Interpretable Cross-Network Attention for Resting-State fMRI Representation Learning

Understanding how large-scale functional brain networks reorganize during cognitive decline remains a central challenge in neuroimaging. While recent self-supervised models have shown promise for learning representations from resting-state fMRI, their internal mechanisms are difficult to interpret, limiting mechanistic insight. We propose BrainInterNet, a network-aware self-supervised framework based on masked reconstruction with cross-attention that explicitly models inter-network dependencies in rs-fMRI. By selectively masking predefined functional networks and reconstructing them from remaining context, our approach enables direct quantification of network predictability and interpretable analysis of cross-network interactions. We train BrainInterNet on multi-cohort fMRI data (from the ABCD, HCP Development, HCP Young Adults, and HCP Aging datasets) and evaluate on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, in total comprising 5,582 recordings. Our method reveals systematic alterations in the brain's network interactions under AD, including in the default mode, limbic, and attention networks. In parallel, the learned representations support accurate Alzheimer's-spectrum classification and yield a compact summary marker that tracks disease severity longitudinally. Together, these results demonstrate that network-guided masked modeling with cross-attention provides an interpretable and effective framework for characterizing functional reorganization in neurodegeneration.

Latent Forcing: Reordering the Diffusion Trajectory for Pixel-Space Image Generation

Latent diffusion models excel at generating high-quality images but lose the benefits of end-to-end modeling. They discard information during image encoding, require a separately trained decoder, and model an auxiliary distribution to the raw data. In this paper, we propose Latent Forcing, a simple modification to existing architectures that achieves the efficiency of latent diffusion while operating on raw natural images. Our approach orders the denoising trajectory by jointly processing latents and pixels with separately tuned noise schedules. This allows the latents to act as a scratchpad for intermediate computation before high-frequency pixel features are generated. We find that the order of conditioning signals is critical, and we analyze this to explain differences between REPA distillation in the tokenizer and the diffusion model, conditional versus unconditional generation, and how tokenizer reconstruction quality relates to diffusability. Applied to ImageNet, Latent Forcing achieves a new state-of-the-art for diffusion transformer-based pixel generation at our compute scale.

Anatomically Guided Latent Diffusion for Brain MRI Progression Modeling

Accurately modeling longitudinal brain MRI progression is crucial for understanding neurodegenerative diseases and predicting individualized structural changes. Existing state-of-the-art approaches, such as Brain Latent Progression (BrLP), often use multi-stage training pipelines with auxiliary conditioning modules but suffer from architectural complexity, suboptimal use of conditional clinical covariates, and limited guarantees of anatomical consistency. We propose Anatomically Guided Latent Diffusion Model (AG-LDM), a segmentation-guided framework that enforces anatomically consistent progression while substantially simplifying the training pipeline. AG-LDM conditions latent diffusion by directly fusing baseline anatomy, noisy follow-up states, and clinical covariates at the input level, a strategy that avoids auxiliary control networks by learning a unified, end-to-end model that represents both anatomy and progression. A lightweight 3D tissue segmentation model (WarpSeg) provides explicit anatomical supervision during both autoencoder fine-tuning and diffusion model training, ensuring consistent brain tissue boundaries and morphometric fidelity. Experiments on 31,713 ADNI longitudinal pairs and zero-shot evaluation on OASIS-3 demonstrate that AG-LDM matches or surpasses more complex diffusion models, achieving state-of-the-art image quality and 15-20\% reduction in volumetric errors in generated images. AG-LDM also exhibits markedly stronger utilization of temporal and clinical covariates (up to 31.5x higher sensitivity than BrLP) and generates biologically plausible counterfactual trajectories, accurately capturing hallmarks of Alzheimer's progression such as limbic atrophy and ventricular expansion. These results highlight AG-LDM as an efficient, anatomically grounded framework for reliable brain MRI progression modeling.

VideoWeave: A Data-Centric Approach for Efficient Video Understanding

Training video-language models is often prohibitively expensive due to the high cost of processing long frame sequences and the limited availability of annotated long videos. We present VideoWeave, a simple yet effective approach to improve data efficiency by constructing synthetic long-context training samples that splice together short, captioned videos from existing datasets. Rather than modifying model architectures or optimization objectives, VideoWeave reorganizes available video-text pairs to expand temporal diversity within fixed compute. We systematically study how different data composition strategies like random versus visually clustered splicing and caption enrichment affect downstream performance on downstream video question answering. Under identical compute constraints, models trained with VideoWeave achieve higher accuracy than conventional video finetuning. Our results highlight that reorganizing training data, rather than altering architectures, may offer a simple and scalable path for training video-language models. We link our code for all experiments here.

A Tool Bottleneck Framework for Clinically-Informed and Interpretable Medical Image Understanding

Recent tool-use frameworks powered by vision-language models (VLMs) improve image understanding by grounding model predictions with specialized tools. Broadly, these frameworks leverage VLMs and a pre-specified toolbox to decompose the prediction task into multiple tool calls (often deep learning models) which are composed to make a prediction. The dominant approach to composing tools is using text, via function calls embedded in VLM-generated code or natural language. However, these methods often perform poorly on medical image understanding, where salient information is encoded as spatially-localized features that are difficult to compose or fuse via text alone. To address this, we propose a tool-use framework for medical image understanding called the Tool Bottleneck Framework (TBF), which composes VLM-selected tools using a learned Tool Bottleneck Model (TBM). For a given image and task, TBF leverages an off-the-shelf medical VLM to select tools from a toolbox that each extract clinically-relevant features. Instead of text-based composition, these tools are composed by the TBM, which computes and fuses the tool outputs using a neural network before outputting the final prediction. We propose a simple and effective strategy for TBMs to make predictions with any arbitrary VLM tool selection. Overall, our framework not only improves tool-use in medical imaging contexts, but also yields more interpretable, clinically-grounded predictors. We evaluate TBF on tasks in histopathology and dermatology and find that these advantages enable our framework to perform on par with or better than deep learning-based classifiers, VLMs, and state-of-the-art tool-use frameworks, with particular gains in data-limited regimes. Our code is available at https://github.com/christinaliu2020/tool-bottleneck-framework.

QuantiPhy: A Quantitative Benchmark Evaluating Physical Reasoning Abilities of Vision-Language Models

Understanding the physical world is essential for generalist AI agents. However, it remains unclear whether state-of-the-art vision perception models (e.g., large VLMs) can reason physical properties quantitatively. Existing evaluations are predominantly VQA-based and qualitative, offering limited insight into whether these models can infer the kinematic quantities of moving objects from video observations. To address this, we present QuantiPhy, the first benchmark designed to quantitatively measure a VLM's physical reasoning ability. Comprising more than 3.3K video-text instances with numerical ground truth, QuantiPhy evaluates a VLM's performance on estimating an object's size, velocity, and acceleration at a given timestamp, using one of these properties as an input prior. The benchmark standardizes prompts and scoring to assess numerical accuracy, enabling fair comparisons across models. Our experiments on state-of-the-art VLMs reveal a consistent gap between their qualitative plausibility and actual numerical correctness. We further provide an in-depth analysis of key factors like background noise, counterfactual priors, and strategic prompting and find that state-of-the-art VLMs lean heavily on pre-trained world knowledge rather than faithfully using the provided visual and textual inputs as references when reasoning kinematic properties quantitatively. QuantiPhy offers the first rigorous, scalable testbed to move VLMs beyond mere verbal plausibility toward a numerically grounded physical understanding.

Repurposing 2D Diffusion Models for 3D Shape Completion

We present a framework that adapts 2D diffusion models for 3D shape completion from incomplete point clouds. While text-to-image diffusion models have achieved remarkable success with abundant 2D data, 3D diffusion models lag due to the scarcity of high-quality 3D datasets and a persistent modality gap between 3D inputs and 2D latent spaces. To overcome these limitations, we introduce the Shape Atlas, a compact 2D representation of 3D geometry that (1) enables full utilization of the generative power of pretrained 2D diffusion models, and (2) aligns the modalities between the conditional input and output spaces, allowing more effective conditioning. This unified 2D formulation facilitates learning from limited 3D data and produces high-quality, detail-preserving shape completions. We validate the effectiveness of our results on the PCN and ShapeNet-55 datasets. Additionally, we show the downstream application of creating artist-created meshes from our completed point clouds, further demonstrating the practicality of our method.

Spherical Leech Quantization for Visual Tokenization and Generation

Non-parametric quantization has received much attention due to its efficiency on parameters and scalability to a large codebook. In this paper, we present a unified formulation of different non-parametric quantization methods through the lens of lattice coding. The geometry of lattice codes explains the necessity of auxiliary loss terms when training auto-encoders with certain existing lookup-free quantization variants such as BSQ. As a step forward, we explore a few possible candidates, including random lattices, generalized Fibonacci lattices, and densest sphere packing lattices. Among all, we find the Leech lattice-based quantization method, which is dubbed as Spherical Leech Quantization ($Λ_{24}$-SQ), leads to both a simplified training recipe and an improved reconstruction-compression tradeoff thanks to its high symmetry and even distribution on the hypersphere. In image tokenization and compression tasks, this quantization approach achieves better reconstruction quality across all metrics than BSQ, the best prior art, while consuming slightly fewer bits. The improvement also extends to state-of-the-art auto-regressive image generation frameworks.

ViBES: A Conversational Agent with Behaviorally-Intelligent 3D Virtual Body

Human communication is inherently multimodal and social: words, prosody, and body language jointly carry intent. Yet most prior systems model human behavior as a translation task co-speech gesture or text-to-motion that maps a fixed utterance to motion clips-without requiring agentic decision-making about when to move, what to do, or how to adapt across multi-turn dialogue. This leads to brittle timing, weak social grounding, and fragmented stacks where speech, text, and motion are trained or inferred in isolation. We introduce ViBES (Voice in Behavioral Expression and Synchrony), a conversational 3D agent that jointly plans language and movement and executes dialogue-conditioned body actions. Concretely, ViBES is a speech-language-behavior (SLB) model with a mixture-of-modality-experts (MoME) backbone: modality-partitioned transformer experts for speech, facial expression, and body motion. The model processes interleaved multimodal token streams with hard routing by modality (parameters are split per expert), while sharing information through cross-expert attention. By leveraging strong pretrained speech-language models, the agent supports mixed-initiative interaction: users can speak, type, or issue body-action directives mid-conversation, and the system exposes controllable behavior hooks for streaming responses. We further benchmark on multi-turn conversation with automatic metrics of dialogue-motion alignment and behavior quality, and observe consistent gains over strong co-speech and text-to-motion baselines. ViBES goes beyond "speech-conditioned motion generation" toward agentic virtual bodies where language, prosody, and movement are jointly generated, enabling controllable, socially competent 3D interaction. Code and data will be made available at: ai.stanford.edu/~juze/ViBES/

Ask WhAI:Probing Belief Formation in Role-Primed LLM Agents

We present Ask WhAI, a systems-level framework for inspecting and perturbing belief states in multi-agent interactions. The framework records and replays agent interactions, supports out-of-band queries into each agent's beliefs and rationale, and enables counterfactual evidence injection to test how belief structures respond to new information. We apply the framework to a medical case simulator notable for its multi-agent shared memory (a time-stamped electronic medical record, or EMR) and an oracle agent (the LabAgent) that holds ground truth lab results revealed only when explicitly queried. We stress-test the system on a multi-specialty diagnostic journey for a child with an abrupt-onset neuropsychiatric presentation. Large language model agents, each primed with strong role-specific priors ("act like a neurologist", "act like an infectious disease specialist"), write to a shared medical record and interact with a moderator across sequential or parallel encounters. Breakpoints at key diagnostic moments enable pre- and post-event belief queries, allowing us to distinguish entrenched priors from reasoning or evidence-integration effects. The simulation reveals that agent beliefs often mirror real-world disciplinary stances, including overreliance on canonical studies and resistance to counterevidence, and that these beliefs can be traced and interrogated in ways not possible with human experts. By making such dynamics visible and testable, Ask WhAI offers a reproducible way to study belief formation and epistemic silos in multi-agent scientific reasoning.