Recently, large language models (LLMs) have shown significant progress, approaching human perception levels. In this work, we demonstrate that despite these advances, LLMs still struggle to reason using molecular structural information. This gap is critical because many molecular properties, including functional groups, depend heavily on such structural details. To address this limitation, we propose an approach that sketches molecular structures for reasoning. Specifically, we introduce Molecular Structural Reasoning (MSR) framework to enhance the understanding of LLMs by explicitly incorporating the key structural features. We present two frameworks for scenarios where the target molecule is known or unknown. We verify that our MSR improves molecular understanding through extensive experiments.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science.A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation.However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings.To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension.These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties.We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks.Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

Generating graphs from a target distribution is a significant challenge across many domains, including drug discovery and social network analysis. In this work, we introduce a novel graph generation method leveraging $K^2$ representation, originally designed for lossless graph compression. The $K^2$ representation enables compact generation while concurrently capturing an inherent hierarchical structure of a graph. In addition, we make contributions by (1) presenting a sequential $K^2$ representation that incorporates pruning, flattening, and tokenization processes and (2) introducing a Transformer-based architecture designed to generate the sequence by incorporating a specialized tree positional encoding scheme. Finally, we extensively evaluate our algorithm on four general and two molecular graph datasets to confirm its superiority for graph generation.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

In this paper, we study hybrid neural representations for spherical data, a domain of increasing relevance in scientific research. In particular, our work focuses on weather and climate data as well as cosmic microwave background (CMB) data. Although previous studies have delved into coordinate-based neural representations for spherical signals, they often fail to capture the intricate details of highly nonlinear signals. To address this limitation, we introduce a novel approach named Hybrid Neural Representations for Spherical data (HNeR-S). Our main idea is to use spherical feature-grids to obtain positional features which are combined with a multi-layer perceptron to predict the target signal. We consider feature-grids with equirectangular and hierarchical equal area isolatitude pixelization structures that align with weather data and CMB data, respectively. We extensively verify the effectiveness of our HNeR-S for regression, super-resolution, temporal interpolation, and compression tasks.

This paper studies Generative Flow Networks (GFlowNets), which learn to sample objects proportionally to a given reward function through the trajectory of state transitions. In this work, we observe that GFlowNets tend to under-exploit the high-reward objects due to training on insufficient number of trajectories, which may lead to a large gap between the estimated flow and the (known) reward value. In response to this challenge, we propose a pessimistic backward policy for GFlowNets (PBP-GFN), which maximizes the observed flow to align closely with the true reward for the object. We extensively evaluate PBP-GFN across eight benchmarks, including hyper-grid environment, bag generation, structured set generation, molecular generation, and four RNA sequence generation tasks. In particular, PBP-GFN enhances the discovery of high-reward objects, maintains the diversity of the objects, and consistently outperforms existing methods.