Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instruction dataset; (ii) ignoring the close correlation between reaction and retrosynthesis prediction for the existing fine-tuning strategies. To address these challenges, we propose ChemDual, a novel LLM framework for accurate chemical synthesis. Specifically, considering the high cost of data acquisition for reaction and retrosynthesis, ChemDual regards the reaction-and-retrosynthesis of molecules as a related recombination-and-fragmentation process and constructs a large-scale of 4.4 million instruction dataset. Furthermore, ChemDual introduces an enhanced LLaMA, equipped with a multi-scale tokenizer and dual-task learning strategy, to jointly optimize the process of recombination and fragmentation as well as the tasks between reaction and retrosynthesis prediction. Extensive experiments on Mol-Instruction and USPTO-50K datasets demonstrate that ChemDual achieves state-of-the-art performance in both predictions of reaction and retrosynthesis, outperforming the existing conventional single-task approaches and the general open-source LLMs. Through molecular docking analysis, ChemDual generates compounds with diverse and strong protein binding affinity, further highlighting its strong potential in drug design.

Quantum-Enhanced Classification of Brain Tumors Using DNA Microarray Gene Expression Profiles

DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the identification of diagnostic genetic signatures. To derive meaningful biological insights from the high-dimensional and complex gene features obtained through this technology and to analyze gene properties in detail, classical AI-based approaches such as machine learning and deep learning are widely employed. However, these methods face various limitations in managing high-dimensional vector spaces and modeling the intricate relationships among genes. In particular, challenges such as hyperparameter tuning, computational costs, and high processing power requirements can hinder their efficiency. To overcome these limitations, quantum computing and quantum AI approaches are gaining increasing attention. Leveraging quantum properties such as superposition and entanglement, quantum methods enable more efficient parallel processing of high-dimensional data and offer faster and more effective solutions to problems that are computationally demanding for classical methods. In this study, a novel model called "Deep VQC" is proposed, based on the Variational Quantum Classifier approach. Developed using microarray data containing 54,676 gene features, the model successfully classified four different types of brain tumors-ependymoma, glioblastoma, medulloblastoma, and pilocytic astrocytoma-alongside healthy samples with high accuracy. Furthermore, compared to classical ML algorithms, our model demonstrated either superior or comparable classification performance. These results highlight the potential of quantum AI methods as an effective and promising approach for the analysis and classification of complex structures such as brain tumors based on gene expression features.

RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation

3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cut-off radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.

BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models

Advances in deep learning and generative modeling have driven interest in data-driven molecule discovery pipelines, whereby machine learning (ML) models are used to filter and design novel molecules without requiring prohibitively expensive first-principles simulations. Although the discovery of novel molecules that extend the boundaries of known chemistry requires accurate out-of-distribution (OOD) predictions, ML models often struggle to generalize OOD. Furthermore, there are currently no systematic benchmarks for molecular OOD prediction tasks. We present BOOM, $\boldsymbol{b}$enchmarks for $\boldsymbol{o}$ut-$\boldsymbol{o}$f-distribution $\boldsymbol{m}$olecular property predictions -- a benchmark study of property-based out-of-distribution models for common molecular property prediction models. We evaluate more than 140 combinations of models and property prediction tasks to benchmark deep learning models on their OOD performance. Overall, we do not find any existing models that achieve strong OOD generalization across all tasks: even the top performing model exhibited an average OOD error 3x larger than in-distribution. We find that deep learning models with high inductive bias can perform well on OOD tasks with simple, specific properties. Although chemical foundation models with transfer and in-context learning offer a promising solution for limited training data scenarios, we find that current foundation models do not show strong OOD extrapolation capabilities. We perform extensive ablation experiments to highlight how OOD performance is impacted by data generation, pre-training, hyperparameter optimization, model architecture, and molecular representation. We propose that developing ML models with strong OOD generalization is a new frontier challenge in chemical ML model development. This open-source benchmark will be made available on Github.

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.

On Simulating Thin-Film Processes at the Atomic Scale Using Machine Learned Force Fields

Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface. Molecular dynamics (MD) is a powerful computational method to study the evolution of a process at the atomic scale, but studies of industrially relevant processes usually require suitable force fields, which are in general not available for all processes of interest. However, machine learned force fields (MLFF) are conquering the field of computational materials and surface science. In this paper, we demonstrate how to efficiently build MLFFs suitable for process simulations and provide two examples for technologically relevant processes: precursor pulse in the atomic layer deposition of HfO2 and atomic layer etching of MoS2.

Monotone Peridynamic Neural Operator for Nonlinear Material Modeling with Conditionally Unique Solutions

Data-driven methods have emerged as powerful tools for modeling the responses of complex nonlinear materials directly from experimental measurements. Among these methods, the data-driven constitutive models present advantages in physical interpretability and generalizability across different boundary conditions/domain settings. However, the well-posedness of these learned models is generally not guaranteed a priori, which makes the models prone to non-physical solutions in downstream simulation tasks. In this study, we introduce monotone peridynamic neural operator (MPNO), a novel data-driven nonlocal constitutive model learning approach based on neural operators. Our approach learns a nonlocal kernel together with a nonlinear constitutive relation, while ensuring solution uniqueness through a monotone gradient network. This architectural constraint on gradient induces convexity of the learnt energy density function, thereby guaranteeing solution uniqueness of MPNO in small deformation regimes. To validate our approach, we evaluate MPNO's performance on both synthetic and real-world datasets. On synthetic datasets with manufactured kernel and constitutive relation, we show that the learnt model converges to the ground-truth as the measurement grid size decreases both theoretically and numerically. Additionally, our MPNO exhibits superior generalization capabilities than the conventional neural networks: it yields smaller displacement solution errors in down-stream tasks with new and unseen loadings. Finally, we showcase the practical utility of our approach through applications in learning a homogenized model from molecular dynamics data, highlighting its expressivity and robustness in real-world scenarios.

A Temporal Broadening-Aware Pulse Width Adaptation Scheme for ISI Mitigation and Energy Efficiency in THz Communication

Terahertz (THz) communication ensures the provision of ultra-high data rates owing to its abundant bandwidth; however, its performance is impeded by complex propagation mechanisms. In particular, molecular absorption induces a temporal broadening effect (TBE), which causes pulse spreading and inter-symbol interference (ISI), especially in ON-OFF keying-based systems. To address this, we propose an adaptive pulse-width transmission scheme that dynamically adjusts pulse durations based on the anticipated TBE. This approach suppresses ISI by confining energy within symbol durations while also exploiting TBE constructively to reduce pulse transmissions in specific bit patterns, leading to improved energy efficiency (EE) as an additional advantage of the proposed scheme. Analytical derivations and simulation results confirm that the proposed scheme substantially improves EE and bit error rate under practical THz channel conditions.

Multi-Hierarchical Fine-Grained Feature Mapping Driven by Feature Contribution for Molecular Odor Prediction

Molecular odor prediction is the process of using a molecule's structure to predict its smell. While accurate prediction remains challenging, AI models can suggest potential odors. Existing methods, however, often rely on basic descriptors or handcrafted fingerprints, which lack expressive power and hinder effective learning. Furthermore, these methods suffer from severe class imbalance, limiting the training effectiveness of AI models. To address these challenges, we propose a Feature Contribution-driven Hierarchical Multi-Feature Mapping Network (HMFNet). Specifically, we introduce a fine-grained, Local Multi-Hierarchy Feature Extraction module (LMFE) that performs deep feature extraction at the atomic level, capturing detailed features crucial for odor prediction. To enhance the extraction of discriminative atomic features, we integrate a Harmonic Modulated Feature Mapping (HMFM). This module dynamically learns feature importance and frequency modulation, improving the model's capability to capture relevant patterns. Additionally, a Global Multi-Hierarchy Feature Extraction module (GMFE) is designed to learn global features from the molecular graph topology, enabling the model to fully leverage global information and enhance its discriminative power for odor prediction. To further mitigate the issue of class imbalance, we propose a Chemically-Informed Loss (CIL). Experimental results demonstrate that our approach significantly improves performance across various deep learning models, highlighting its potential to advance molecular structure representation and accelerate the development of AI-driven technologies.

Design, Integration, and Evaluation of a Dual-Arm Robotic System for High Throughput Tissue Sampling from Potato Tubers

Manual tissue extraction from potato tubers for molecular pathogen detection is highly laborious. This study presents a machine-vision-guided, dual-arm coordinated inline robotic system integrating tuber grasping and tissue sampling mechanisms. Tubers are transported on a conveyor that halts when a YOLOv11-based vision system detects a tuber within the workspace of a one-prismatic-degree-of-freedom (P-DoF) robotic arm. This arm, equipped with a gripping end-effector, secures and positions the tuber for sampling. The second arm, a 3-P-DoF Cartesian manipulator with a biopsy punch-based end-effector, then performs tissue extraction guided by a YOLOv10-based vision system that identifies the sampling sites on the tuber such as eyes or stolon scars. The sampling involves four stages: insertion of the punch into the tuber, punch rotation for tissue detachment, biopsy punch retraction, and deposition of the tissue core onto a collection site. The system achieved an average positional error of 1.84 mm along the tuber surface and a depth deviation of 1.79 mm from a 7.00 mm target. The success rate for core extraction and deposition was 81.5%, with an average sampling cycle of 10.4 seconds. The total cost of the system components was under $1,900, demonstrating the system's potential as a cost-effective alternative to labor-intensive manual tissue sampling. Future work will focus on optimizing for multi-site sampling from a single tuber and validation in commercial settings.