In biotechnology Raman Spectroscopy is rapidly gaining popularity as a process analytical technology (PAT) that measures cell densities, substrate- and product concentrations. As it records vibrational modes of molecules it provides that information non-invasively in a single spectrum. Typically, partial least squares (PLS) is the model of choice to infer information about variables of interest from the spectra. However, biological processes are known for their complexity where convolutional neural networks (CNN) present a powerful alternative. They can handle non-Gaussian noise and account for beam misalignment, pixel malfunctions or the presence of additional substances. However, they require a lot of data during model training, and they pick up non-linear dependencies in the process variables. In this work, we exploit the additive nature of spectra in order to generate additional data points from a given dataset that have statistically independent labels so that a network trained on such data exhibits low correlations between the model predictions. We show that training a CNN on these generated data points improves the performance on datasets where the annotations do not bear the same correlation as the dataset that was used for model training. This data augmentation technique enables us to reuse spectra as training data for new contexts that exhibit different correlations. The additional data allows for building a better and more robust model. This is of interest in scenarios where large amounts of historical data are available but are currently not used for model training. We demonstrate the capabilities of the proposed method using synthetic spectra of Ralstonia eutropha batch cultivations to monitor substrate, biomass and polyhydroxyalkanoate (PHA) biopolymer concentrations during of the experiments.

Most vision-based tactile sensors use elastomer deformation to infer tactile information, which can not sense some modalities, like temperature. As an important part of human tactile perception, temperature sensing can help robots better interact with the environment. In this work, we propose a novel multimodal vision-based tactile sensor, SATac, which can simultaneously perceive information of temperature, pressure, and shear. SATac utilizes thermoluminescence of strontium aluminate (SA) to sense a wide range of temperatures with exceptional resolution. Additionally, the pressure and shear can also be perceived by analyzing Voronoi diagram. A series of experiments are conducted to verify the performance of our proposed sensor. We also discuss the possible application scenarios and demonstrate how SATac could benefit robot perception capabilities.

Large language models (LLMs), such as GPT4 and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data is associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data is paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graphs (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-attributed graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we discuss the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Anomaly detection (AD) tasks have been solved using machine learning algorithms in various domains and applications. The great majority of these algorithms use normal data to train a residual-based model and assign anomaly scores to unseen samples based on their dissimilarity with the learned normal regime. The underlying assumption of these approaches is that anomaly-free data is available for training. This is, however, often not the case in real-world operational settings, where the training data may be contaminated with an unknown fraction of abnormal samples. Training with contaminated data, in turn, inevitably leads to a deteriorated AD performance of the residual-based algorithms. In this paper we introduce a framework for a fully unsupervised refinement of contaminated training data for AD tasks. The framework is generic and can be applied to any residual-based machine learning model. We demonstrate the application of the framework to two public datasets of multivariate time series machine data from different application fields. We show its clear superiority over the naive approach of training with contaminated data without refinement. Moreover, we compare it to the ideal, unrealistic reference in which anomaly-free data would be available for training. The method is based on evaluating the contribution of individual samples to the generalization ability of a given model, and contrasting the contribution of anomalies with the one of normal samples. As a result, the proposed approach is comparable to, and often outperforms training with normal samples only.

Recent AI research plots a promising future of automatic chemical reactions within the chemistry society. This study proposes Chemist-X, a transformative AI agent that automates the reaction condition recommendation (RCR) task in chemical synthesis with retrieval-augmented generation (RAG) technology. To emulate expert chemists' strategies when solving RCR tasks, Chemist-X utilizes advanced RAG schemes to interrogate online molecular databases and distill critical data from the latest literature database. Further, the agent leverages state-of-the-art computer-aided design (CAD) tools with a large language model (LLM) supervised programming interface. With the ability to utilize updated chemical knowledge and CAD tools, our agent significantly outperforms conventional synthesis AIs confined to the fixed knowledge within its training data. Chemist-X considerably reduces chemists' workload and allows them to focus on more fundamental and creative problems, thereby bringing closer computational techniques and chemical research and making a remarkable leap toward harnessing AI's full capabilities in scientific discovery.

Accurate detection and analysis of traces of persistent organic pollutants in water is important in many areas, including environmental monitoring and food quality control, due to their long environmental stability and potential bioaccumulation. While conventional analysis of organic pollutants requires expensive equipment, surface enhanced Raman spectroscopy (SERS) has demonstrated great potential for accurate detection of these contaminants. However, SERS analytical difficulties, such as spectral preprocessing, denoising, and substrate-based spectral variation, have hindered widespread use of the technique. Here, we demonstrate an approach for predicting the concentration of sample pollutants from messy, unprocessed Raman data using machine learning. Frequency domain transform methods, including the Fourier and Walsh Hadamard transforms, are applied to sets of Raman spectra of three model micropollutants in water (rhodamine 6G, chlorpyrifos, and triclosan), which are then used to train machine learning algorithms. Using standard machine learning models, the concentration of sample pollutants are predicted with more than 80 percent cross-validation accuracy from raw Raman data. cross-validation accuracy of 85 percent was achieved using deep learning for a moderately sized dataset (100 spectra), and 70 to 80 percent cross-validation accuracy was achieved even for very small datasets (50 spectra). Additionally, standard models were shown to accurately identify characteristic peaks via analysis of their importance scores. The approach shown here has the potential to be applied to facilitate accurate detection and analysis of persistent organic pollutants by surface-enhanced Raman spectroscopy.

Conceptual architecture involves a highly creative exploration of novel ideas, often taken from other disciplines as architects consider radical new forms, materials, textures and colors for buildings. While today's generative AI systems can produce remarkable results, they lack the creativity demonstrated for decades by evolutionary algorithms. SCAPE, our proposed tool, combines evolutionary search with generative AI, enabling users to explore creative and good quality designs inspired by their initial input through a simple point and click interface. SCAPE injects randomness into generative AI, and enables memory, making use of the built-in language skills of GPT-4 to vary prompts via text-based mutation and crossover. We demonstrate that compared to DALL-E 3, SCAPE enables a 67% improvement in image novelty, plus improvements in quality and effectiveness of use; we show that in just 3 iterations SCAPE has a 24% image novelty increase enabling effective exploration, plus optimization of images by users. We use more than 20 independent architects to assess SCAPE, who provide markedly positive feedback.

Aqueous solubility is a valuable yet challenging property to predict. Computing solubility using first-principles methods requires accounting for the competing effects of entropy and enthalpy, resulting in long computations for relatively poor accuracy. Data-driven approaches, such as deep learning, offer improved accuracy and computational efficiency but typically lack uncertainty quantification. Additionally, ease of use remains a concern for any computational technique, resulting in the sustained popularity of group-based contribution methods. In this work, we addressed these problems with a deep learning model with predictive uncertainty that runs on a static website (without a server). This approach moves computing needs onto the website visitor without requiring installation, removing the need to pay for and maintain servers. Our model achieves satisfactory results in solubility prediction. Furthermore, we demonstrate how to create molecular property prediction models that balance uncertainty and ease of use. The code is available at https://github.com/ur-whitelab/mol.dev, and the model is usable at https://mol.dev.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Chemical reactivity models are developed to predict chemical reaction outcomes in the form of classification (success/failure) or regression (product yield) tasks. The vast majority of the reported models are trained solely on chemical information such as reactants, products, reagents, and solvents, but not on the details of a synthetic protocol. Herein incorporation of procedural text with the aim to augment the Graphormer reactivity model and improve its accuracy is presented. Two major approaches are used: training an adapter Graphormer model that is provided with a GPT-2-derived latent representation of the text procedure (ReacLLaMA-Adapter) and labeling an unlabeled part of a dataset with the LLaMA 2 model followed by training the Graphormer on an extended dataset (Zero-Shot Labeling ReacLLaMA). Both methodologies enhance the discernment of unpromising reactions, thereby providing more accurate models with improved specificity.