Molecular Property Prediction (MPP) is a critical task in computational drug discovery, aimed at identifying molecules with desirable pharmacological and ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties. Machine learning models have been widely used in this fast-growing field, with two types of models being commonly employed: traditional non-deep models and deep models.

As quantum chemical properties have a dependence on their geometries, graph neural networks (GNNs) using 3D geometric information have achieved high prediction accuracy in many tasks.

We propose a neural network weight encoding method for network property prediction that utilizes set-to-set and set-to-vector functionsto efficiently encode neural network parameters. Our approach is capable of encoding neural networks in a model zoo of mixed architecture and different parameter sizes as opposed to previous approaches that require custom encoding models for different architectures. Furthermore, our \textbf{S}et-based \textbf{N}eural network \textbf{E}ncoder (SNE) takes into consideration the hierarchical computational structure of neural networks. To respect symmetries inherent in network weight space, we utilize Logit Invariance to learn the required minimal invariance properties. Additionally, we introduce a \textit{pad-chunk-encode} pipeline to efficiently encode neural network layers that is adjustable to computational and memory constraints. We also introduce two new tasks for neural network property prediction: cross-dataset and cross-architecture. In cross-dataset property prediction, we evaluate how well property predictors generalize across model zoos trained on different datasets but of the same architecture. In cross-architecture property prediction, we evaluate how well property predictors transfer to model zoos of different architecture not seen during training. We show that SNE outperforms the relevant baselines on standard benchmarks.

Molecular property prediction (MPP) is integral to drug discovery and material science, but often faces the challenge of data scarcity in real-world scenarios. Addressing this, few-shot molecular property prediction (FSMPP) has been developed. Unlike other few-shot tasks, FSMPP typically employs a pre-trained molecular encoder and a context-aware classifier, benefiting from molecular pre-training and molecular context information.

Molecular property prediction plays a fundamental role in drug discovery to identify candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem, which makes it hard to use regular machine learning models. In this paper, we propose Property-Aware Relation networks (PAR) to handle this problem. In comparison to existing works, we leverage the fact that both relevant substructures and relationships among molecules change across different molecular properties. We first introduce a property-aware embedding function to transform the generic molecular embeddings to substructure-aware space relevant to the target property. Further, we design an adaptive relation graph learning module to jointly estimate molecular relation graph and refine molecular embeddings w.r.t. the target property, such that the limited labels can be effectively propagated among similar molecules. We adopt a meta-learning strategy where the parameters are selectively updated within tasks in order to model generic and property-aware knowledge separately. Extensive experiments on benchmark molecular property prediction datasets show that PAR consistently outperforms existing methods and can obtain property-aware molecular embeddings and model molecular relation graph properly.

The discovery of next-generation photoinitiators for two-photon polymerization (TPP) is hindered by the absence of large, open datasets containing the quantum-chemical and photophysical properties required to model photodissociation and excited-state behavior. Existing molecular datasets typically provide only basic physicochemical descriptors and therefore cannot support data-driven screening or AI-assisted design of photoinitiators. To address this gap, we introduce QuantumChem-200K, a large-scale dataset of over 200,000 organic molecules annotated with eleven quantum-chemical properties, including two-photon absorption (TPA) cross sections, TPA spectral ranges, singlet-triplet intersystem crossing (ISC) energies, toxicity and synthetic accessibility scores, hydrophilicity, solubility, boiling point, molecular weight, and aromaticity. These values are computed using a hybrid workflow that integrates density function theory (DFT), semi-empirical excited-state methods, atomistic quantum solvers, and neural-network predictors. Using QuantumChem-200K, we fine tune the open-source Qwen2.5-32B large language model to create a chemistry AI assistant capable of forward property prediction from SMILES. Benchmarking on 3000 unseen molecules from VQM24 and ZINC20 demonstrates that domain-specific fine-tuning significantly improves accuracy over GPT-4o, Llama-3.1-70B, and the base Qwen2.5-32B model, particularly for TPA and ISC predictions central to photoinitiator design. QuantumChem-200K and the corresponding AI assistant together provide the first scalable platform for high-throughput, LLM-driven photoinitiator screening and accelerated discovery of photosensitive materials.

Pretrained transformers provide rich, general-purpose embeddings, which are transferred to downstream tasks. However, current transfer strategies: fine-tuning and probing, either distort the pretrained geometric structure of the embeddings or lack sufficient expressivity to capture task-relevant signals. These issues become even more pronounced when supervised data are scarce. Here, we introduce Freeze, Diffuse, Decode (FDD), a novel diffusion-based framework that adapts pre-trained embeddings to downstream tasks while preserving their underlying geometric structure. FDD propagates supervised signal along the intrinsic manifold of frozen embeddings, enabling a geometry-aware adaptation of the embedding space. Applied to antimicrobial peptide design, FDD yields low-dimensional, predictive, and interpretable representations that support property prediction, retrieval, and latent-space interpolation.