AI Research Papers Daily

Vision-Language-Action (VLA) models aim to provide a single generalist controller for robots, but today's systems fall short on the criteria that matter for real-world deployment. Frontier models are closed, open-weight alternatives are tied to expensive hardware, reasoning-augmented policies pay prohibitive latency for their grounding, and fine-tuned success rates remain below the threshold for dependable use. We present MolmoAct2, a fully open action reasoning model built for practical deployment, advancing its predecessor along five axes. We introduce MolmoER, a VLM backbone specialized for spatial and embodied reasoning, trained on a 3.3M-sample corpus with a specialize-then-rehearse recipe. We release three new datasets spanning low-to-medium cost platforms, including MolmoAct2-BimanualYAM, 720 hours of teleoperated bimanual trajectories that constitute the largest open bimanual dataset to date, together with quality-filtered Franka (DROID) and SO100/101 subsets. We provide OpenFAST, an open-weight, open-data action tokenizer trained on millions of trajectories across five embodiments. We redesign the architecture to graft a flow-matching continuous-action expert onto a discrete-token VLM via per-layer KV-cache conditioning. Finally, we propose MolmoThink, an adaptive-depth reasoning variant that re-predicts depth tokens only for scene regions that change between timesteps, retaining geometric grounding at a fraction of prior latency. In the most extensive empirical study of any open VLA to date, spanning 7 simulation and real-world benchmarks, MolmoAct2 outperforms strong baselines including Pi-05, while MolmoER surpasses GPT-5 and Gemini Robotics ER-1.5 across 13 embodied-reasoning benchmarks. We release model weights, training code, and complete training data. Project page: https://allenai.org/blog/molmoact2

Many real-world tasks require language models (LMs) to reason over complex contexts that exceed their parametric knowledge. This calls for context learning, where LMs directly learn relevant knowledge from the given context. An intuitive solution is inference-time skill augmentation: extracting the rules and procedures from context into natural-language skills. However, constructing such skills for context learning scenarios faces two challenges: the prohibitive cost of manual skill annotation for long, technically dense contexts, and the lack of external feedback for automated skill construction. In this paper, we propose Ctx2Skill, a self-evolving framework that autonomously discovers, refines, and selects context-specific skills without human supervision or external feedback. At its core, a multi-agent self-play loop has a Challenger that generates probing tasks and rubrics, a Reasoner that attempts to solve them guided by an evolving skill set, and a neutral Judge that provides binary feedback. Crucially, both the Challenger and the Reasoner evolve through accumulated skills: dedicated Proposer and Generator agents analyze failure cases and synthesize them into targeted skill updates for both sides, enabling automated skill discovery and refinement. To prevent adversarial collapse caused by increasingly extreme task generation and over-specialized skill accumulation, we further introduce a Cross-time Replay mechanism that identifies the skill set achieving the best balance across representative cases for the Reasoner side, ensuring robust and generalizable skill evolution. The resulting skills can be plugged into any language model to obtain better context learning capability. Evaluated on four context learning tasks from CL-bench, Ctx2Skill consistently improves solving rates across backbone models.

Recent research has shown that filtering massive English web corpora into high-quality subsets significantly improves training efficiency. However, for high-resource non-English languages like German, French, or Japanese, aggressive filtering creates a strategic dilemma: should practitioners prioritize diversity by training once on large amounts of lightly filtered web data, or prioritize quality by strictly filtering for a high-quality core and repeating it over multiple epochs? We investigate this trade-off for German by constructing hierarchical quality filters applied to 500M web documents, comparing multi-epoch training on the filtered subsets against single-pass training on a diverse corpus. Our experiments across multiple model scales and token budgets show that repeating high-quality data consistently outperforms single-pass training on larger, less filtered sets. Notably, the performance gap persists even after 7 epochs. Our findings suggest that for non-English LLMs, semantic concentration through quality filtering offers a more viable path to efficient language modeling than simply maximizing unique data volume. We release our German language models (called Boldt), as well as our cleaned evaluation benchmarks to the research community. Our experiments indicate that they achieve state-of-the-art results despite training on 10-360x fewer tokens than comparable models.

While autoregressive Large Vision-Language Models (LVLMs) demonstrate remarkable proficiency in multimodal tasks, they face a "Visual Signal Dilution" phenomenon, where the accumulation of textual history expands the attention partition function, causing visual attention to decay inversely with generated sequence length. To counteract this, we propose Persistent Visual Memory (PVM), a lightweight learnable module designed to ensure sustained, on-demand visual perception. Integrated as a parallel branch alongside the Feed-Forward Network (FFN) in LVLMs, PVM establishes a distance-agnostic retrieval pathway that directly provides visual embeddings for precise visual perception, thereby structurally mitigating the signal suppression inherent to deep generation. Extensive experiments on Qwen3-VL models demonstrate that PVM brings notable improvements with negligible parameter overhead, delivering consistent average accuracy gains across both 4B and 8B scales, particularly in complex reasoning tasks that demand persistent visual perception. Furthermore, in-depth analysis reveals that PVM can resist length-induced signal decay and accelerate internal prediction convergence.

The vast and underexplored ocean plays a critical role in regulating global climate and supporting marine biodiversity, yet artificial intelligence has so far delivered limited impact in this domain due to a fundamental data bottleneck. Specifically, ocean data are highly fragmented across disparate sources and inherently exhibit multi-modal, high-noise, and weakly labeled characteristics, lacking unified schemas and semantic alignment. Although Multimodal Large Language Models (MLLMs) have achieved remarkable success in general domains, their application to ocean science remains severely constrained by the absence of large-scale, well-aligned multimodal datasets tailored to marine environments. To bridge this gap, we introduce OceanPile, a large-scale multimodal corpus designed for ocean foundation models. It comprises three key components: OceanCorpus, a unified collection integrating sonar data, underwater imagery, marine science visuals, and scientific text from diverse authoritative sources; OceanInstruction, a high-quality instruction dataset synthesized via a novel pipeline guided by a hierarchical Ocean Concept Knowledge Graph; and OceanBenchmark, a manually curated evaluation benchmark for rigorous assessment. We establish a multi-stage quality control process to ensure scientific validity and alignment across modalities. Experimental validation demonstrates significant performance improvements for models trained on our data. All datasets are publicly released to advance the field of marine artificial intelligence and empower domain-specific MLLMs.

Despite significant strides in factual reliability, errors -- often termed hallucinations -- remain a major concern for generative AI, especially as LLMs are increasingly expected to be helpful in more complex or nuanced setups. Yet even in the simplest setting -- factoid question-answering with clear ground truth-frontier models without external tools continue to hallucinate. We argue that most factuality gains in this domain have come from expanding the model's knowledge boundary (encoding more facts) rather than improving awareness of that boundary (distinguishing known from unknown). We conjecture that the latter is inherently difficult: models may lack the discriminative power to perfectly separate truths from errors, creating an unavoidable tradeoff between eliminating hallucinations and preserving utility. This tradeoff dissolves under a different framing. If we understand hallucinations as confident errors -- incorrect information delivered without appropriate qualification -- a third path emerges beyond the answer-or-abstain dichotomy: expressing uncertainty. We propose faithful uncertainty: aligning linguistic uncertainty with intrinsic uncertainty. This is one facet of metacognition -- the ability to be aware of one's own uncertainty and to act on it. For direct interaction, acting on uncertainty means communicating it honestly; for agentic systems, it becomes the control layer governing when to search and what to trust. Metacognition is thus essential for LLMs to be both trustworthy and capable; we conclude by highlighting open problems for progress towards this objective.

Benchmarks within the OpenClaw ecosystem have thus far evaluated exclusively assistant-level tasks, leaving the academic-level capabilities of OpenClaw largely unexamined. We introduce AcademiClaw, a bilingual benchmark of 80 complex, long-horizon tasks sourced directly from university students' real academic workflows -- homework, research projects, competitions, and personal projects -- that they found current AI agents unable to solve effectively. Curated from 230 student-submitted candidates through rigorous expert review, the final task set spans 25+ professional domains, ranging from olympiad-level mathematics and linguistics problems to GPU-intensive reinforcement learning and full-stack system debugging, with 16 tasks requiring CUDA GPU execution. Each task executes in an isolated Docker sandbox and is scored on task completion by multi-dimensional rubrics combining six complementary techniques, with an independent five-category safety audit providing additional behavioral analysis. Experiments on six frontier models show that even the best achieves only a 55\% pass rate. Further analysis uncovers sharp capability boundaries across task domains, divergent behavioral strategies among models, and a disconnect between token consumption and output quality, providing fine-grained diagnostic signals beyond what aggregate metrics reveal. We hope that AcademiClaw and its open-sourced data and code can serve as a useful resource for the OpenClaw community, driving progress toward agents that are more capable and versatile across the full breadth of real-world academic demands. All data and code are available at https://github.com/GAIR-NLP/AcademiClaw.

In this paper, we study an under-explored but important factor of diffusion generative models, i.e., the combinatorial complexity. Data samples are generally high-dimensional, and for various structured generation tasks, additional attributes are combined to associate with data samples. We show that the space spanned by the combination of dimensions and attributes can be insufficiently covered by existing training schemes of diffusion generative models, potentially limiting test time performance. We present a simple fix to this problem by constructing stochastic processes that fully exploit the combinatorial structures, hence the name ComboStoc. Using this simple strategy, we show that network training is significantly accelerated across diverse data modalities, including images and 3D structured shapes. Moreover, ComboStoc enables a new way of test time generation which uses asynchronous time steps for different dimensions and attributes, thus allowing for varying degrees of control over them. Our code is available at: https://github.com/Xrvitd/ComboStoc

We introduce PhysicianBench, a benchmark for evaluating LLM agents on physician tasks grounded in real clinical setting within electronic health record (EHR) environments. Existing medical agent benchmarks primarily focus on static knowledge recall, single-step atomic actions, or action intent without verifiable execution against the environment. As a result, they fail to capture the long-horizon, composite workflows that characterize real clinical systems. PhysicianBench comprises 100 long-horizon tasks adapted from real consultation cases between primary care and subspecialty physicians, with each task independently reviewed by a separate panel of physicians. Tasks are instantiated in an EHR environment with real patient records and accessed through the same standard APIs used by commercial EHR vendors. Tasks span 21 specialties (e.g., cardiology, endocrinology, oncology, psychiatry) and diverse workflow types (e.g., diagnosis interpretation, medication prescribing, treatment planning), requiring an average of 27 tool calls per task. Solving each task requires retrieving data across encounters, reasoning over heterogeneous clinical information, executing consequential clinical actions, and producing clinical documentation. Each task is decomposed into structured checkpoints (670 in total across the benchmark) capturing distinct stages of completion graded by task-specific scripts with execution-grounded verification. Across 13 proprietary and open-source LLM agents, the best-performing model achieves only 46% success rate (pass@1), while open-source models reach at most 19%, revealing a substantial gap between current agent capabilities and the demands of real-world clinical workflows. PhysicianBench provides a realistic and execution-grounded benchmark for measuring progress toward autonomous clinical agents.

Recent progress in multi-turn reinforcement learning (RL) has significantly improved reasoning LLMs' performances on complex interactive tasks. Despite advances in stabilization techniques such as fine-grained credit assignment and trajectory filtering, instability remains pervasive and often leads to training collapse. We argue that this instability stems from inefficient exploration in multi-turn settings, where policies continue to generate low-information actions that neither reduce uncertainty nor advance task progress. To address this issue, we propose Token- and Turn-level Policy Optimization (T^2PO), an uncertainty-aware framework that explicitly controls exploration at fine-grained levels. At the token level, T^2PO monitors uncertainty dynamics and triggers a thinking intervention once the marginal uncertainty change falls below a threshold. At the turn level, T^2PO identifies interactions with negligible exploration progress and dynamically resamples such turns to avoid wasted rollouts. We evaluate T^2PO in diverse environments, including WebShop, ALFWorld, and Search QA, demonstrating substantial gains in training stability and performance improvements with better exploration efficiency. Code is available at: https://github.com/WillDreamer/T2PO.

Retrieval-augmented generation (RAG) enhances large language models with external knowledge, and tree-based RAG organizes documents into hierarchical indexes to support queries at multiple granularities. However, existing Tree-RAG methods designed for single-document retrieval face critical challenges in scaling to cross-document multi-hop questions: (1) poor distribution adaptability, where k-means clustering introduces noise due to rigid distribution assumptions; (2) structural isolation, as tree indexes lack explicit cross-document connections; and (3) coarse abstraction, which obscures fine-grained details. To address these limitations, we propose Ψ-RAG, a tree-RAG framework with two key components. First, a hierarchical abstract tree index built through an iterative "merging and collapse" process that adapts to data distributions without a priori assumption. Second, a multi-granular retrieval agent that intelligently interacts with the knowledge base with reorganized queries and an agent-powered hybrid retriever. Ψ-RAG supports diverse tasks from token-level question answering to document-level summarization. On cross-document multi-hop QA benchmarks, it outperforms RAPTOR by 25.9% and HippoRAG 2 by 7.4% in average F1 score. Code is available at https://github.com/Newiz430/Psi-RAG.

Despite the success of Large-Vision Language Models (LVLMs), general optimization objectives (e.g., standard MLE) fail to constrain visual trajectories, leading to language bias and hallucination. To mitigate this, current methods introduce geometric priors from visual experts as additional supervision. However, we observe that such supervision is typically suboptimal: it is biased toward geometric precision and offers limited reasoning utility. To bridge this gap, we propose Perceptual Flow Network (PFlowNet), which eschews rigid alignment with the expert priors and achieves interpretable yet more effective visual reasoning. Specifically, PFlowNet decouples perception from reasoning to establish a self-conditioned generation process. Based on this, it integrates multi-dimensional rewards with vicinal geometric shaping via variational reinforcement learning, thereby facilitating reasoning-oriented perceptual behaviors while preserving visual reliability. PFlowNet delivers a provable performance guarantee and competitive empirical results, particularly setting new SOTA records on V* Bench (90.6%) and MME-RealWorld-lite (67.0%).

Frontier coding agents solve complex tasks when given complete context but collapse when specifications are incomplete or ambiguous. The bottleneck is not raw capability, but judgment: knowing when to act autonomously and when to ask for help. Current benchmarks are blind to this failure mode. They supply unambiguous detailed instructions and solely reward execution correctness, so an agent that makes a lucky guess for a missing requirement will score identically to one that would have asked to be certain. We present HiL-Bench (Human-in-the-Loop Benchmark) to measure this selective escalation skill. Each task contains human-validated blockers (missing information, ambiguous requests, contradictory information) that surface only through progressive exploration, not upfront inspection. Our core metric, Ask-F1, the harmonic mean of question precision and blocker recall, captures the tension between over-asking and silent guessing; its structure architecturally prevents gaming through question spam. Evaluation across SWE and text-to-SQL domains reveals a large universal judgment gap: no frontier model recovers more than a fraction of its full-information performance when deciding whether to ask. Failure analysis identifies three key help-seeking patterns: overconfident wrong beliefs with no gap detection; high uncertainty detection yet persistent errors; broad, imprecise escalation without self-correction. These consistent patterns confirm poor help-seeking is a model-level flaw, not task-specific. RL training on shaped Ask-F1 reward shows judgment is trainable: a 32B model improves both help-seeking quality and task pass rate, with gains that transfer across domains. The model does not learn domain-specific heuristics for when to ask; it learns to detect unresolvable uncertainty and act on it.

We present Orbit-Space Geometric Probability Paths (OGPP), a particle-native flow-matching framework for generative modeling of particle systems. OGPP is motivated by two insights: (i) particles are defined up to permutation symmetries, so anonymous indexing inflates per-index target variance and yields curved, hard-to-learn flows; and (ii) particles live in physical space, so the flow terminal velocity has physical meaning and can encode geometric attributes, e.g., surface normals. OGPP instantiates three key components: (1) orbit-space canonicalization of the probability-path terminal endpoint, (2) particle index embeddings for role specialization, and (3) geometric probability paths with arc-length-aware terminal velocities that generate normals as a byproduct of the flow. We evaluate OGPP on minimal-surface benchmarks, where it reduces metric error by up to two orders of magnitude in a single inference step; on ShapeNet, where it matches the state of the art with 5x fewer steps and reaches airplane EMD comparable to DiT-3D with 26x fewer parameters and 5x fewer steps; and on single-shape encoding, where it produces normals and reconstructions competitive with 6D generators while operating entirely in 3D.

Existing research largely attributes the global sequence modeling capability of Transformers to the explicit computation of attention weights, a process that inherently incurs quadratic computational complexity. In this work, we offer a novel perspective: we demonstrate that attention can be mathematically reframed as a Multi-Layer Perceptron (MLP) equipped with dynamically predicted parameters. Through this lens, we explain attention's global modeling power not as explicit token-wise aggregation, but as an implicit process where dynamically generated parameters act as a compressed representation of the global context. Inspired by this insight, we investigate a fundamental question: can we achieve Transformer-level sequence global modeling entirely through dynamic parameterization while maintaining linear complexity, effectively replacing explicit attention? To explore this, we design various dynamic parameter prediction strategies and integrate them into standard network layers. Extensive empirical studies on vision models demonstrate that dynamic parameterization can indeed serve as a highly effective, linear-complexity alternative to explicit attention, opening new pathways for efficient sequence modeling. Code is available at https://github.com/LeapLabTHU/WeightFormer.

This position paper argues that agentic AI systems should be designed and evaluated as marginal token allocation economies rather than as text generators priced by the unit. We follow a single request -- a developer asking a coding agent to fix a failing test -- through four economic layers that today are designed in isolation: a router that decides which model answers, an agent that decides whether to plan, act, verify, or defer, a serving stack that decides how to produce each token, and a training pipeline that decides whether the trace is worth learning from. We show that all four layers are solving the same first-order condition -- marginal benefit equals marginal cost plus latency cost plus risk cost -- with different index sets and different prices. The framing is deliberately minimal: we do not propose a complete theory of AI economics. But adopting marginal token allocation as the shared accounting object explains why systems that locally minimize tokens globally misallocate them, predicts a small set of recurring failure modes (over-routing, over-delegation, under-verification, serving congestion, stale rollouts, cache misuse), and points to a concrete research agenda in token-aware evaluation, autonomy pricing, congestion-priced serving, and risk-adjusted RL budgeting.

Large language models perform strongly on benchmarks in mathematical reasoning, coding and document analysis, suggesting a broad ability to follow instructions. However, it remains unclear whether such success reflects general logical competence, repeated application of learned procedures, or pattern matching that mimics rule execution. We investigate this question by introducing Stable Counting Capacity, an assay in which models count repeated symbols until failure. The assay removes knowledge dependencies, semantics and ambiguity from evaluation, avoids lexical and tokenization confounds, and provides a direct measure of procedural reliability beyond standard knowledge-based benchmarks. Here we show, across more than 100 model variants, that stable counting capacity remains far below advertised context limits. Model behavior is consistent neither with open-ended logic nor with stable application of a learned rule, but instead with use of a finite set of count-like internal states, analogous to counting on fingers. Once this resource is exhausted, the appearance of rule following disappears and exact execution collapses into guessing, even with additional test-time compute. These findings show that fluent performance in current language models does not guarantee general, reliable rule following.

This report documents the preparedness assessment of Code World Model (CWM), a model for code generation and reasoning about code from Meta. We conducted pre-release testing across domains identified in our Frontier AI Framework as potentially presenting catastrophic risks, and also evaluated the model's misaligned propensities. Our assessment found that CWM does not pose additional frontier risks beyond those present in the current AI ecosystem. We therefore release it as an open-weight model.

Surgical resection remains the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC), and eligibility depends on accurate assessment of vascular invasion (VI), i.e., tumor extension into adjacent critical vessels. Despite its importance for preoperative staging and surgical planning, computational VI assessment remains underexplored. Two major challenges are the lack of public datasets and the diagnostic ambiguity at the tumor-vessel interface, which leads to substantial inter-rater variability even among expert radiologists. To address these limitations, we introduce the CURVAS-PDACVI Dataset and Challenge, an open benchmark for uncertainty-aware AI in PDAC staging based on a densely annotated dataset with five independent expert annotations per scan. We also propose a multi-metric evaluation framework that extends beyond spatial overlap to include probabilistic calibration and VI assessment. Evaluation of six state-of-the-art methods shows that strong global volumetric overlap does not necessarily translate into reliable performance at clinically critical tumor-vessel interfaces. In particular, methods optimized for binary segmentation perform competitively on average overlap metrics, but often degrade in high-complexity cases with low expert consensus, either collapsing in volume or overextending at uncertain boundaries. In contrast, methods that model inter-rater disagreement produce better calibrated probabilistic maps and show greater robustness in these ambiguous cases. The benchmark highlights the limitations of volumetric accuracy as a proxy for localized surgical utility, motivating uncertainty-aware probabilistic models for preoperative decision-making.

Tabular Foundation Models (TFMs) achieve state-of-the-art zero-shot accuracy on small tabular datasets by meta-learning over synthetic data-generating processes -- making them highly attractive for practitioners who cannot afford large annotated corpora. However, their in-context learning mechanism assumes approximately clean inputs: missing values, outliers, and duplicates in the real-world data create a prior mismatch that degrades both accuracy and confidence calibration simultaneously. Correcting this mismatch requires sequential decisions over cleaning operators whose interactions no static preprocessing rule can anticipate -a natural fit for reinforcement learning~(RL). We introduce L2C2, the first deep RL framework framing tabular data cleaning as prior alignment: a learned policy sequences operators to minimize the distributional gap between dirty input and the TFM's synthetic prior. Six experiments on ten OpenML benchmark datasets establish: 1) three of seven reward designs collapse to degenerate trivial cleaning strategies -- principled reward engineering is scientifically non-trivial; 2) the novel TFMAwareReward reward we propose selects structurally distinct pipelines on 4/10 datasets and achieves higher TabPFN accuracy on those diverging cases (mean 0.851 vs. 0.843; Wilcoxon p=0.063, n=4) while never underperforming; 3) parameterized cleaning actions improve best-found pipeline reward on 9/10 datasets (Wilcoxon p=0.004); and 4) a policy pre-trained on one single source dataset exceeds scratch training at the 2,000-step fine-tuning checkpoint on all three held-out datasets (up to +28.8% after full fine-tuning) demonstrating cross-dataset transfer of prior-alignment knowledge. These findings establish that prior alignment is a principled data preparation strategy for TFM deployment on real-world tabular data.

Autoregressive video generation paradigms offer theoretical promise for long video synthesis, yet their practical deployment is hindered by the computational burden of sequential iterative denoising. While cache reuse strategies can accelerate generation by skipping redundant denoising steps, existing methods rely on coarse-grained chunk-level skipping that fails to capture fine-grained pixel dynamics. This oversight is critical: pixels with high motion require more denoising steps to prevent error accumulation, while static pixels tolerate aggressive skipping. We formalize this insight theoretically by linking cache errors to residual instability, and propose MotionCache, a motion-aware cache framework that exploits inter-frame differences as a lightweight proxy for pixel-level motion characteristics. MotionCache employs a coarse-to-fine strategy: an initial warm-up phase establishes semantic coherence, followed by motion-weighted cache reuse that dynamically adjusts update frequencies per token. Extensive experiments on state-of-the-art models like SkyReels-V2 and MAGI-1 demonstrate that MotionCache achieves significant speedups of 6.28times and 1.64times respectively, while effectively preserving generation quality (VBench: 1%downarrow and 0.01%downarrow respectively). The code is available at https://github.com/ywlq/MotionCache.

Automatic generation of executable Blender code from natural language remains challenging, with state-of-the-art LLMs producing frequent syntactic errors and geometrically inconsistent objects. We present BlenderRAG, a retrieval-augmented generation system that operates on a curated multimodal dataset of 500 expert-validated examples (text, code, image) across 50 object categories. By retrieving semantically similar examples during generation, BlenderRAG improves compilation success rates from 40.8% to 70.0% and semantic normalized alignment from 0.41 to 0.77 (CLIP similarity) across four state-of-the-art LLMs, without requiring fine-tuning or specialized hardware, making it immediately accessible for deployment. The dataset and code will be available at https://github.com/MaxRondelli/BlenderRAG.

Video game engines have been an important source for generating large volumes of visual synthetic datasets for training and evaluating computer vision algorithms that are to be deployed in the real world. While the visual fidelity of modern game engines has been significantly improved with technologies such as ray-tracing, a notable sim2real appearance gap between the synthetic and the real-world images still remains, which limits the utilization of synthetic datasets in real-world applications. In this letter, we investigate the ability of a state-of-the-art image generation and editing diffusion model (FLUX.2-4B Klein) to enhance the photorealism of synthetic datasets and compare its performance against a traditional image-to-image translation model (REGEN). Furthermore, we propose a hybrid approach that combines the strong geometry and material transformations of diffusion-based methods with the distribution-matching capabilities of image-to-image translation techniques. Through experiments, it is demonstrated that REGEN outperforms FLUX.2-4B Klein and that by combining both FLUX.2-4B Klein and REGEN models, better visual realism can be achieved compared to using each model individually, while maintaining semantic consistency. The code is available at: https://github.com/stefanos50/Hybrid-Sim2Real

Integrating molecular, morphological, and clinical data is essential for basic and translational biomedical research, yet systematic frameworks for jointly modeling these modalities remain limited. Here we present Haiku, a tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF). It comprises 26.7 million spatial proteomics patches from 3,218 tissue sections across 1,606 patients spanning 11 organ types, with matched hematoxylin and eosin (H&E) histology and clinical metadata aligned in a shared embedding space. Haiku enables three-way cross-modal retrieval, improves downstream classification and clinical prediction tasks over unimodal baselines, and supports zero-shot biomarker inference through fusion retrieval conditioned on clinical metadata-only text descriptions. Across tasks, Haiku outperforms competing approaches, achieving cross-modal retrieval (Recall@50 up to 0.611 versus near-zero baseline), survival prediction (C-index 0.737, +7.91% relative improvement), and zero-shot biomarker inference (mean Pearson correlation 0.718 across 52 biomarkers). Furthermore, we introduce a counterfactual prediction framework in which modifying only clinical metadata while fixing tissue morphology surfaces niche-specific molecular shifts associated with breast cancer stage progression and lung cancer survival outcomes. In a lung adenocarcinoma case study, the counterfactual analysis recovers niche-specific shifts characterized by increased CD8 and granzyme B, reduced PD-L1, and decreased Ki67, broadly consistent with patterns reported for favorable outcomes. We present these counterfactual results as exploratory, hypothesis-generating signals rather than mechanistic claims. These capabilities demonstrate that tri-modal alignment via Haiku enables integrative analysis of spatial biology, bridging molecular measurements with clinical context for biological exploration.