Graphical models have been widely used as parsimonious encoders of assumptions of the underlying causal system and provide a basis for causal inferences. Models encoding stronger constraints tend to require higher expressive power, which are also harder, and sometimes impossible to empirically falsify. In this paper, we introduce two new collections of distributions that include counterfactual quantities which are experimentally accessible under counterfactual randomizations. Correspondingly, we define two new classes of graphical models for encoding empirically testable constraints in these distributions. We further present a sound and complete calculus, based on counterfactual calculus, which licenses inferences in these two new models with rules that are within the empirically falsifiable boundary. Finally, we formulate a hierarchy over several graphical models based on the constraints they encode and study the fundamental trade-off between the expressive power and empirical falsifiability of different models across the hierarchy.

Diffusion-based generative methods have shown promising potential for modeling trajectories from offline reinforcement learning (RL) datasets, and hierarchical diffusion has been introduced to mitigate variance accumulation and computational challenges in long-horizon planning tasks. However, existing approaches typically assume a fixed two-layer diffusion hierarchy with a single predefined temporal scale, which limits adaptability to diverse downstream tasks and reduces flexibility in decision making. In this work, we propose SIHD, a novel Structural Information-based Hierarchical Diffusion framework for effective and stable offline policy learning in long-horizon environments with sparse rewards. Specifically, we analyze structural information embedded in offline trajectories to construct the diffusion hierarchy adaptively, enabling flexible trajectory modeling across multiple temporal scales. Rather than relying on reward predictions from localized sub-trajectories, we quantify the structural information gain of each state community and use it as a conditioning signal within the corresponding diffusion layer. To reduce overreliance on offline datasets, we introduce a structural entropy regularizer that encourages exploration of underrepresented states while avoiding extrapolation errors from distributional shifts. Extensive evaluations show that SIHD significantly outperforms state-of-the-art baselines in decision-making performance and demonstrates superior generalization across diverse scenarios.

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the new task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent literature show that our method consistently outperforms strong baselines.1

Invariant object recognition-the ability to identify objects despite changes in appearance-is a hallmark of visual processing in the brain, yet its understanding remains a central challenge in systems neuroscience. Artificial neural networks trained to predict neural responses to visual stimuli ("digital twins") could provide a powerful framework for studying such complex computations in silico. However, while current models accurately capture single-neuron responses within individual visual areas, their ability to reproduce how populations of neurons represent object identity, and how these representations transform across the cortical hierarchy, remains largely unexplored. Here we examine key functional signatures observed experimentally and find that current models account for hierarchical changes in basic single-neuron properties, such as receptive field size, but fail to capture more complex population-level phenomena, particularly invariant object representations. To address this gap, we introduce a biologically inspired hierarchical readout scheme that mirrors cortical anatomy, modeling each visual area as a projection from a distinct depth within a shared core network. This approach significantly improves the prediction of population-level representational transformations, outperforming standard models that use only the final layer, as well as alternatives with modified architecture, regularization, and loss function. Our results suggest that incorporating anatomical information provides a strong inductive bias in digital twin models, enabling them to better capture general principles of brain function.

In this work, we introduce TreeGen, a novel generative framework modeling distributions over hierarchies. We extend Bayesian Flow Networks (BFNs) to enable transitions between probabilistic and discrete hierarchies parametrized via categorical distributions. Our proposed scheduler provides smooth and consistent entropy decay across varying numbers of categories. We empirically evaluate TreeGen on the jet-clustering task in high-energy physics, demonstrating that it consistently generates valid trees that adhere to physical constraints and closely align with ground-truth log-likelihoods. Finally, by comparing TreeGen's samples to the exact posterior distribution and performing likelihood maximization via rejection sampling, we demonstrate that TreeGen outperforms various baselines.

Understanding objects at the level of their constituent parts is fundamental to advancing computer vision, graphics, and robotics. While datasets like PartNet have driven progress in 3D part understanding, their reliance on untextured geometries and expert-dependent annotation limits scalability and usability. We introduce PartNeXt, a next-generation dataset addressing these gaps with over 23,000 highquality, textured 3D models annotated with fine-grained, hierarchical part labels across 50 categories. We benchmark PartNeXt on two tasks: (1) class-agnostic part segmentation, where state-of-the-art methods (e.g., PartField, SAMPart3D) struggle with fine-grained and leaf-level parts, and (2) 3D part-centric question answering, a new benchmark for 3D-LLMs that reveals significant gaps in open-vocabulary part grounding. Additionally, training Point-SAM on PartNeXt yields substantial gains over PartNet, underscoring the dataset's superior quality and diversity.

Hierarchical structures of motion exist across research fields, including computer vision, graphics, and robotics, where complex dynamics typically arise from coordinated interactions among simpler motion components. Existing methods to model such dynamics typically rely on manually-defined or heuristic hierarchies with fixed motion primitives, limiting their generalizability across different tasks. In this work, we propose a general hierarchical motion modeling method that learns structured, interpretable motion relationships directly from data. Our method represents observed motions using graph-based hierarchies, explicitly decomposing global absolute motions into parent-inherited patterns and local motion residuals. We formulate hierarchy inference as a differentiable graph learning problem, where vertices represent elemental motions and directed edges capture learned parentchild dependencies through graph neural networks. We evaluate our hierarchical reconstruction approach on three examples: 1D translational motion, 2D rotational motion, and dynamic 3D scene deformation via Gaussian splatting. Experimental results show that our method reconstructs the intrinsic motion hierarchy in 1D and 2D cases, and produces more realistic and interpretable deformations compared to the baseline on dynamic 3DGaussian splatting scenes. By providing an adaptable, data-driven hierarchical modeling paradigm, our method offers a formulation applicable to a broad range of motion-centric tasks.

Biological and artificial vision systems both rely on hierarchical architectures, yet it remains unclear how their representational geometry evolves across processing stages, and what functional consequences may arise from potential differences. In this work, we systematically quantify and compare the linear and nonlinear dimensionality of human brain activity (fMRI) and artificial neural networks (ANNs) during natural image viewing. In the human ventral visual stream, both dimensionality measures increase along the visual hierarchy, supporting the emergence of semantic and abstract representations. For linear dimensionality, most ANNs show a similar increase, but only for pooled features, emphasizing the importance of appropriate feature readouts in brain-model comparisons. In contrast, nonlinear dimensionality shows a collapse in the later layers of ANNs, pointing at a mismatch in representational geometry between the human and artificial visual systems. This mismatch may have functional consequences: while high-dimensional brain representations support flexible generalization to abstract features, ANNs appear to lose this capacity in later layers, where their representations become overly compressed. Overall, our findings propose dimensionality alignment as a benchmark for building more flexible and biologically grounded vision models.

In this paper we introduce Hierarchical Diffusion Language Models (HDLM) - a novel family of discrete diffusion models for language modeling. HDLM builds on a hierarchical vocabulary where low-level tokens with detailed semantics are surjectively mapped to high-level tokens with coarse-grained meanings. In the forward process, each token is independently perturbed to its higher-level ancestor with more abstract semantics according to the scheduler, while in the reverse process the model progressively predicts the next, more detailed semantics. Taken together, HDLM provides a general time-varying next semantic scale prediction process for language modeling. We derive closed-form expressions for the diffusion Evidence Lower Bound (ELBO), and show that HDLM can be implemented in a flexible manner while including the existing MDLM as a special case. We also propose practical training techniques based on the insights. Extensive text generation experiments validate the effectiveness of HDLM, which demonstrates consistently lower validation and generative perplexity than baselines.

It has been observed that transformers with greater depth (that is, more layers) have more capabilities, but can we establish formally which capabilities are gained? We answer this question with a theoretical proof followed by an empirical study. First, we consider transformers that round to fixed precision except inside attention. We show that this subclass of transformers is expressively equivalent to the programming language C-RASP and this equivalence preserves depth. Second, we prove that deeper C-RASP programs are more expressive than shallower C-RASP programs, implying that deeper transformers are more expressive than shallower transformers (within the subclass mentioned above). The same is also proven for transformers with positional encodings (like RoPE and ALiBi). These results are established by studying a temporal logic with counting operators equivalent to C-RASP. Finally, we provide empirical evidence that our theory predicts the depth required for transformers without positional encodings to length-generalize on a family of sequential dependency tasks.