The task here is to predict the toxicological activity of chemical compounds based on the Tox21 dataset, a benchmark in computational toxicology. After a domain-specific overview of chemical toxicity, we discuss current computational strategies, focusing on machine learning and deep learning. Several architectures are compared in terms of performance, robustness, and interpretability. This research introduces a novel image-based pipeline based on DenseNet121, which processes 2D graphical representations of chemical structures. Additionally, we employ Grad-CAM visualizations, an explainable AI technique, to interpret the model's predictions and highlight molecular regions contributing to toxicity classification. The proposed architecture achieves competitive results compared to traditional models, demonstrating the potential of deep convolutional networks in cheminformatics. Our findings emphasize the value of combining image-based representations with explainable AI methods to improve both predictive accuracy and model transparency in toxicology.

Jackie (short for jack-o'-lantern) owes her unique colors to a mixture of chemical compounds. Breakthroughs, discoveries, and DIY tips sent every weekday. A rare and seasonally-colored lobster is joining spiders, bats, and even some oozing fungi as some of nature's best Halloween ambassadors. Jackie is a calico lobster and the odds of catching a crustacean like this are about one-in-20 million, according to the Marine Science Center outreach coordinator Sierra Munoz. This makes Jackie even more rare than the center's other recent star, Neptune the blue lobster .

Artificial Intelligence algorithms are introduced in this work as a tool to predict the performance of new chemical compounds as alternative propellants for electric propulsion, focusing on predicting their ionisation characteristics and fragmentation patterns. The chemical properties and structure of the compounds are encoded using a chemical fingerprint, and the training datasets are extracted from the NIST WebBook. The AI-predicted ionisation energy and minimum appearance energy have a mean relative error of 6.87% and 7.99%, respectively, and a predicted ion mass with a 23.89% relative error. In the cases of full mass spectra due to electron ionisation, the predictions have a cosine similarity of 0.6395 and align with the top 10 most similar mass spectra in 78% of instances within a 30 Da range.

In this Section, we visualize four "hidden graphs" for each of the

Recently, a novel two-phase framework named mol-infer for inference of chemical compounds with prescribed abstract structures and desired property values has been proposed. The framework mol-infer is primarily based on using mixed integer linear programming (MILP) to simulate the computational process of machine learning methods and describe the necessary and sufficient conditions to ensure such a chemical graph exists. The existing approaches usually first convert the chemical compounds into handcrafted feature vectors to construct prediction functions, but because of the limit on the kinds of descriptors originated from the need for tractability in the MILP formulation, the learning performances on datasets of some properties are not good enough. A lack of good learning performance can greatly lower the quality of the inferred chemical graphs, and thus improving learning performance is of great importance. On the other hand, graph neural networks (GNN) offer a promising machine learning method to directly utilize the chemical graphs as the input, and many existing GNN-based approaches to the molecular property prediction problem have shown that they can enjoy better learning performances compared to the traditional approaches that are based on feature vectors. In this study, we develop a molecular inference framework based on mol-infer, namely mol-infer-GNN, that utilizes GNN as the learning method while keeping the great flexibility originated from the two-layered model on the abstract structure of the chemical graph to be inferred. We conducted computational experiments on the QM9 dataset to show that our proposed GNN model can obtain satisfying learning performances for some properties despite its simple structure, and can infer small chemical graphs comprising up to 20 non-hydrogen atoms within reasonable computational time.

Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only learn from images, despite many screens being inherently multimodal, as they involve both a chemical or genetic perturbation as well as an image-based readout. We hypothesized that incorporating chemical compound structure during self-supervised pre-training could improve learned representations of images in high-throughput microscopy screens. We introduce a representation learning framework, MICON (Molecular-Image Contrastive Learning), that models chemical compounds as treatments that induce counterfactual transformations of cell phenotypes. MICON significantly outperforms classical hand-crafted features such as CellProfiler and existing deep-learning-based representation learning methods in challenging evaluation settings where models must identify reproducible effects of drugs across independent replicates and data-generating centers. We demonstrate that incorporating chemical compound information into the learning process provides consistent improvements in our evaluation setting and that modeling compounds specifically as treatments in a causal framework outperforms approaches that directly align images and compounds in a single representation space. Our findings point to a new direction for representation learning in morphological profiling, suggesting that methods should explicitly account for the multimodal nature of microscopy screening data.

In recent years, machine learning has profoundly reshaped the field of chemistry, facilitating significant advancements across various applications, including the prediction of molecular properties and the generation of molecular structures. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of tasks. However, the prevailing practice of representing chemical compounds in the SMILES format -- used by most datasets and many language models -- presents notable limitations as a training data format. In contrast, chemical fingerprints offer a more physically informed representation of compounds, thereby enhancing their suitability for model training. This study aims to develop a language model that is specifically trained on fingerprints. Furthermore, we introduce a bimodal architecture that integrates this language model with a graph model. Our proposed methodology synthesizes these approaches, utilizing RoBERTa as the language model and employing Graph Isomorphism Networks (GIN), Graph Convolutional Networks (GCN) and Graphormer as graph models. This integration results in a significant improvement in predictive performance compared to conventional strategies for tasks such as Quantitative Structure-Activity Relationship (QSAR) and the prediction of nuclear magnetic resonance (NMR) spectra, among others.

The study of food pairing has evolved beyond subjective expertise with the advent of machine learning. This paper presents FlavorDiffusion, a novel framework leveraging diffusion models to predict food-chemical interactions and ingredient pairings without relying on chromatography. By integrating graph-based embeddings, diffusion processes, and chemical property encoding, FlavorDiffusion addresses data imbalances and enhances clustering quality. Using a heterogeneous graph derived from datasets like Recipe1M and FlavorDB, our model demonstrates superior performance in reconstructing ingredient-ingredient relationships. The addition of a Chemical Structure Prediction (CSP) layer further refines the embedding space, achieving state-of-the-art NMI scores and enabling meaningful discovery of novel ingredient combinations. The proposed framework represents a significant step forward in computational gastronomy, offering scalable, interpretable, and chemically informed solutions for food science.

Recent years have witnessed extensive efforts to enhance Large Language Models (LLMs) across various domains, alongside growing attention to their ethical implications. However, a critical challenge remains largely overlooked: LLMs must balance between rejecting harmful requests for safety and accommodating legitimate ones for utility. This paper presents a Direct Preference Optimization (DPO) based alignment framework that achieves better overall performance by addressing this ethical-utility trade-off, using chemical domain applications as a proof-of-concept. Our alignment pipeline starts with a GPT-assisted three-phase data generation scheme, in which we create LibraChemQA, a chemical question-answering dataset comprising 31.6k triplet instances. By incorporating an innovative balanced seed in the data generation process, our framework systematically considers both legitimate and illegitimate requests. The framework also introduces a rephrasing mechanism for efficient data augmentation that enhances the model's chemical comprehension. We further develop a novel hybrid evaluation scheme with LLM judges for precise assessment of both safety and utility. Experimental results demonstrate our model's substantial improvements in overall performance where both safety and utility are considered - our resulting model, LibraChem, outperforms leading LLMs including Claude-3, GPT-4o, and LLaMA-3 by margins of 13.44%, 7.16%, and 7.10% respectively on our released benchmark.