arXiv subjects

Yossi Matias

Publications and source records attributed to Yossi Matias.

At least 55 records · Page 3Linked to original sources

arXiv2025

Selective Attention Improves Transformer

Unneeded elements in the attention's context degrade performance. We introduce Selective Attention, a simple parameter-free change to the standard attention mechanism which reduces attention to unneeded elements. Selective attention consistently improves language modeling and downstream task performance in a variety of model sizes and context lengths. For example, transformers trained with the language modeling objective on C4 with selective attention perform language modeling equivalently to standard transformers with ~2X more heads and parameters in their attention modules. Selective attention also allows decreasing the size of the attention's context buffer, leading to meaningful reductions in the memory and compute requirements during inference. For example, transformers trained on C4 with context sizes of 512, 1,024, and 2,048 need 16X, 25X, and 47X less memory for their attention module, respectively, when equipped with selective attention, as those without selective attention, with the same validation perplexity.

cs.CL↗

arXiv2025

Evaluating AI systems under uncertain ground truth: a case study in dermatology

For safety, medical AI systems undergo thorough evaluations before deployment, validating their predictions against a ground truth which is assumed to be fixed and certain. However, this ground truth is often curated in the form of differential diagnoses. While a single differential diagnosis reflects the uncertainty in one expert assessment, multiple experts introduce another layer of uncertainty through disagreement. Both forms of uncertainty are ignored in standard evaluation which aggregates these differential diagnoses to a single label. In this paper, we show that ignoring uncertainty leads to overly optimistic estimates of model performance, therefore underestimating risk associated with particular diagnostic decisions. To this end, we propose a statistical aggregation approach, where we infer a distribution on probabilities of underlying medical condition candidates themselves, based on observed annotations. This formulation naturally accounts for the potential disagreements between different experts, as well as uncertainty stemming from individual differential diagnoses, capturing the entire ground truth uncertainty. Our approach boils down to generating multiple samples of medical condition probabilities, then evaluating and averaging performance metrics based on these sampled probabilities. In skin condition classification, we find that a large portion of the dataset exhibits significant ground truth uncertainty and standard evaluation severely over-estimates performance without providing uncertainty estimates. In contrast, our framework provides uncertainty estimates on common metrics of interest such as top-k accuracy and average overlap, showing that performance can change multiple percentage points. We conclude that, while assuming a crisp ground truth can be acceptable for many AI applications, a more nuanced evaluation protocol should be utilized in medical diagnosis.

cs.LG↗

arXiv2025

TxGemma: Efficient and Agentic LLMs for Therapeutics

Therapeutic development is a costly and high-risk endeavor that is often plagued by high failure rates. To address this, we introduce TxGemma, a suite of efficient, generalist large language models (LLMs) capable of therapeutic property prediction as well as interactive reasoning and explainability. Unlike task-specific models, TxGemma synthesizes information from diverse sources, enabling broad application across the therapeutic development pipeline. The suite includes 2B, 9B, and 27B parameter models, fine-tuned from Gemma-2 on a comprehensive dataset of small molecules, proteins, nucleic acids, diseases, and cell lines. Across 66 therapeutic development tasks, TxGemma achieved superior or comparable performance to the state-of-the-art generalist model on 64 (superior on 45), and against state-of-the-art specialist models on 50 (superior on 26). Fine-tuning TxGemma models on therapeutic downstream tasks, such as clinical trial adverse event prediction, requires less training data than fine-tuning base LLMs, making TxGemma suitable for data-limited applications. Beyond these predictive capabilities, TxGemma features conversational models that bridge the gap between general LLMs and specialized property predictors. These allow scientists to interact in natural language, provide mechanistic reasoning for predictions based on molecular structure, and engage in scientific discussions. Building on this, we further introduce Agentic-Tx, a generalist therapeutic agentic system powered by Gemini 2.5 that reasons, acts, manages diverse workflows, and acquires external domain knowledge. Agentic-Tx surpasses prior leading models on the Humanity's Last Exam benchmark (Chemistry & Biology) with 52.3% relative improvement over o3-mini (high) and 26.7% over o3-mini (high) on GPQA (Chemistry) and excels with improvements of 6.3% (ChemBench-Preference) and 2.4% (ChemBench-Mini) over o3-mini (high).

cs.AI↗

arXiv2025

Towards Conversational AI for Disease Management

While large language models (LLMs) have shown promise in diagnostic dialogue, their capabilities for effective management reasoning - including disease progression, therapeutic response, and safe medication prescription - remain under-explored. We advance the previously demonstrated diagnostic capabilities of the Articulate Medical Intelligence Explorer (AMIE) through a new LLM-based agentic system optimised for clinical management and dialogue, incorporating reasoning over the evolution of disease and multiple patient visit encounters, response to therapy, and professional competence in medication prescription. To ground its reasoning in authoritative clinical knowledge, AMIE leverages Gemini's long-context capabilities, combining in-context retrieval with structured reasoning to align its output with relevant and up-to-date clinical practice guidelines and drug formularies. In a randomized, blinded virtual Objective Structured Clinical Examination (OSCE) study, AMIE was compared to 21 primary care physicians (PCPs) across 100 multi-visit case scenarios designed to reflect UK NICE Guidance and BMJ Best Practice guidelines. AMIE was non-inferior to PCPs in management reasoning as assessed by specialist physicians and scored better in both preciseness of treatments and investigations, and in its alignment with and grounding of management plans in clinical guidelines. To benchmark medication reasoning, we developed RxQA, a multiple-choice question benchmark derived from two national drug formularies (US, UK) and validated by board-certified pharmacists. While AMIE and PCPs both benefited from the ability to access external drug information, AMIE outperformed PCPs on higher difficulty questions. While further research would be needed before real-world translation, AMIE's strong performance across evaluations marks a significant step towards conversational AI as a tool in disease management.

cs.CL↗

arXiv2025

Existence of Deadlock-Free Routing for Arbitrary Networks

Given a network of routing nodes, represented as a directed graph, we prove the following necessary and sufficient condition for the existence of deadlock-free message routing: The directed graph must contain two edge-disjoint directed trees rooted at the same node, one tree directed into the root node and the other directed away from the root node. While the sufficiency of this condition is known, its necessity, to the best of our knowledge, has not been previously recognized or proven. Although not directly applicable to the construction of deadlock-free routing schemes, this result provides a fundamental insight into the nature of deadlock-free networks and may lead to the development of improved tools for designing and verifying such schemes.

math.CO↗

arXiv2025

CoCa-CXR: Contrastive Captioners Learn Strong Temporal Structures for Chest X-Ray Vision-Language Understanding

Vision-language models have proven to be of great benefit for medical image analysis since they learn rich semantics from both images and reports. Prior efforts have focused on better alignment of image and text representations to enhance image understanding. However, though explicit reference to a prior image is common in Chest X-Ray (CXR) reports, aligning progression descriptions with the semantics differences in image pairs remains under-explored. In this work, we propose two components to address this issue. (1) A CXR report processing pipeline to extract temporal structure. It processes reports with a large language model (LLM) to separate the description and comparison contexts, and extracts fine-grained annotations from reports. (2) A contrastive captioner model for CXR, namely CoCa-CXR, to learn how to both describe images and their temporal progressions. CoCa-CXR incorporates a novel regional cross-attention module to identify local differences between paired CXR images. Extensive experiments show the superiority of CoCa-CXR on both progression analysis and report generation compared to previous methods. Notably, on MS-CXR-T progression classification, CoCa-CXR obtains 65.0% average testing accuracy on five pulmonary conditions, outperforming the previous state-of-the-art (SOTA) model BioViL-T by 4.8%. It also achieves a RadGraph F1 of 24.2% on MIMIC-CXR, which is comparable to the Med-Gemini foundation model.

cs.CV↗

arXiv2025

PolyPath: Adapting a Large Multimodal Model for Multi-slide Pathology Report Generation

The interpretation of histopathology cases underlies many important diagnostic and treatment decisions in medicine. Notably, this process typically requires pathologists to integrate and summarize findings across multiple slides per case. Existing vision-language capabilities in computational pathology have so far been largely limited to small regions of interest, larger regions at low magnification, or single whole-slide images (WSIs). This limits interpretation of findings that span multiple high-magnification regions across multiple WSIs. By making use of Gemini 1.5 Flash, a large multimodal model (LMM) with a 1-million token context window, we demonstrate the ability to generate bottom-line diagnoses from up to 40,000 768x768 pixel image patches from multiple WSIs at 10X magnification. This is the equivalent of up to 11 hours of video at 1 fps. Expert pathologist evaluations demonstrate that the generated report text is clinically accurate and equivalent to or preferred over the original reporting for 68% (95% CI: [60%, 76%]) of multi-slide examples with up to 5 slides. While performance decreased for examples with 6 or more slides, this study demonstrates the promise of leveraging the long-context capabilities of modern LMMs for the uniquely challenging task of medical report generation where each case can contain thousands of image patches.

cs.CV↗

arXiv2024

Multi-turn Reinforcement Learning from Preference Human Feedback

Reinforcement Learning from Human Feedback (RLHF) has become the standard approach for aligning Large Language Models (LLMs) with human preferences, allowing LLMs to demonstrate remarkable abilities in various tasks. Existing methods work by emulating the preferences at the single decision (turn) level, limiting their capabilities in settings that require planning or multi-turn interactions to achieve a long-term goal. In this paper, we address this issue by developing novel methods for Reinforcement Learning (RL) from preference feedback between two full multi-turn conversations. In the tabular setting, we present a novel mirror-descent-based policy optimization algorithm for the general multi-turn preference-based RL problem, and prove its convergence to Nash equilibrium. To evaluate performance, we create a new environment, Education Dialogue, where a teacher agent guides a student in learning a random topic, and show that a deep RL variant of our algorithm outperforms RLHF baselines. Finally, we show that in an environment with explicit rewards, our algorithm recovers the same performance as a reward-based RL baseline, despite relying solely on a weaker preference signal.

cs.LG↗

arXiv2024

Health AI Developer Foundations

Robust medical Machine Learning (ML) models have the potential to revolutionize healthcare by accelerating clinical research, improving workflows and outcomes, and producing novel insights or capabilities. Developing such ML models from scratch is cost prohibitive and requires substantial compute, data, and time (e.g., expert labeling). To address these challenges, we introduce Health AI Developer Foundations (HAI-DEF), a suite of pre-trained, domain-specific foundation models, tools, and recipes to accelerate building ML for health applications. The models cover various modalities and domains, including radiology (X-rays and computed tomography), histopathology, dermatological imaging, and audio. These models provide domain specific embeddings that facilitate AI development with less labeled data, shorter training times, and reduced computational costs compared to traditional approaches. In addition, we utilize a common interface and style across these models, and prioritize usability to enable developers to integrate HAI-DEF efficiently. We present model evaluations across various tasks and conclude with a discussion of their application and evaluation, covering the importance of ensuring efficacy, fairness, and equity. Finally, while HAI-DEF and specifically the foundation models lower the barrier to entry for ML in healthcare, we emphasize the importance of validation with problem- and population-specific data for each desired usage setting. This technical report will be updated over time as more modalities and features are added.

cs.LG↗

arXiv2024

A Toolbox for Surfacing Health Equity Harms and Biases in Large Language Models

Large language models (LLMs) hold promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. We present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and conduct a large-scale empirical case study with the Med-PaLM 2 LLM. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases, and EquityMedQA, a collection of seven datasets enriched for adversarial queries. Both our human assessment framework and dataset design process are grounded in an iterative participatory approach and review of Med-PaLM 2 answers. Through our empirical study, we find that our approach surfaces biases that may be missed via narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. While our approach is not sufficient to holistically assess whether the deployment of an AI system promotes equitable health outcomes, we hope that it can be leveraged and built upon towards a shared goal of LLMs that promote accessible and equitable healthcare.

cs.CY↗

arXiv2024

Using generative AI to investigate medical imagery models and datasets

AI models have shown promise in many medical imaging tasks. However, our ability to explain what signals these models have learned is severely lacking. Explanations are needed in order to increase the trust in AI-based models, and could enable novel scientific discovery by uncovering signals in the data that are not yet known to experts. In this paper, we present a method for automatic visual explanations leveraging team-based expertise by generating hypotheses of what visual signals in the images are correlated with the task. We propose the following 4 steps: (i) Train a classifier to perform a given task (ii) Train a classifier guided StyleGAN-based image generator (StylEx) (iii) Automatically detect and visualize the top visual attributes that the classifier is sensitive towards (iv) Formulate hypotheses for the underlying mechanisms, to stimulate future research. Specifically, we present the discovered attributes to an interdisciplinary panel of experts so that hypotheses can account for social and structural determinants of health. We demonstrate results on eight prediction tasks across three medical imaging modalities: retinal fundus photographs, external eye photographs, and chest radiographs. We showcase examples of attributes that capture clinically known features, confounders that arise from factors beyond physiological mechanisms, and reveal a number of physiologically plausible novel attributes. Our approach has the potential to enable researchers to better understand, improve their assessment, and extract new knowledge from AI-based models. Importantly, we highlight that attributes generated by our framework can capture phenomena beyond physiology or pathophysiology, reflecting the real world nature of healthcare delivery and socio-cultural factors. Finally, we intend to release code to enable researchers to train their own StylEx models and analyze their predictive tasks.

eess.IV↗

arXiv2024

AI in Action: Accelerating Progress Towards the Sustainable Development Goals

Advances in Artificial Intelligence (AI) are helping tackle a growing number of societal challenges, demonstrating technology's increasing capability to address complex issues, including those outlined in the United Nations (UN) Sustainable Development Goals (SDGs). Despite global efforts, 80 percent of SDG targets have deviated, stalled, or regressed, and only 15 percent are on track as of 2023, illustrating the urgency of accelerating efforts to meet the goals by 2030. We draw on Google's internal and collaborative research, technical work, and social impact initiatives to show AI's potential to accelerate action on the SDGs and make substantive progress to help address humanity's most pressing challenges. The paper highlights AI capabilities (including computer vision, generative AI, natural language processing, and multimodal AI) and showcases how AI is altering how we approach problem-solving across all 17 SDGs through use cases, with a spotlight on AI-powered innovation in health, education, and climate. We then offer insights on AI development and deployment to drive bold and responsible innovation, enhance impact, close the accessibility gap, and ensure that everyone, everywhere, can benefit from AI.

cs.CY↗

arXiv2024

PathAlign: A vision-language model for whole slide images in histopathology

Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.

cs.CV↗

arXiv2024

Towards a Personal Health Large Language Model

In health, most large language model (LLM) research has focused on clinical tasks. However, mobile and wearable devices, which are rarely integrated into such tasks, provide rich, longitudinal data for personal health monitoring. Here we present Personal Health Large Language Model (PH-LLM), fine-tuned from Gemini for understanding and reasoning over numerical time-series personal health data. We created and curated three datasets that test 1) production of personalized insights and recommendations from sleep patterns, physical activity, and physiological responses, 2) expert domain knowledge, and 3) prediction of self-reported sleep outcomes. For the first task we designed 857 case studies in collaboration with domain experts to assess real-world scenarios in sleep and fitness. Through comprehensive evaluation of domain-specific rubrics, we observed that Gemini Ultra 1.0 and PH-LLM are not statistically different from expert performance in fitness and, while experts remain superior for sleep, fine-tuning PH-LLM provided significant improvements in using relevant domain knowledge and personalizing information for sleep insights. We evaluated PH-LLM domain knowledge using multiple choice sleep medicine and fitness examinations. PH-LLM achieved 79% on sleep and 88% on fitness, exceeding average scores from a sample of human experts. Finally, we trained PH-LLM to predict self-reported sleep quality outcomes from textual and multimodal encoding representations of wearable data, and demonstrate that multimodal encoding is required to match performance of specialized discriminative models. Although further development and evaluation are necessary in the safety-critical personal health domain, these results demonstrate both the broad knowledge and capabilities of Gemini models and the benefit of contextualizing physiological data for personal health applications as done with PH-LLM.

cs.AI↗

arXiv2024

Advancing Multimodal Medical Capabilities of Gemini

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

cs.CV↗

arXiv2024

Capabilities of Gemini Models in Medicine

Excellence in a wide variety of medical applications poses considerable challenges for AI, requiring advanced reasoning, access to up-to-date medical knowledge and understanding of complex multimodal data. Gemini models, with strong general capabilities in multimodal and long-context reasoning, offer exciting possibilities in medicine. Building on these core strengths of Gemini, we introduce Med-Gemini, a family of highly capable multimodal models that are specialized in medicine with the ability to seamlessly use web search, and that can be efficiently tailored to novel modalities using custom encoders. We evaluate Med-Gemini on 14 medical benchmarks, establishing new state-of-the-art (SoTA) performance on 10 of them, and surpass the GPT-4 model family on every benchmark where a direct comparison is viable, often by a wide margin. On the popular MedQA (USMLE) benchmark, our best-performing Med-Gemini model achieves SoTA performance of 91.1% accuracy, using a novel uncertainty-guided search strategy. On 7 multimodal benchmarks including NEJM Image Challenges and MMMU (health & medicine), Med-Gemini improves over GPT-4V by an average relative margin of 44.5%. We demonstrate the effectiveness of Med-Gemini's long-context capabilities through SoTA performance on a needle-in-a-haystack retrieval task from long de-identified health records and medical video question answering, surpassing prior bespoke methods using only in-context learning. Finally, Med-Gemini's performance suggests real-world utility by surpassing human experts on tasks such as medical text summarization, alongside demonstrations of promising potential for multimodal medical dialogue, medical research and education. Taken together, our results offer compelling evidence for Med-Gemini's potential, although further rigorous evaluation will be crucial before real-world deployment in this safety-critical domain.

cs.AI↗

arXiv2024

HeAR -- Health Acoustic Representations

Health acoustic sounds such as coughs and breaths are known to contain useful health signals with significant potential for monitoring health and disease, yet are underexplored in the medical machine learning community. The existing deep learning systems for health acoustics are often narrowly trained and evaluated on a single task, which is limited by data and may hinder generalization to other tasks. To mitigate these gaps, we develop HeAR, a scalable self-supervised learning-based deep learning system using masked autoencoders trained on a large dataset of 313 million two-second long audio clips. Through linear probes, we establish HeAR as a state-of-the-art health audio embedding model on a benchmark of 33 health acoustic tasks across 6 datasets. By introducing this work, we hope to enable and accelerate further health acoustics research.

cs.LG↗

arXiv2024

Breaking the Language Barrier: Can Direct Inference Outperform Pre-Translation in Multilingual LLM Applications?

Large language models hold significant promise in multilingual applications. However, inherent biases stemming from predominantly English-centric pre-training have led to the widespread practice of pre-translation, i.e., translating non-English inputs to English before inference, leading to complexity and information loss. This study re-evaluates the need for pre-translation in the context of PaLM2 models (Anil et al., 2023), which have been established as highly performant in multilingual tasks. We offer a comprehensive investigation across 108 languages and 6 diverse benchmarks, including open-end generative tasks, which were excluded from previous similar studies. Our findings challenge the pre-translation paradigm established in prior research, highlighting the advantages of direct inference in PaLM2. Specifically, PaLM2-L consistently outperforms pre-translation in 94 out of 108 languages. These findings pave the way for more efficient and effective multilingual applications, alleviating the limitations associated with pre-translation and unlocking linguistic authenticity.

cs.CL↗