Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields, including drug discovery and materials science. Existing studies adopt a global alignment approach to learn the knowledge from different modalities. These global alignment approaches fail to capture fine-grained information, such as molecular fragments and their corresponding textual description, which is crucial for downstream tasks. Furthermore, it is incapable to model such information using a similar global alignment strategy due to data scarcity of paired local part annotated data from existing datasets. In this paper, we propose Atomas, a multi-modal molecular representation learning framework to jointly learn representations from SMILES string and text. We design a Hierarchical Adaptive Alignment model to concurrently learn the fine-grained fragment correspondence between two modalities and align these representations of fragments in three levels. Additionally, Atomas's end-to-end training framework incorporates the tasks of understanding and generating molecule, thereby supporting a wider range of downstream tasks. In the retrieval task, Atomas exhibits robust generalization ability and outperforms the baseline by 30.8% of recall@1 on average. In the generation task, Atomas achieves state-of-the-art results in both molecule captioning task and molecule generation task. Moreover, the visualization of the Hierarchical Adaptive Alignment model further confirms the chemical significance of our approach. Our codes can be found at https://anonymous.4open.science/r/Atomas-03C3.

In this paper, we explore the optimization of metal recycling with a focus on real-time differentiation between alloys of copper and aluminium. Spectral data, obtained through Prompt Gamma Neutron Activation Analysis (PGNAA), is utilized for classification. The study compares data from two detectors, cerium bromide (CeBr$_{3}$) and high purity germanium (HPGe), considering their energy resolution and sensitivity. We test various data generation, preprocessing, and classification methods, with Maximum Likelihood Classifier (MLC) and Conditional Variational Autoencoder (CVAE) yielding the best results. The study also highlights the impact of different detector types on classification accuracy, with CeBr$_{3}$ excelling in short measurement times and HPGe performing better in longer durations. The findings suggest the importance of selecting the appropriate detector and methodology based on specific application requirements.

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts in which enzymes and the chemical reactions they catalyze are annotated using identifiers from the UniProt Knowledgebase (UniProtKB) and the ontology of Chemical Entities of Biological Interest (ChEBI). We show that fine-tuning pre-trained language models with EnzChemRED can significantly boost their ability to identify mentions of proteins and chemicals in text (Named Entity Recognition, or NER) and to extract the chemical conversions in which they participate (Relation Extraction, or RE), with average F1 score of 86.30% for NER, 86.66% for RE for chemical conversion pairs, and 83.79% for RE for chemical conversion pairs and linked enzymes. We combine the best performing methods after fine-tuning using EnzChemRED to create an end-to-end pipeline for knowledge extraction from text and apply this to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea. The EnzChemRED corpus is freely available at https://ftp.expasy.org/databases/rhea/nlp/.

This paper presents a study on the integration of domain-specific knowledge in prompt engineering to enhance the performance of large language models (LLMs) in scientific domains. A benchmark dataset is curated to encapsulate the intricate physical-chemical properties of small molecules, their drugability for pharmacology, alongside the functional attributes of enzymes and crystal materials, underscoring the relevance and applicability across biological and chemical domains.The proposed domain-knowledge embedded prompt engineering method outperforms traditional prompt engineering strategies on various metrics, including capability, accuracy, F1 score, and hallucination drop. The effectiveness of the method is demonstrated through case studies on complex materials including the MacMillan catalyst, paclitaxel, and lithium cobalt oxide. The results suggest that domain-knowledge prompts can guide LLMs to generate more accurate and relevant responses, highlighting the potential of LLMs as powerful tools for scientific discovery and innovation when equipped with domain-specific prompts. The study also discusses limitations and future directions for domain-specific prompt engineering development.

For robot arms to perform everyday tasks in unstructured environments, these robots must be able to manipulate a diverse range of objects. Today's robots often grasp objects with either soft grippers or rigid end-effectors. However, purely rigid or purely soft grippers have fundamental limitations: soft grippers struggle with irregular, heavy objects, while rigid grippers often cannot grasp small, numerous items. In this paper we therefore introduce RISOs, a mechanics and controls approach for unifying traditional RIgid end-effectors with a novel class of SOft adhesives. When grasping an object, RISOs can use either the rigid end-effector (pinching the item between non-deformable fingers) and/or the soft materials (attaching and releasing items with switchable adhesives). This enhances manipulation capabilities by combining and decoupling rigid and soft mechanisms. With RISOs robots can perform grasps along a spectrum from fully rigid, to fully soft, to rigid-soft, enabling real time object manipulation across a 1 million times range in weight (from 2 mg to 2 kg). To develop RISOs we first model and characterize the soft switchable adhesives. We then mount sheets of these soft adhesives on the surfaces of rigid end-effectors, and develop control strategies that make it easier for robot arms and human operators to utilize RISOs. The resulting RISO grippers were able to pick-up, carry, and release a larger set of objects than existing grippers, and participants also preferred using RISO. Overall, our experimental and user study results suggest that RISOs provide an exceptional gripper range in both capacity and object diversity. See videos of our user studies here: https://youtu.be/du085R0gPFI

Transition states (TSs) are transient structures that are key in understanding reaction mechanisms and designing catalysts but challenging to be captured in experiments. Alternatively, many optimization algorithms have been developed to search for TSs computationally. Yet the cost of these algorithms driven by quantum chemistry methods (usually density functional theory) is still high, posing challenges for their applications in building large reaction networks for reaction exploration. Here we developed React-OT, an optimal transport approach for generating unique TS structures from reactants and products. React-OT generates highly accurate TS structures with a median structural root mean square deviation (RMSD) of 0.053{\AA} and median barrier height error of 1.06 kcal/mol requiring only 0.4 second per reaction. The RMSD and barrier height error is further improved by roughly 25% through pretraining React-OT on a large reaction dataset obtained with a lower level of theory, GFN2-xTB. We envision the great accuracy and fast inference of React-OT useful in targeting TSs when exploring chemical reactions with unknown mechanisms.

This paper examines the impact of Generative Artificial Intelligence (GenAI) tools like ChatGPT on the creation and consumption of terminological definitions. From the terminologist's point of view, the strategic use of GenAI tools can streamline the process of crafting definitions, reducing both time and effort, while potentially enhancing quality. GenAI tools enable AI-assisted terminography, notably post-editing terminography, where the machine produces a definition that the terminologist then corrects or refines. However, the potential of GenAI tools to fulfill all the terminological needs of a user, including term definitions, challenges the very existence of terminological definitions and resources as we know them. Unlike terminological definitions, GenAI tools can describe the knowledge activated by a term in a specific context. However, a main drawback of these tools is that their output can contain errors. For this reason, users requiring reliability will likely still resort to terminological resources for definitions. Nevertheless, with the inevitable integration of AI into terminology work, the distinction between human-created and AI-created content will become increasingly blurred.

Hyperspectral imaging technology has a wide range of applications, including forest management, mineral resource exploration, and Earth surface monitoring. Endmember extraction of hyperspectral images is a key step in leveraging this technology for applications. It aims to identifying the spectral signatures of materials, i.e., the major components in the observed scenes. Theoretically speaking, Hottopixx methods should be effective on problems involving extracting endmembers from hyperspectral images. Yet, these methods are challenging to perform in practice, due to high computational costs. They require us to solve LP problems, called Hottopixx models, whose size grows quadratically with the number of pixels in the image. It is thus still unclear as to whether they are actually effective or not. This study clarifies this situation. We propose an efficient and effective implementation of Hottopixx. Our implementation follows the framework of column generation, which is known as a classical but powerful means of solving large-scale LPs. We show in experiments that our implementation is applicable to the endmember extraction from real hyperspectral images and can provide estimations of endmember signatures with higher accuracy than the existing methods can.

In the steel production domain, recycling ferrous scrap is essential for environmental and economic sustainability, as it reduces both energy consumption and greenhouse gas emissions. However, the classification of scrap materials poses a significant challenge, requiring advancements in automation technology. Additionally, building trust among human operators is a major obstacle. Traditional approaches often fail to quantify uncertainty and lack clarity in model decision-making, which complicates acceptance. In this article, we describe how conformal prediction can be employed to quantify uncertainty and add robustness in scrap classification. We have adapted the Split Conformal Prediction technique to seamlessly integrate with state-of-the-art computer vision models, such as the Vision Transformer (ViT), Swin Transformer, and ResNet-50, while also incorporating Explainable Artificial Intelligence (XAI) methods. We evaluate the approach using a comprehensive dataset of 8147 images spanning nine ferrous scrap classes. The application of the Split Conformal Prediction method allowed for the quantification of each model's uncertainties, which enhanced the understanding of predictions and increased the reliability of the results. Specifically, the Swin Transformer model demonstrated more reliable outcomes than the others, as evidenced by its smaller average size of prediction sets and achieving an average classification accuracy exceeding 95%. Furthermore, the Score-CAM method proved highly effective in clarifying visual features, significantly enhancing the explainability of the classification decisions.

Motivation: Retrosynthesis planning poses a formidable challenge in the organic chemical industry. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. Results: This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.