Large Language Models (LLMs) have demonstrated remarkable success across various NLP benchmarks. However, excelling in complex tasks that require nuanced reasoning and precise decision-making demands more than raw language proficiency--LLMs must reason, i.e., think logically, draw from past experiences, and synthesize information to reach conclusions and take action. To enhance reasoning abilities, approaches such as prompting and fine-tuning have been widely explored. While these methods have led to clear improvements in reasoning, their impact on LLM safety remains less understood. In this work, we investigate the interplay between reasoning and safety in LLMs. We highlight the latent safety risks that arise as reasoning capabilities improve, shedding light on previously overlooked vulnerabilities. At the same time, we explore how reasoning itself can be leveraged to enhance safety, uncovering potential mitigation strategies. By examining both the risks and opportunities in reasoning-driven LLM safety, our study provides valuable insights for developing models that are not only more capable but also more trustworthy in real-world deployments.

The rapid advent of machine learning (ML) and artificial intelligence (AI) has catalyzed major transformations in chemistry, yet the application of these methods to spectroscopic and spectrometric data, referred to as Spectroscopy Machine Learning (SpectraML), remains relatively underexplored. Modern spectroscopic techniques (MS, NMR, IR, Raman, UV-Vis) generate an ever-growing volume of high-dimensional data, creating a pressing need for automated and intelligent analysis beyond traditional expert-based workflows. In this survey, we provide a unified review of SpectraML, systematically examining state-of-the-art approaches for both forward tasks (molecule-to-spectrum prediction) and inverse tasks (spectrum-to-molecule inference). We trace the historical evolution of ML in spectroscopy, from early pattern recognition to the latest foundation models capable of advanced reasoning, and offer a taxonomy of representative neural architectures, including graph-based and transformer-based methods. Addressing key challenges such as data quality, multimodal integration, and computational scalability, we highlight emerging directions such as synthetic data generation, large-scale pretraining, and few- or zero-shot learning. To foster reproducible research, we also release an open-source repository containing recent papers and their corresponding curated datasets (https://github.com/MINE-Lab-ND/SpectrumML_Survey_Papers). Our survey serves as a roadmap for researchers, guiding progress at the intersection of spectroscopy and AI.

While deep generative models~(DGMs) have demonstrated remarkable success in capturing complex data distributions, they consistently fail to learn constraints that encode domain knowledge and thus require constraint integration. Existing solutions to this challenge have primarily relied on heuristic methods and often ignore the underlying data distribution, harming the generative performance. In this work, we propose a probabilistically sound approach for enforcing the hard constraints into DGMs to generate constraint-compliant and realistic data. This is achieved by our proposed gradient estimators that allow the constrained distribution, the data distribution conditioned on constraints, to be differentiably learned. We carry out extensive experiments with various DGM model architectures over five image datasets and three scientific applications in which domain knowledge is governed by linear equality constraints. We validate that the standard DGMs almost surely generate data violating the constraints. Among all the constraint integration strategies, ours not only guarantees the satisfaction of constraints in generation but also archives superior generative performance than the other methods across every benchmark.

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of physics and chemistry, which constrains their generalization capabilities. To address this challenge, we introduce a novel self-supervised approach termed Equivariant Masked Position Prediction (EMPP), grounded in intramolecular potential and force theory. Unlike conventional attribute masking techniques, EMPP formulates a nuanced position prediction task that is more well-defined and enhances the learning of quantum mechanical features. EMPP also bypasses the approximation of the Gaussian mixture distribution commonly used in denoising methods, allowing for more accurate acquisition of physical properties. Experimental results indicate that EMPP significantly enhances performance of advanced molecular architectures, surpassing state-of-the-art self-supervised approaches. Graph neural networks (GNNs) have found widespread application in computational chemistry. However, unlike other fields such as natural language processing (NLP), the limited availability of molecular data hampers the development of GNNs in this domain. For example, one of the largest molecular dataset, OC20 (Chanussot et al., 2021), contains only 1.38 million samples, and collecting more molecular data with ab initio calculations is both challenging and expensive. To address this limitation, molecular self-supervised learning has gained increasing attention. This approach enables molecular GNNs to learn more general physical and chemical knowledge, enhancing performance in various computational chemistry tasks, such as drug discovery (Hasselgren & Oprea, 2024) and catalyst design (Chanussot et al., 2021). Current self-supervised methods for molecular learning contain two mainstream categories: masking and denoising. Masking methods (Hu et al., 2020; Hou et al., 2022; Inae et al., 2023) adapt the concept of masked token prediction from natural language processing (NLP) to graph learning, where graph information, such as node attribute, is masked instead of token. However, there are two major limitations: underdetermined reconstruction and lack of deep quantum mechanical (QM) insight.

Growing concerns about climate change and sustainability are driving manufacturers to take significant steps toward reducing their carbon footprints. For these manufacturers, a first step towards this goal is to identify the environmental impact of the individual components of their products. We propose a system leveraging large language models (LLMs) to automatically map components from manufacturer Bills of Materials (BOMs) to Life Cycle Assessment (LCA) database entries by using LLMs to expand on available component information. Our approach reduces the need for manual data processing, paving the way for more accessible sustainability practices.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

In this study, we propose Explainable Multimodal Machine Learning (EMML), which integrates the analysis of diverse data types (multimodal data) using factor analysis for feature extraction with Explainable AI (XAI), for carbon nanotube (CNT) fibers prepared from aqueous dispersions. This method is a powerful approach to elucidate the mechanisms governing material properties, where multi-stage fabrication conditions and multiscale structures have complex influences. Thus, in our case, this approach helps us understand how different processing steps and structures at various scales impact the final properties of CNT fibers. The analysis targeted structures ranging from the nanoscale to the macroscale, including aggregation size distributions of CNT dispersions and the effective length of CNTs. Furthermore, because some types of data were difficult to interpret using standard methods, challenging-to-interpret distribution data were analyzed using Negative Matrix Factorization (NMF) for extracting key features that determine the outcome. Contribution analysis with SHapley Additive exPlanations (SHAP) demonstrated that small, uniformly distributed aggregates are crucial for improving fracture strength, while CNTs with long effective lengths are significant factors for enhancing electrical conductivity. The analysis also identified thresholds and trends for these key factors to assist in defining the conditions needed to optimize CNT fiber properties. EMML is not limited to CNT fibers but can be applied to the design of other materials derived from nanomaterials, making it a useful tool for developing a wide range of advanced materials. This approach provides a foundation for advancing data-driven materials research.

Large Language Models (LLMs) have shown significant capability across various tasks, with their real-world effectiveness often driven by prompt design. While recent research has focused on optimizing prompt content, the role of prompt formatting, a critical but often overlooked dimension, has received limited systematic investigation. In this paper, we introduce Content-Format Integrated Prompt Optimization (CFPO), an innovative methodology that jointly optimizes both prompt content and formatting through an iterative refinement process. CFPO leverages natural language mutations to explore content variations and employs a dynamic format exploration strategy that systematically evaluates diverse format options. Our extensive evaluations across multiple tasks and open-source LLMs demonstrate that CFPO demonstrates measurable performance improvements compared to content-only optimization methods. This highlights the importance of integrated content-format optimization and offers a practical, model-agnostic approach to enhancing LLM performance. Code is available at https://github.com/HenryLau7/CFPO.

Hard computing generally deals with precise data, which provides ideal solutions to problems. However, in the civil engineering field, amongst other disciplines, that is not always the case as real-world systems are continuously changing. Here lies the need to explore soft computing methods and artificial intelligence to solve civil engineering shortcomings. The integration of advanced computational models, including Artificial Neural Networks (ANNs), Fuzzy Logic, Genetic Algorithms (GAs), and Probabilistic Reasoning, has revolutionized the domain of civil engineering. These models have significantly advanced diverse sub-fields by offering innovative solutions and improved analysis capabilities. Sub-fields such as: slope stability analysis, bearing capacity, water quality and treatment, transportation systems, air quality, structural materials, etc. ANNs predict non-linearities and provide accurate estimates. Fuzzy logic uses an efficient decision-making process to provide a more precise assessment of systems. Lastly, while GAs optimizes models (based on evolutionary processes) for better outcomes, probabilistic reasoning lowers their statistical uncertainties.

Lightweight, durable textile-based inflatable soft actuators are widely used in soft robotics, particularly for wearable robots in rehabilitation and in enhancing human performance in demanding jobs. Fabricating these actuators typically involves multiple steps: heat-sealable fabrics are fused with a heat press, and non-stick masking layers define internal chambers. These layers must be carefully removed post-fabrication, often making the process labor-intensive and prone to errors. To address these challenges and improve the accuracy and performance of inflatable actuators, we introduce the Weld n'Cut platform-an open-source, automated manufacturing process that combines ultrasonic welding for fusing textile layers with an oscillating knife for precise cuts, enabling the creation of complex inflatable structures. We demonstrate the machine's performance across various materials and designs with arbitrarily complex geometries.