Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}.

The advancements in precision agriculture are vital to support the increasing demand for global food supply. Precision spot spraying is a major step towards reducing chemical usage for pest and weed control in agriculture. A novel spot spraying algorithm that autonomously detects weeds and performs trajectory planning for the sprayer nozzle has been proposed. Furthermore, this research introduces a vision-based autonomous navigation system that operates through the detected crop row, effectively synchronizing with an autonomous spraying algorithm. This proposed system is characterized by its cost effectiveness that enable the autonomous spraying of herbicides onto detected weeds.

Solvation free energy, and notably hydration free energy, is generally recognized as a fundamental thermodynamic quantity of interest in computational chemistry. Defined as the work done when transferring a molecule from the gas phase to the solution (water in the case of hydration free energy), it enables the computation of several key physicochemical properties of molecules, such as solubility, partition coefficients, activity coefficients, and binding free energies in solutions [1, 2]. These properties are of great importance to the pharmaceutical, environmental, and materials sciences [3-9], prompting the organization of blind prediction SAMPL challenges [10-12] with hydration free energy as one of the main targets. In addition, Mobley et al. compiled and curated a FreeSolv database of experimentally measured hydration free energies for small neutral molecules in water [13, 14]. A wide spectrum of methods is available to calculate solvation free energy, ranging from traditional approaches such as continuum solvation models [15, 16] to recent machine learning (ML) algorithms [17-26] and their combinations [27-29]. The alchemical methods with Molecular Dynamics (MD) simulations [14, 30, 31] are typically assumed to be highly accurate but computationally expensive [32, 33]. However, both the fidelity and the efficiency highly depend on the explicitly treated degrees of freedom and the employed potential energy model.

Fine-tuning on task-specific question-answer pairs is a predominant method for enhancing the performance of instruction-tuned large language models (LLMs) on downstream tasks. However, in certain specialized domains, such as healthcare or harmless content generation, it is nearly impossible to obtain a large volume of high-quality data that matches the downstream distribution. To improve the performance of LLMs in data-scarce domains with domain-mismatched data, we re-evaluated the Transformer architecture and discovered that not all parameter updates during fine-tuning contribute positively to downstream performance. Our analysis reveals that within the self-attention and feed-forward networks, only the fine-tuned attention parameters are particularly beneficial when the training set's distribution does not fully align with the test set. Based on this insight, we propose an effective inference-time intervention method: Training All parameters but Inferring with only Attention (\trainallInfAttn). We empirically validate \trainallInfAttn using two general instruction-tuning datasets and evaluate it on seven downstream tasks involving math, reasoning, and knowledge understanding across LLMs of different parameter sizes and fine-tuning techniques. Our comprehensive experiments demonstrate that \trainallInfAttn achieves superior improvements compared to both the fully fine-tuned model and the base model in most scenarios, with significant performance gains. The high tolerance of \trainallInfAttn to data mismatches makes it resistant to jailbreaking tuning and enhances specialized tasks using general data.

Yoshimura origami is a classical folding pattern that has inspired many deployable structure designs. Its applications span from space exploration, kinetic architectures, and soft robots to even everyday household items. However, despite its wide usage, Yoshimura has been fixated on a set of design constraints to ensure its flat-foldability. Through extensive kinematic analysis and prototype tests, this study presents a new Yoshimura that intentionally defies these constraints. Remarkably, one can impart a unique meta-stability by using the Golden Ratio angle to define the triangular facets of a generalized Yoshimura. As a result, when its facets are strategically popped out, a ``Golden Ratio Yoshimura'' boom with $m$ modules can be theoretically reconfigured into $8^m$ geometrically unique and load-bearing shapes. This result not only challenges the existing design norms but also opens up a new avenue to create deployable and versatile structural systems.

The increasing popularity of machine learning (ML) in catalysis has spurred interest in leveraging these techniques to enhance catalyst design. Our study aims to bridge the gap between physics-based studies and data-driven methodologies by integrating ML techniques with eXplainable AI (XAI). Specifically, we employ two XAI techniques: Post-hoc XAI analysis and Symbolic Regression. These techniques help us unravel the correlation between adsorption energy and the properties of the adsorbate-catalyst system. Leveraging a large dataset such as the Open Catalyst Dataset (OC20), we employ a combination of shallow ML techniques and XAI methodologies. Our investigation involves utilizing multiple shallow machine learning techniques to predict adsorption energy, followed by post-hoc analysis for feature importance, inter-feature correlations, and the influence of various feature values on the prediction of adsorption energy. The post-hoc analysis reveals that adsorbate properties exert a greater influence than catalyst properties in our dataset. The top five features based on higher Shapley values are adsorbate electronegativity, the number of adsorbate atoms, catalyst electronegativity, effective coordination number, and the sum of atomic numbers of the adsorbate molecule. There is a positive correlation between catalyst and adsorbate electronegativity with the prediction of adsorption energy. Additionally, symbolic regression yields results consistent with SHAP analysis. It deduces a mathematical relationship indicating that the square of the catalyst electronegativity is directly proportional to the adsorption energy. These consistent correlations resemble those derived from physics-based equations in previous research. Our work establishes a robust framework that integrates ML techniques with XAI, leveraging large datasets like OC20 to enhance catalyst design through model explainability.

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. Yet, addressing complex urban and environmental management problems normally requires in-depth domain science and informatics expertise. This expertise is essential for deriving data and simulation-driven for informed decision support. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs). By adopting ChatGPT API as the reasoning core, we outline an integrated workflow that encompasses natural language processing, methontology-based prompt tuning, and transformers. This workflow automates the creation of scenario-based ontology using existing research articles and technical manuals of urban datasets and simulations. The outcomes of our methodology are knowledge graphs in widely adopted ontology languages (e.g., OWL, RDF, SPARQL). These facilitate the development of urban decision support systems by enhancing the data and metadata modeling, the integration of complex datasets, the coupling of multi-domain simulation models, and the formulation of decision-making metrics and workflow. The feasibility of our methodology is evaluated through a comparative analysis that juxtaposes our AI-generated ontology with the well-known Pizza Ontology employed in tutorials for popular ontology software (e.g., prot\'eg\'e). We close with a real-world case study of optimizing the complex urban system of multi-modal freight transportation by generating anthologies of various domain data and simulations to support informed decision-making.

Landslide susceptibility mapping (LSM) is crucial for identifying high-risk areas and informing prevention strategies. This study investigates the interpretability of statistical, machine learning (ML), and deep learning (DL) models in predicting landslide susceptibility. This is achieved by incorporating various relevant interpretation methods and two types of input factors: a comprehensive set of 19 contributing factors that are statistically relevant to landslides, as well as a dedicated set of 9 triggering factors directly associated with triggering landslides. Given that model performance is a crucial metric in LSM, our investigations into interpretability naturally involve assessing and comparing LSM accuracy across different models considered. In our investigation, the convolutional neural network model achieved the highest accuracy (0.8447 with 19 factors; 0.8048 with 9 factors), while Extreme Gradient Boosting and Support Vector Machine also demonstrated strong predictive capabilities, outperforming conventional statistical models. These findings indicate that DL and sophisticated ML algorithms can effectively capture the complex relationships between input factors and landslide occurrence. However, the interpretability of predictions varied among different models, particularly when using the broader set of 19 contributing factors. Explanation methods like SHAP, LIME, and DeepLIFT also led to variations in interpretation results. Using a comprehensive set of 19 contributing factors improved prediction accuracy but introduced complexities and inconsistency in model interpretations. Focusing on a dedicated set of 9 triggering factors sacrificed some predictive power but enhanced interpretability, as evidenced by more consistent key factors identified across various models and alignment with the findings of field investigation reports....

The startling success of ChatGPT and other large language models (LLMs) using transformer-based generative neural network architecture in applications such as natural language processing and image synthesis has many researchers excited about potential opportunities in process systems engineering (PSE). The almost human-like performance of LLMs in these areas is indeed very impressive, surprising, and a major breakthrough. Their capabilities are very useful in certain tasks, such as writing first drafts of documents, code writing assistance, text summarization, etc. However, their success is limited in highly scientific domains as they cannot yet reason, plan, or explain due to their lack of in-depth domain knowledge. This is a problem in domains such as chemical engineering as they are governed by fundamental laws of physics and chemistry (and biology), constitutive relations, and highly technical knowledge about materials, processes, and systems. Although purely data-driven machine learning has its immediate uses, the long-term success of AI in scientific and engineering domains would depend on developing hybrid AI systems that use first principles and technical knowledge effectively. We call these hybrid AI systems Large Knowledge Models (LKMs), as they will not be limited to only NLP-based techniques or NLP-like applications. In this paper, we discuss the challenges and opportunities in developing such systems in chemical engineering.

Deep learning foundation models are revolutionizing many facets of science by leveraging vast amounts of data to learn general-purpose representations that can be adapted to tackle diverse downstream tasks. Foundation models hold the promise to also transform our ability to model our planet and its subsystems by exploiting the vast expanse of Earth system data. Here we introduce Aurora, a large-scale foundation model of the atmosphere trained on over a million hours of diverse weather and climate data. Aurora leverages the strengths of the foundation modelling approach to produce operational forecasts for a wide variety of atmospheric prediction problems, including those with limited training data, heterogeneous variables, and extreme events. In under a minute, Aurora produces 5-day global air pollution predictions and 10-day high-resolution weather forecasts that outperform state-of-the-art classical simulation tools and the best specialized deep learning models. Taken together, these results indicate that foundation models can transform environmental forecasting.