Drug design, particularly in the discovery of lead compounds, is of core strategic importance to combating disease and enhancing human well-being. Prevailing computational methods, however, struggle to effectively integrate domain-specific knowledge, severely limiting their capacity to identify novel lead compounds with validated binding modes and new scaffolds. Here, we propose AutoLeadDesign, a lead compounds design framework that inspires extensive domain knowledge encoded in large language models with chemical fragments to progressively implement efficient exploration of vast chemical space. The comprehensive experiments indicate that AutoLeadDesign outperforms baseline methods. Significantly, empirical lead design campaigns targeting two clinically relevant targets (PRMT5 and SARS-CoV-2 PLpro) demonstrate AutoLeadDesign's competence in de novo generation of lead compounds, achieving expert-competitive design efficacy. Structural analysis further confirms their mechanism-validated inhibitory patterns. By tracing the process of design, we find that AutoLeadDesign shares analogous mechanisms with fragment-based drug design, which traditionally rely on expert decision-making, further revealing why it works. Overall, AutoLeadDesign offers an efficient approach for lead compound design, suggesting its potential utility in drug design.

We have developed Aitomia - a platform powered by AI to assist in performing AI-driven atomistic and quantum chemical (QC) simulations. This evolving intelligent assistant platform is equipped with chatbots and AI agents to help experts and guide non-experts in setting up and running atomistic simulations, monitoring their computational status, analyzing simulation results, and summarizing them for the user in both textual and graphical forms. We achieve these goals by exploiting large language models that leverage the versatility of our MLatom ecosystem, supporting AI-enhanced computational chemistry tasks ranging from ground-state to excited-state calculations, including geometry optimizations, thermochemistry, and spectral calculations. The multi-agent implementation enables autonomous executions of the complex computational workflows, such as the computation of the reaction enthalpies. Aitomia is the first intelligent assistant publicly accessible online on a cloud computing platform for atomistic simulations of broad scope (Aitomistic Hub at https://aitomistic.xyz). It may also be deployed locally as described at http://mlatom.com/aitomia. Aitomia is expected to lower the barrier to performing atomistic simulations, thereby democratizing simulations and accelerating research and development in relevant fields.

Large Language Models (LLMs) are increasingly applied in the fields of mechanical engineering and materials science. As models that establish connections through the interface of language, LLMs can be applied for step-wise reasoning through the Processing-Structure-Property-Performance chain of material science and engineering. Current LLMs are built for adequately representing a dataset, which is the most part of the accessible internet. However, the internet mostly contains non-scientific content. If LLMs should be applied for engineering purposes, it is valuable to investigate models for their intrinsic knowledge -- here: the capacity to generate correct information about materials. In the current work, for the example of the Periodic Table of Elements, we highlight the role of vocabulary and tokenization for the uniqueness of material fingerprints, and the LLMs' capabilities of generating factually correct output of different state-of-the-art open models. This leads to a material knowledge benchmark for an informed choice, for which steps in the PSPP chain LLMs are applicable, and where specialized models are required.

In causal inference, whether through randomized controlled trials or observational studies, access to both treated and control units is essential for estimating the effect of a treatment on an outcome of interest. When treatment assignment is random, the average treatment effect (ATE) can be estimated directly by comparing outcomes between groups. In non-randomized settings, various techniques are employed to adjust for confounding and approximate the counterfactual scenario to recover an unbiased ATE. A common challenge, especially in observational studies, is the absence of units clearly labeled as controls-that is, units known not to have received the treatment. To address this, we propose positive-unlabeled (PU) learning as a framework for identifying, with high confidence, control units from a pool of unlabeled ones, using only the available treated (positive) units. We evaluate this approach using both simulated and real-world data. We construct a causal graph with diverse relationships and use it to generate synthetic data under various scenarios, assessing how reliably the method recovers control groups that allow estimates of true ATE. We also apply our approach to real-world data on optimal sowing and fertilizer treatments in sustainable agriculture. Our findings show that PU learning can successfully identify control (negative) units from unlabeled data based only on treated units and, through the resulting control group, estimate an ATE that closely approximates the true value. This work has important implications for observational causal inference, especially in fields where randomized experiments are difficult or costly. In domains such as earth, environmental, and agricultural sciences, it enables a plethora of quasi-experiments by leveraging available earth observation and climate data, particularly when treated units are available but control units are lacking.

Structured pruning aims to reduce the size and computational cost of deep neural networks by removing entire filters or channels. The traditional regularizers such as L1 or Group Lasso and its variants lead to magnitude-biased pruning decisions, such that the filters with small magnitudes are likely to be pruned. Also, they often entail pruning results with almost zero margin around pruning decision boundary, such that tiny perturbation in a filter magnitude can flip the pruning decision. In this paper, we identify the precise algebraic condition under which pruning operations preserve model performance, and use the condition to construct a novel regularizer defined in an extended parameter space via auxiliary catalyst variables. The proposed Catalyst regularization ensures fair pruning chance for each filters with theoretically provable zero bias to their magnitude and robust pruning behavior achieved by wide-margin bifurcation of magnitudes between the preserved and the pruned filters. The theoretical properties naturally lead to real-world effectiveness, as shown by empirical validations of Catalyst Pruning algorithm. Pruning results on various datasets and models are superior to state-of-the-art filter pruning methods, and at the same time confirm the predicted robust and fair pruning characteristics of Catalyst pruning.

Due to the computational complexity of evaluating interatomic forces from first principles, the creation of interatomic machine learning force fields has become a highly active field of research. However, the generation of training datasets of sufficient size and sample diversity itself comes with a computational burden that can make this approach impractical for modeling rare events or systems with a large configuration space. Fine-tuning foundation models that have been pre-trained on large-scale material or molecular databases offers a promising opportunity to reduce the amount of training data necessary to reach a desired level of accuracy. However, even if this approach requires less training data overall, creating a suitable training dataset can still be a very challenging problem, especially for systems with rare events and for end-users who don't have an extensive background in machine learning. In on-the-fly learning, the creation of a training dataset can be largely automated by using model uncertainty during the simulation to decide if the model is accurate enough or if a structure should be recalculated with classical methods and used to update the model. A key challenge for applying this form of active learning to the fine-tuning of foundation models is how to assess the uncertainty of those models during the fine-tuning process, even though most foundation models lack any form of uncertainty quantification. In this paper, we overcome this challenge by introducing a fine-tuning approach based on Bayesian neural network methods and a subsequent on-the-fly workflow that automatically fine-tunes the model while maintaining a pre-specified accuracy and can detect rare events such as transition states and sample them at an increased rate relative to their occurrence.

The development of Large Language Models (LLMs) requires robust benchmarks that encompass not only academic domains but also industrial fields to effectively evaluate their applicability in real-world scenarios. In this paper, we introduce two Korean expert-level benchmarks. KMMLU-Redux, reconstructed from the existing KMMLU, consists of questions from the Korean National Technical Qualification exams, with critical errors removed to enhance reliability. KMMLU-Pro is based on Korean National Professional Licensure exams to reflect professional knowledge in Korea. Our experiments demonstrate that these benchmarks comprehensively represent industrial knowledge in Korea. We release our dataset publicly available.

In recent years, various artificial intelligence-based surrogate models have been proposed to provide rapid manufacturability predictions of material forming processes. However, traditional AI-based surrogate models, typically built with scalar or image-based neural networks, are limited in their ability to capture complex 3D spatial relationships and to operate in a permutation-invariant manner. To overcome these issues, emerging graph-based surrogate models are developed using graph neural networks. This study developed a new graph neural network surrogate model named Recurrent U Net-based Graph Neural Network (RUGNN). The RUGNN model can achieve accurate predictions of sheet material deformation fields across multiple forming timesteps. The RUGNN model incorporates Gated Recurrent Units (GRUs) to model temporal dynamics and a U-Net inspired graph-based downsample/upsample mechanism to handle spatial long-range dependencies. A novel 'node-to-surface' contact representation method was proposed, offering significant improvements in computational efficiency for large-scale contact interactions. The RUGNN model was validated using a cold forming case study and a more complex hot forming case study using aluminium alloys. Results demonstrate that the RUGNN model provides accurate deformation predictions closely matching ground truth FE simulations and outperforming several baseline GNN architectures. Model tuning was also performed to identify suitable hyperparameters, training strategies, and input feature representations. These results demonstrate that RUGNN is a reliable approach to support sheet material forming design by enabling accurate manufacturability predictions.

Understanding and predicting the activity of oxide perovskite catalysts for the oxygen evolution reaction (OER) requires descriptors that are both accurate and physically interpretable. While symbolic regression (SR) offers a path to discover such formulas, its performance degrades with high-dimensional inputs and small datasets. We present a two-phase framework that combines neural networks (NN), feature importance analysis, and symbolic regression (SR) to discover interpretable descriptors for OER activity in oxide perovskites. In Phase I, using a small dataset and seven structural features, we reproduce and improve the known μ/t descriptor by engineering composite features and applying symbolic regression, achieving training and validation MAEs of 22.8 and 20.8 meV, respectively. In Phase II, we expand to 164 features, reduce dimensionality, and identify LUMO energy as a key electronic descriptor. A final formula using μ/t, μ/RA, and LUMO energy achieves improved accuracy (training and validation MAEs of 22.1 and 20.6 meV) with strong physical interpretability. Our results demonstrate that NN-guided symbolic regression enables accurate, interpretable, and physically meaningful descriptor discovery in data-scarce regimes, indicating interpretability need not sacrifice accuracy for materials informatics.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.