Adam Yala

Victor Quach, Adam Fisch, Tal Schuster et al. · berkeley, mit

We propose a novel approach to conformal prediction for generative language models (LMs). Standard conformal prediction produces prediction sets -- in place of single predictions -- that have rigorous, statistical performance guarantees. LM responses are typically sampled from the model's predicted distribution over the large, combinatorial output space of natural language. Translating this process to conformal prediction, we calibrate a stopping rule for sampling different outputs from the LM that get added to a growing set of candidates until we are confident that the output set is sufficient. Since some samples may be low-quality, we also simultaneously calibrate and apply a rejection rule for removing candidates from the output set to reduce noise. Similar to conformal prediction, we prove that the sampled set returned by our procedure contains at least one acceptable answer with high probability, while still being empirically precise (i.e., small) on average. Furthermore, within this set of candidate responses, we show that we can also accurately identify subsets of individual components -- such as phrases or sentences -- that are each independently correct (e.g., that are not "hallucinations"), again with statistical guarantees. We demonstrate the promise of our approach on multiple tasks in open-domain question answering, text summarization, and radiology report generation using different LM variants.

Long Lian, Baifeng Shi, Adam Yala et al. · berkeley

Text-conditioned diffusion models have emerged as a promising tool for neural video generation. However, current models still struggle with intricate spatiotemporal prompts and often generate restricted or incorrect motion. To address these limitations, we introduce LLM-grounded Video Diffusion (LVD). Instead of directly generating videos from the text inputs, LVD first leverages a large language model (LLM) to generate dynamic scene layouts based on the text inputs and subsequently uses the generated layouts to guide a diffusion model for video generation. We show that LLMs are able to understand complex spatiotemporal dynamics from text alone and generate layouts that align closely with both the prompts and the object motion patterns typically observed in the real world. We then propose to guide video diffusion models with these layouts by adjusting the attention maps. Our approach is training-free and can be integrated into any video diffusion model that admits classifier guidance. Our results demonstrate that LVD significantly outperforms its base video diffusion model and several strong baseline methods in faithfully generating videos with the desired attributes and motion patterns.

Homa Esfahanizadeh, Adam Yala, Rafael G. L. D'Oliveira et al. · berkeley, mit

Allowing organizations to share their data for training of machine learning (ML) models without unintended information leakage is an open problem in practice. A promising technique for this still-open problem is to train models on the encoded data. Our approach, called Privately Encoded Open Datasets with Public Labels (PEOPL), uses a certain class of randomly constructed transforms to encode sensitive data. Organizations publish their randomly encoded data and associated raw labels for ML training, where training is done without knowledge of the encoding realization. We investigate several important aspects of this problem: We introduce information-theoretic scores for privacy and utility, which quantify the average performance of an unfaithful user (e.g., adversary) and a faithful user (e.g., model developer) that have access to the published encoded data. We then theoretically characterize primitives in building families of encoding schemes that motivate the use of random deep neural networks. Empirically, we compare the performance of our randomized encoding scheme and a linear scheme to a suite of computational attacks, and we also show that our scheme achieves competitive prediction accuracy to raw-sample baselines. Moreover, we demonstrate that multiple institutions, using independent random encoders, can collaborate to train improved ML models.

Zirui Wang, Junwei Yu, Adam Yala et al.

Vision-language models (VLMs) are increasingly used in multi-image, multi-turn agentic settings where decisions depend on visual changes. However, in existing open-weight VLMs, visual comparisons happen only inside the language model, while the visual encoder itself remains stateless: each image is encoded independently, without access to the prior visual context. As a result, small but task-critical changes may be attenuated before the language model has a chance to compare them, especially when those changes do not affect the high-level semantics of the scene. We introduce a Stateful Visual Encoder, which conditions each visual representation on prior visual features. Under supervised finetuning, VLMs equipped with stateful encoders achieve consistent improvements on controlled tasks involving cross-image spatial aggregation, multi-object visual differencing, and visual trajectory behavior cloning. These improvements are consistent across input resolutions, language model sizes, and VLM backbones. Finally, we validate our model on real-world tasks, including longitudinal radiology, fine-grained image comparison, and remote sensing, where stateful encoders consistently improve generalist VLM baselines and can match or surpass specialized models in selected domains. Project page: https://statefulvisualencoders.github.io/

Janice Yang, Ludvig Karstens, Casey Ross et al. · berkeley

This study is a technical supplement to "AI gone astray: How subtle shifts in patient data send popular algorithms reeling, undermining patient safety." from STAT News, which investigates the effect of time drift on clinically deployed machine learning models. We use MIMIC-IV, a publicly available dataset, to train models that replicate commercial approaches by Dascena and Epic to predict the onset of sepsis, a deadly and yet treatable condition. We observe some of these models degrade overtime; most notably an RNN built on Epic features degrades from a 0.729 AUC to a 0.525 AUC over a decade, leading us to investigate technical and clinical drift as root causes of this performance drop.

Zineng Tang, Long Lian, Seun Eisape et al.

Despite the recent success of image-text contrastive models like CLIP and SigLIP, these models often struggle with vision-centric tasks that demand high-fidelity image understanding, such as counting, depth estimation, and fine-grained object recognition. These models, by performing language alignment, tend to prioritize high-level semantics over visual understanding, weakening their image understanding. On the other hand, vision-focused models are great at processing visual information but struggle to understand language, limiting their flexibility for language-driven tasks. In this work, we introduce TULIP, an open-source, drop-in replacement for existing CLIP-like models. Our method leverages generative data augmentation, enhanced image-image and text-text contrastive learning, and image/text reconstruction regularization to learn fine-grained visual features while preserving global semantic alignment. Our approach, scaling to over 1B parameters, outperforms existing state-of-the-art (SOTA) models across multiple benchmarks, establishing a new SOTA zero-shot performance on ImageNet-1K, delivering up to a $2\times$ enhancement over SigLIP on RxRx1 in linear probing for few-shot classification, and improving vision-language models, achieving over $3\times$ higher scores than SigLIP on MMVP. Our code/checkpoints are available at https://tulip-berkeley.github.io

Michael Nercessian, Wenxin Zhang, Alexander Schubert et al.

Randomized controlled trials (RCTs) are indispensable for establishing the clinical value of medical artificial-intelligence (AI) tools, yet their high cost and long timelines hinder timely validation as new models emerge rapidly. Here, we propose BRIDGE, a data-reuse RCT design for AI-based risk models. AI risk models support a broad range of interventions, including screening, treatment selection, and clinical alerts. BRIDGE trials recycle participant-level data from completed trials of AI models when legacy and updated models make concordant predictions, thereby reducing the enrollment requirement for subsequent trials. We provide a practical checklist for investigators to assess whether reusing data from previous trials allows for valid causal inference and preserves type I error. Using real-world datasets across breast cancer, cardiovascular disease, and sepsis, we demonstrate concordance between successive AI models, with up to 64.8% overlap in top 5% high-risk cohorts. We then simulate a series of breast cancer screening studies, where our design reduced required enrollment by 46.6%--saving over US$2.8 million--while maintaining 80% power. By transforming trials into adaptive, modular studies, our proposed design makes Level I evidence generation feasible for every model iteration, thereby accelerating cost-effective translation of AI into routine care.

Kumar Krishna Agrawal, Long Lian, Longchao Liu et al.

Efficiently modeling massive images is a long-standing challenge in machine learning. To this end, we introduce Multi-Scale Attention (MSA). MSA relies on two key ideas, (i) multi-scale representations (ii) bi-directional cross-scale communication. MSA creates O(log N) scales to represent the image across progressively coarser features and leverages cross-attention to propagate information across scales. We then introduce Atlas, a novel neural network architecture based on MSA. We demonstrate that Atlas significantly improves the compute-performance tradeoff of long-context image modeling in a high-resolution variant of ImageNet 100. At 1024px resolution, Atlas-B achieves 91.04% accuracy, comparable to ConvNext-B (91.92%) while being 4.3x faster. Atlas is 2.95x faster and 7.38% better than FasterViT, 2.25x faster and 4.96% better than LongViT. In comparisons against MambaVision-S, we find Atlas-S achieves 5%, 16% and 32% higher accuracy at 1024px, 2048px and 4096px respectively, while obtaining similar runtimes. Code for reproducing our experiments and pretrained models is available at https://github.com/yalalab/atlas.

Louis Blankemeier, Ashwin Kumar, Joseph Paul Cohen et al.

The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.

Jiayi Pan, Xiuyu Li, Long Lian et al. · berkeley

Scaling inference-time computation has substantially improved the reasoning capabilities of language models. However, existing methods have significant limitations: serialized chain-of-thought approaches generate overly long outputs, leading to increased latency and exhausted context windows, while parallel methods such as self-consistency suffer from insufficient coordination, resulting in redundant computations and limited performance gains. To address these shortcomings, we propose Adaptive Parallel Reasoning (APR), a novel reasoning framework that enables language models to orchestrate both serialized and parallel computations end-to-end. APR generalizes existing reasoning methods by enabling adaptive multi-threaded inference using spawn() and join() operations. A key innovation is our end-to-end reinforcement learning strategy, optimizing both parent and child inference threads to enhance task success rate without requiring predefined reasoning structures. Experiments on the Countdown reasoning task demonstrate significant benefits of APR: (1) higher performance within the same context window (83.4% vs. 60.0% at 4k context); (2) superior scalability with increased computation (80.1% vs. 66.6% at 20k total tokens); (3) improved accuracy at equivalent latency (75.2% vs. 57.3% at approximately 5,000ms). APR represents a step towards enabling language models to autonomously optimize their reasoning processes through adaptive allocation of computation.

Long Lian, Yifan Ding, Yunhao Ge et al.

Generating detailed and accurate descriptions for specific regions in images and videos remains a fundamental challenge for vision-language models. We introduce the Describe Anything Model (DAM), a model designed for detailed localized captioning (DLC). DAM preserves both local details and global context through two key innovations: a focal prompt, which ensures high-resolution encoding of targeted regions, and a localized vision backbone, which integrates precise localization with its broader context. To tackle the scarcity of high-quality DLC data, we propose a Semi-supervised learning (SSL)-based Data Pipeline (DLC-SDP). DLC-SDP starts with existing segmentation datasets and expands to unlabeled web images using SSL. We introduce DLC-Bench, a benchmark designed to evaluate DLC without relying on reference captions. DAM sets new state-of-the-art on 7 benchmarks spanning keyword-level, phrase-level, and detailed multi-sentence localized image and video captioning.

Long Lian, Sida Wang, Felix Juefei-Xu et al.

Scaling inference-time computation has enabled Large Language Models (LLMs) to achieve strong reasoning performance, but inherently sequential decoding leads to substantial latency, especially on complex tasks. Recent work on adaptive parallel reasoning aims to improve inference efficiency by decomposing the problem-solving process into concurrent reasoning threads when beneficial. However, existing methods on realistic tasks are either limited to supervised behavior cloning or exhibit significant accuracy drops compared to widely-used sequential long chain-of-thought (CoT) baselines. Moreover, many require customized inference engines, complicating deployment. We introduce ThreadWeaver, a framework for adaptive parallel reasoning that achieves accuracy on par with popular sequential reasoning models of comparable size while significantly reducing inference latency. ThreadWeaver's performance stems from three key innovations: 1) a two-stage parallel trajectory generator that produces large-scale, high-quality CoT data with parallel annotations for supervised fine-tuning; 2) a trie-based training-inference co-design that enables parallel reasoning on any off-the-shelf autoregressive inference engine without modifying position embeddings or KV caches; and 3) a parallelization-aware reinforcement learning framework that teaches the model to balance accuracy with effective parallelization. Across six challenging mathematical reasoning benchmarks, ThreadWeaver trained atop Qwen3-8B achieves accuracy comparable to cutting-edge sequential reasoning models (71.9% on average and 79.9% on AIME24) while delivering up to 1.53x average speedup in token latency, establishing a new Pareto frontier between accuracy and efficiency.

Kumar Krishna Agrawal, Longchao Liu, Long Lian et al.

Radiology plays an integral role in modern medicine, yet rising imaging volumes have far outpaced workforce growth. Foundation models offer a path toward assisting with the full spectrum of radiology tasks, but existing medical models remain limited: they process volumetric CT and MRI as low-fidelity 2D slices, discard critical grayscale contrast information, and lack evaluation frameworks that reflect real clinical practice. We introduce Pillar-0, a radiology foundation model pretrained on 42,990 abdomen-pelvis CTs, 86,411 chest CTs, 14,348 head CTs, and 11,543 breast MRIs from a large academic center, together with RATE, a scalable framework that extracts structured labels for 366 radiologic findings with near-perfect accuracy using LLMs. Across internal test sets of 14,230 abdomen-pelvis CTs, 10,646 chest CTs, 4,906 head CTs, and 1,585 breast MRIs, Pillar-0 establishes a new performance frontier, achieving mean AUROCs of 86.4, 88.0, 90.1, and 82.9, outperforming MedGemma (Google), MedImageInsight (Microsoft), Lingshu (Alibaba), and Merlin (Stanford) by 7.8-15.8 AUROC points and ranking best in 87.2\% (319/366) tasks. Pillar-0 similarly outperforms all baselines in an external validation on the Stanford Abdominal CT dataset, including Merlin (82.2 vs 80.6 AUROC). Pillar-0 extends to tasks beyond its pretraining, such as long-horizon lung cancer risk prediction, where it improves upon the state-of-the-art Sybil by 3.0 C-index points on NLST, and generalizes with gains of 5.9 (MGH) and 1.9 (CGMH). In brain hemorrhage detection, Pillar-0 obtained a >95 AUROC when using only 1/20th of the data of the next most sample efficient baseline. Pillar-0 and RATE together provide an open, clinically rigorous foundation for building high-performance radiology systems, enabling applications that were previously infeasible due to computational, data, and evaluation constraints.

Letian Fu, Long Lian, Renhao Wang et al.

In this work, we examine the impact of inter-patch dependencies in the decoder of masked autoencoders (MAE) on representation learning. We decompose the decoding mechanism for masked reconstruction into self-attention between mask tokens and cross-attention between masked and visible tokens. Our findings reveal that MAE reconstructs coherent images from visible patches not through interactions between patches in the decoder but by learning a global representation within the encoder. This discovery leads us to propose a simple visual pretraining framework: cross-attention masked autoencoders (CrossMAE). This framework employs only cross-attention in the decoder to independently read out reconstructions for a small subset of masked patches from encoder outputs. This approach achieves comparable or superior performance to traditional MAE across models ranging from ViT-S to ViT-H and significantly reduces computational requirements. By its design, CrossMAE challenges the necessity of interaction between mask tokens for effective masked pretraining. Code and models are publicly available: https://crossmae.github.io

Long Lian, Boyi Li, Adam Yala et al.

Recent advancements in text-to-image diffusion models have yielded impressive results in generating realistic and diverse images. However, these models still struggle with complex prompts, such as those that involve numeracy and spatial reasoning. This work proposes to enhance prompt understanding capabilities in diffusion models. Our method leverages a pretrained large language model (LLM) for grounded generation in a novel two-stage process. In the first stage, the LLM generates a scene layout that comprises captioned bounding boxes from a given prompt describing the desired image. In the second stage, a novel controller guides an off-the-shelf diffusion model for layout-grounded image generation. Both stages utilize existing pretrained models without additional model parameter optimization. Our method significantly outperforms the base diffusion model and several strong baselines in accurately generating images according to prompts that require various capabilities, doubling the generation accuracy across four tasks on average. Furthermore, our method enables instruction-based multi-round scene specification and can handle prompts in languages not supported by the underlying diffusion model. We anticipate that our method will unleash users' creativity by accurately following more complex prompts. Our code, demo, and benchmark are available at: https://llm-grounded-diffusion.github.io

Adam Yala, Victor Quach, Homa Esfahanizadeh et al.

Balancing privacy and predictive utility remains a central challenge for machine learning in healthcare. In this paper, we develop Syfer, a neural obfuscation method to protect against re-identification attacks. Syfer composes trained layers with random neural networks to encode the original data (e.g. X-rays) while maintaining the ability to predict diagnoses from the encoded data. The randomness in the encoder acts as the private key for the data owner. We quantify privacy as the number of attacker guesses required to re-identify a single image (guesswork). We propose a contrastive learning algorithm to estimate guesswork. We show empirically that differentially private methods, such as DP-Image, obtain privacy at a significant loss of utility. In contrast, Syfer achieves strong privacy while preserving utility. For example, X-ray classifiers built with DP-image, Syfer, and original data achieve average AUCs of 0.53, 0.78, and 0.86, respectively.

Adam Yala, Homa Esfahanizadeh, Rafael G. L. D' Oliveira et al.

Balancing the needs of data privacy and predictive utility is a central challenge for machine learning in healthcare. In particular, privacy concerns have led to a dearth of public datasets, complicated the construction of multi-hospital cohorts and limited the utilization of external machine learning resources. To remedy this, new methods are required to enable data owners, such as hospitals, to share their datasets publicly, while preserving both patient privacy and modeling utility. We propose NeuraCrypt, a private encoding scheme based on random deep neural networks. NeuraCrypt encodes raw patient data using a randomly constructed neural network known only to the data-owner, and publishes both the encoded data and associated labels publicly. From a theoretical perspective, we demonstrate that sampling from a sufficiently rich family of encoding functions offers a well-defined and meaningful notion of privacy against a computationally unbounded adversary with full knowledge of the underlying data-distribution. We propose to approximate this family of encoding functions through random deep neural networks. Empirically, we demonstrate the robustness of our encoding to a suite of adversarial attacks and show that NeuraCrypt achieves competitive accuracy to non-private baselines on a variety of x-ray tasks. Moreover, we demonstrate that multiple hospitals, using independent private encoders, can collaborate to train improved x-ray models. Finally, we release a challenge dataset to encourage the development of new attacks on NeuraCrypt.

Karthik Narasimhan, Adam Yala, Regina Barzilay

Most successful information extraction systems operate with access to a large collection of documents. In this work, we explore the task of acquiring and incorporating external evidence to improve extraction accuracy in domains where the amount of training data is scarce. This process entails issuing search queries, extraction from new sources and reconciliation of extracted values, which are repeated until sufficient evidence is collected. We approach the problem using a reinforcement learning framework where our model learns to select optimal actions based on contextual information. We employ a deep Q-network, trained to optimize a reward function that reflects extraction accuracy while penalizing extra effort. Our experiments on two databases -- of shooting incidents, and food adulteration cases -- demonstrate that our system significantly outperforms traditional extractors and a competitive meta-classifier baseline.