Tensor Decomposition Networks for Fast Machine Learning Interatomic Potential Computations

$\rm{SO}(3)$-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks whose CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of $\rm{SO}(3)$-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the $O(L^3)$ CG paths into a single path without compromising equivariance, where $L$ is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from $O(L^6)$ to $O(L^4)$. We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations.

Natural Language Guided Ligand-Binding Protein Design

Can AI protein models follow human language instructions and design proteins with desired functions (e.g. binding to a ligand)? Designing proteins that bind to a given ligand is crucial in a wide range of applications in biology and chemistry. Most prior AI models are trained on protein-ligand complex data, which is scarce due to the high cost and time requirements of laboratory experiments. In contrast, there is a substantial body of human-curated text descriptions about protein-ligand interactions and ligand formula. In this paper, we propose InstructPro, a family of protein generative models that follow natural language instructions to design ligand-binding proteins. Given a textual description of the desired function and a ligand formula in SMILES, InstructPro generates protein sequences that are functionally consistent with the specified instructions. We develop the model architecture, training strategy, and a large-scale dataset, InstructProBench, to support both training and evaluation. InstructProBench consists of 9,592,829 triples of (function description, ligand formula, protein sequence). We train two model variants: InstructPro-1B (with 1 billion parameters) and InstructPro-3B~(with 3 billion parameters). Both variants consistently outperform strong baselines, including ProGen2, ESM3, and Pinal. Notably, InstructPro-1B achieves the highest docking success rate (81.52% at moderate confidence) and the lowest average root mean square deviation (RMSD) compared to ground truth structures (4.026{\AA}). InstructPro-3B further descreases the average RMSD to 2.527{\AA}, demonstrating InstructPro's ability to generate ligand-binding proteins that align with the functional specifications.

DEL-ToM: Inference-Time Scaling for Theory-of-Mind Reasoning via Dynamic Epistemic Logic

Theory-of-Mind (ToM) tasks pose a unique challenge for small language models (SLMs) with limited scale, which often lack the capacity to perform deep social reasoning. In this work, we propose DEL-ToM, a framework that improves ToM reasoning through inference-time scaling rather than architectural changes. Our approach decomposes ToM tasks into a sequence of belief updates grounded in Dynamic Epistemic Logic (DEL), enabling structured and transparent reasoning. We train a verifier, called the Process Belief Model (PBM), to score each belief update step using labels generated automatically via a DEL simulator. During inference, candidate belief traces generated by a language model are evaluated by the PBM, and the highest-scoring trace is selected. This allows SLMs to emulate more deliberate reasoning by allocating additional compute at test time. Experiments across multiple model scales and benchmarks show that DEL-ToM consistently improves performance, demonstrating that verifiable belief supervision can significantly enhance ToM abilities of SLMs without retraining.

Latent Adaptive Planner for Dynamic Manipulation

This paper presents Latent Adaptive Planner (LAP), a novel approach for dynamic nonprehensile manipulation tasks that formulates planning as latent space inference, effectively learned from human demonstration videos. Our method addresses key challenges in visuomotor policy learning through a principled variational replanning framework that maintains temporal consistency while efficiently adapting to environmental changes. LAP employs Bayesian updating in latent space to incrementally refine plans as new observations become available, striking an optimal balance between computational efficiency and real-time adaptability. We bridge the embodiment gap between humans and robots through model-based proportional mapping that regenerates accurate kinematic-dynamic joint states and object positions from human demonstrations. Experimental evaluations across multiple complex manipulation benchmarks demonstrate that LAP achieves state-of-the-art performance, outperforming existing approaches in success rate, trajectory smoothness, and energy efficiency, particularly in dynamic adaptation scenarios. Our approach enables robots to perform complex interactions with human-like adaptability while providing an expandable framework applicable to diverse robotic platforms using the same human demonstration videos.

SpatialReasoner: Towards Explicit and Generalizable 3D Spatial Reasoning

Recent studies in 3D spatial reasoning explore data-driven approaches and achieve enhanced spatial reasoning performance with reinforcement learning (RL). However, these methods typically perform spatial reasoning in an implicit manner, and it remains underexplored whether the acquired 3D knowledge generalizes to unseen question types at any stage of the training. In this work we introduce SpatialReasoner, a novel large vision-language model (LVLM) that address 3D spatial reasoning with explicit 3D representations shared between stages -- 3D perception, computation, and reasoning. Explicit 3D representations provide a coherent interface that supports advanced 3D spatial reasoning and enable us to study the factual errors made by LVLMs. Results show that our SpatialReasoner achieve improved performance on a variety of spatial reasoning benchmarks and generalizes better when evaluating on novel 3D spatial reasoning questions. Our study bridges the 3D parsing capabilities of prior visual foundation models with the powerful reasoning abilities of large language models, opening new directions for 3D spatial reasoning.

Video-MMLU: A Massive Multi-Discipline Lecture Understanding Benchmark

Recent advancements in language multimodal models (LMMs) for video have demonstrated their potential for understanding video content, yet the task of comprehending multi-discipline lectures remains largely unexplored. We introduce Video-MMLU, a massive benchmark designed to evaluate the capabilities of LMMs in understanding Multi-Discipline Lectures. We evaluate over 90 open-source and proprietary models, ranging from 0.5B to 40B parameters. Our results highlight the limitations of current models in addressing the cognitive challenges presented by these lectures, especially in tasks requiring both perception and reasoning. Additionally, we explore how the number of visual tokens and the large language models influence performance, offering insights into the interplay between multimodal perception and reasoning in lecture comprehension.

Scalable Language Models with Posterior Inference of Latent Thought Vectors

We propose a novel family of language models, Latent-Thought Language Models (LTMs), which incorporate explicit latent thought vectors that follow an explicit prior model in latent space. These latent thought vectors guide the autoregressive generation of ground tokens through a Transformer decoder. Training employs a dual-rate optimization process within the classical variational Bayes framework: fast learning of local variational parameters for the posterior distribution of latent vectors, and slow learning of global decoder parameters. Empirical studies reveal that LTMs possess additional scaling dimensions beyond traditional LLMs, yielding a structured design space. Higher sample efficiency can be achieved by increasing training compute per token, with further gains possible by trading model size for more inference steps. Designed based on these scaling properties, LTMs demonstrate superior sample and parameter efficiency compared to conventional autoregressive models and discrete diffusion models. They significantly outperform these counterparts in validation perplexity and zero-shot language modeling. Additionally, LTMs exhibit emergent few-shot in-context reasoning capabilities that scale with model and latent size, and achieve competitive performance in conditional and unconditional text generation.

Latent Space Energy-based Neural ODEs

This paper introduces a novel family of deep dynamical models designed to represent continuous-time sequence data. This family of models generates each data point in the time series by a neural emission model, which is a non-linear transformation of a latent state vector. The trajectory of the latent states is implicitly described by a neural ordinary differential equation (ODE), with the initial state following an informative prior distribution parameterized by an energy-based model. Furthermore, we can extend this model to disentangle dynamic states from underlying static factors of variation, represented as time-invariant variables in the latent space. We train the model using maximum likelihood estimation with Markov chain Monte Carlo (MCMC) in an end-to-end manner, without requiring additional assisting components such as an inference network. Our experiments on oscillating systems, videos and real-world state sequences (MuJoCo) illustrate that ODEs with the learnable energy-based prior outperform existing counterparts, and can generalize to new dynamic parameterization, enabling long-horizon predictions.

Latent Energy-Based Odyssey: Black-Box Optimization via Expanded Exploration in the Energy-Based Latent Space

Offline Black-Box Optimization (BBO) aims at optimizing a black-box function using the knowledge from a pre-collected offline dataset of function values and corresponding input designs. However, the high-dimensional and highly-multimodal input design space of black-box function pose inherent challenges for most existing methods that model and operate directly upon input designs. These issues include but are not limited to high sample complexity, which relates to inaccurate approximation of black-box function; and insufficient coverage and exploration of input design modes, which leads to suboptimal proposal of new input designs. In this work, we consider finding a latent space that serves as a compressed yet accurate representation of the design-value joint space, enabling effective latent exploration of high-value input design modes. To this end, we formulate an learnable energy-based latent space, and propose Noise-intensified Telescoping density-Ratio Estimation (NTRE) scheme for variational learning of an accurate latent space model without costly Markov Chain Monte Carlo. The optimization process is then exploration of high-value designs guided by the learned energy-based model in the latent space, formulated as gradient-based sampling from a latent-variable-parameterized inverse model. We show that our particular parameterization encourages expanded exploration around high-value design modes, motivated by inversion thinking of a fundamental result of conditional covariance matrix typically used for variance reduction. We observe that our method, backed by an accurately learned informative latent space and an expanding-exploration model design, yields significant improvements over strong previous methods on both synthetic and real world datasets such as the design-bench suite.

Dual-Space Optimization: Improved Molecule Sequence Design by Latent Prompt Transformer

Designing molecules with desirable properties, such as drug-likeliness and high binding affinities towards protein targets, is a challenging problem. In this paper, we propose the Dual-Space Optimization (DSO) method that integrates latent space sampling and data space selection to solve this problem. DSO iteratively updates a latent space generative model and a synthetic dataset in an optimization process that gradually shifts the generative model and the synthetic data towards regions of desired property values. Our generative model takes the form of a Latent Prompt Transformer (LPT) where the latent vector serves as the prompt of a causal transformer. Our extensive experiments demonstrate effectiveness of the proposed method, which sets new performance benchmarks across single-objective, multi-objective and constrained molecule design tasks.