Related papers: GraphT5: Unified Molecular Graph-Language Modeling…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific…

Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN)…

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies…

Building cross-model intelligence that can understand charts and communicate the salient information hidden behind them is an appealing challenge in the vision and language(V+L) community. The capability to uncover the underlined table data…

Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for…

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative…

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge…

Large language models have made significant strides in natural language processing, enabling innovative applications in molecular science by processing textual representations of molecules. However, most existing language models cannot…

Most machine learning models for molecular property prediction rely on a single molecular representation (either a sequence, a graph, or a 3D structure) and treat molecular geometry as static. We present MolFM-Lite, a multi-modal model that…

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language…

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled…

Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in…

Molecular optimization, which transforms a given input molecule X into another Y with desirable properties, is essential in molecular drug discovery. The traditional translating approaches, generating the molecular graphs from scratch by…

SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…

Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these…