RNE: a plug-and-play framework for diffusion density estimation and inference-time control

In this paper, we introduce the Radon-Nikodym Estimator (RNE), a flexible, plug-and-play framework for diffusion inference-time density estimation and control, based on the concept of the density ratio between path distributions. RNE connects and unifies a variety of existing density estimation and inference-time control methods under a single and intuitive perspective, stemming from basic variational inference and probabilistic principles therefore offering both theoretical clarity and practical versatility. Experiments demonstrate that RNE achieves promising performances in diffusion density estimation and inference-time control tasks, including annealing, composition of diffusion models, and reward-tilting.

Building-Block Aware Generative Modeling for 3D Crystals of Metal Organic Frameworks

Metal-organic frameworks (MOFs) marry inorganic nodes, organic edges, and topological nets into programmable porous crystals, yet their astronomical design space defies brute-force synthesis. Generative modeling holds ultimate promise, but existing models either recycle known building blocks or are restricted to small unit cells. We introduce Building-Block-Aware MOF Diffusion (BBA MOF Diffusion), an SE(3)-equivariant diffusion model that learns 3D all-atom representations of individual building blocks, encoding crystallographic topological nets explicitly. Trained on the CoRE-MOF database, BBA MOF Diffusion readily samples MOFs with unit cells containing 1000 atoms with great geometric validity, novelty, and diversity mirroring experimental databases. Its native building-block representation produces unprecedented metal nodes and organic edges, expanding accessible chemical space by orders of magnitude. One high-scoring [Zn(1,4-TDC)(EtOH)2] MOF predicted by the model was synthesized, where powder X-ray diffraction, thermogravimetric analysis, and N2 sorption confirm its structural fidelity. BBA-Diff thus furnishes a practical pathway to synthesizable and high-performing MOFs.

LLM-Augmented Chemical Synthesis and Design Decision Programs

Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has advanced single-step retrosynthetic modeling and subsequent route searches, these solutions remain restricted by the extensive combinatorial space of possible pathways. Concurrently, large language models (LLMs) have exhibited remarkable chemical knowledge, hinting at their potential to tackle complex decision-making tasks in chemistry. In this work, we explore whether LLMs can successfully navigate the highly constrained, multi-step retrosynthesis planning problem. We introduce an efficient scheme for encoding reaction pathways and present a new route-level search strategy, moving beyond the conventional step-by-step reactant prediction. Through comprehensive evaluations, we show that our LLM-augmented approach excels at retrosynthesis planning and extends naturally to the broader challenge of synthesizable molecular design.

FEAT: Free energy Estimators with Adaptive Transport

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation -- a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates improvements over existing learning-based methods.

Large Language Models Are Innate Crystal Structure Generators

Crystal structure generation is fundamental to materials discovery, enabling the prediction of novel materials with desired properties. While existing approaches leverage Large Language Models (LLMs) through extensive fine-tuning on materials databases, we show that pre-trained LLMs can inherently generate stable crystal structures without additional training. Our novel framework MatLLMSearch integrates pre-trained LLMs with evolutionary search algorithms, achieving a 78.38% metastable rate validated by machine learning interatomic potentials and 31.7% DFT-verified stability via quantum mechanical calculations, outperforming specialized models such as CrystalTextLLM. Beyond crystal structure generation, we further demonstrate that our framework can be readily adapted to diverse materials design tasks, including crystal structure prediction and multi-objective optimization of properties such as deformation energy and bulk modulus, all without fine-tuning. These results establish pre-trained LLMs as versatile and effective tools for materials discovery, opening up new venues for crystal structure generation with reduced computational overhead and broader accessibility.

No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.

Large Language Model is Secretly a Protein Sequence Optimizer

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an iterative process to generate variants and select via experimental feedback. We demonstrate large language models (LLMs), despite being trained on massive texts, are secretly protein sequence optimizers. With a directed evolutionary method, LLM can perform protein engineering through Pareto and experiment-budget constrained optimization, demonstrating success on both synthetic and experimental fitness landscapes.

AlphaNet: Scaling Up Local Frame-based Atomistic Foundation Model

We present AlphaNet, a local frame-based equivariant model designed to achieve both accurate and efficient simulations for atomistic systems. Recently, machine learning force fields (MLFFs) have gained prominence in molecular dynamics simulations due to their advantageous efficiency-accuracy balance compared to classical force fields and quantum mechanical calculations, alongside their transferability across various systems. Despite the advancements in improving model accuracy, the efficiency and scalability of MLFFs remain significant obstacles in practical applications. AlphaNet enhances computational efficiency and accuracy by leveraging the local geometric structures of atomic environments through the construction of equivariant local frames and learnable frame transitions. We substantiate the efficacy of AlphaNet across diverse datasets, including defected graphene, formate decomposition, zeolites, and surface reactions. AlphaNet consistently surpasses well-established models, such as NequIP and DeepPot, in terms of both energy and force prediction accuracy. Notably, AlphaNet offers one of the best trade-offs between computational efficiency and accuracy among existing models. Moreover, AlphaNet exhibits scalability across a broad spectrum of system and dataset sizes, affirming its versatility.

Graph Generative Pre-trained Transformer

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models

Designing functional transition metal complexes (TMCs) faces challenges due to the vast search space of metals and ligands, requiring efficient optimization strategies. Traditional genetic algorithms (GAs) are commonly used, employing random mutations and crossovers driven by explicit mathematical objectives to explore this space. Transferring knowledge between different GA tasks, however, is difficult. We integrate large language models (LLMs) into the evolutionary optimization framework (LLM-EO) and apply it in both single- and multi-objective optimization for TMCs. We find that LLM-EO surpasses traditional GAs by leveraging the chemical knowledge of LLMs gained during their extensive pretraining. Remarkably, without supervised fine-tuning, LLMs utilize the full historical data from optimization processes, outperforming those focusing only on top-performing TMCs. LLM-EO successfully identifies eight of the top-20 TMCs with the largest HOMO-LUMO gaps by proposing only 200 candidates out of a 1.37 million TMCs space. Through prompt engineering using natural language, LLM-EO introduces unparalleled flexibility into multi-objective optimizations, thereby circumventing the necessity for intricate mathematical formulations. As generative models, LLMs can suggest new ligands and TMCs with unique properties by merging both internal knowledge and external chemistry data, thus combining the benefits of efficient optimization and molecular generation. With increasing potential of LLMs as pretrained foundational models and new post-training inference strategies, we foresee broad applications of LLM-based evolutionary optimization in chemistry and materials design.