios.

Cliff Wong, Sam Preston, Qianchu Liu et al. · microsoft-research

A significant fraction of real-world patient information resides in unstructured clinical text. Medical abstraction extracts and normalizes key structured attributes from free-text clinical notes, which is the prerequisite for a variety of important downstream applications, including registry curation, clinical trial operations, and real-world evidence generation. Prior medical abstraction methods typically resort to building attribute-specific models, each of which requires extensive manual effort such as rule creation or supervised label annotation for the individual attribute, thus limiting scalability. In this paper, we show that existing frontier models already possess the universal abstraction capability for scaling medical abstraction to a wide range of clinical attributes. We present UniMedAbstractor (UMA), a unifying framework for zero-shot medical abstraction with a modular, customizable prompt template and the selection of any frontier large language models. Given a new attribute for abstraction, users only need to conduct lightweight prompt adaptation in UMA to adjust the specification in natural languages. Compared to traditional methods, UMA eliminates the need for attribute-specific training labels or handcrafted rules, thus substantially reducing the development time and cost. We conducted a comprehensive evaluation of UMA in oncology using a wide range of marquee attributes representing the cancer patient journey. These include relatively simple attributes typically specified within a single clinical note (e.g. performance status), as well as complex attributes requiring sophisticated reasoning across multiple notes at various time points (e.g. tumor staging). Based on a single frontier model such as GPT-4o, UMA matched or even exceeded the performance of state-of-the-art attribute-specific methods, each of which was tailored to the individual attribute.

Theodore Zhao, Sid Kiblawi, Naoto Usuyama et al.

Detecting and segmenting small objects, such as lung nodules and tumor lesions, remains a critical challenge in image analysis. These objects often occupy less than 0.1% of an image, making traditional transformer architectures inefficient and prone to performance degradation due to redundant attention computations on irrelevant regions. Existing sparse attention mechanisms rely on rigid hierarchical structures, which are poorly suited for detecting small, variable, and uncertain object locations. In this paper, we propose BoltzFormer, a novel transformer-based architecture designed to address these challenges through dynamic sparse attention. BoltzFormer identifies and focuses attention on relevant areas by modeling uncertainty using a Boltzmann distribution with an annealing schedule. Initially, a higher temperature allows broader area sampling in early layers, when object location uncertainty is greatest. As the temperature decreases in later layers, attention becomes more focused, enhancing efficiency and accuracy. BoltzFormer seamlessly integrates into existing transformer architectures via a modular Boltzmann attention sampling mechanism. Comprehensive evaluations on benchmark datasets demonstrate that BoltzFormer significantly improves segmentation performance for small objects while reducing attention computation by an order of magnitude compared to previous state-of-the-art methods.