nach0: multimodal natural and chemical languages foundation model

A Perspective on Foundation Models in Chemistry

Foundation models are an emerging paradigm in artificial intelligence (AI), with successful examples like ChatGPT transforming daily workflows. Generally, foundation models are large-scale, pretrained models capable of adapting to various downstream tasks by leveraging extensive data and model scaling. Their success has inspired researchers to develop foundation models for a wide range of chemical challenges, from materials discovery to understanding structure-property relationships, areas where conventional machine learning (ML) models often face limitations. In addition, foundation models hold promise for addressing persistent ML challenges in chemistry, such as data scarcity and poor generalization. In this perspective, we review recent progress in the development of foundation models in chemistry across applications of varying scope. We also discuss emerging trends and provide an outlook on promising approaches for advancing foundation models in chemistry.

Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem

Deep learning has revolutionized difficult tasks in chemistry and biology, yet existing language models often treat these domains separately, relying on concatenated architectures and independently pretrained weights. These approaches fail to fully exploit the shared atomic foundations of molecular and protein sequences. Here, we introduce T5ProtChem, a unified model based on the T5 architecture, designed to simultaneously process molecular and protein sequences. Using a new pretraining objective, ProtiSMILES, T5ProtChem bridges the molecular and protein domains, enabling efficient, generalizable protein-chemical modeling. The model achieves a state-of-the-art performance in tasks such as binding affinity prediction and reaction prediction, while having a strong performance in protein function prediction. Additionally, it supports novel applications, including covalent binder classification and sequence-level adduct prediction. These results demonstrate the versatility of unified language models for drug discovery, protein engineering, and other interdisciplinary efforts in computational biology and chemistry.

Cross-disciplinary perspectives on the potential for artificial intelligence across chemistry

From accelerating simulations and exploring chemical space, to experimental planning and integrating automation within experimental labs, artificial intelligence (AI) is changing the landscape of chemistry. We are seeing a significant increase in the number of publications leveraging these powerful data-driven insights and models to accelerate all aspects of chemical research. For example, how we represent molecules and materials to computer algorithms for predictive and generative models, as well as the physical mechanisms by which we perform experiments in the lab for automation. Here, we present ten diverse perspectives on the impact of AI coming from those with a range of backgrounds from experimental chemistry, computational chemistry, computer science, engineering and across different areas of chemistry, including drug discovery, catalysis, chemical automation, chemical physics, materials chemistry. The ten perspectives presented here cover a range of themes, including AI for computation, facilitating discovery, supporting experiments, and enabling technologies for transformation. We highlight and discuss imminent challenges and ways in which we are redefining problems to accelerate the impact of chemical research via AI.

Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools

Antibodies play a crucial role in defending the human body against diseases, including life-threatening conditions like cancer. They mediate immune responses against foreign antigens and, in some cases, self-antigens. Over time, antibody-based technologies have evolved from monoclonal antibodies (mAbs) to chimeric antigen receptor T cells (CAR-T cells), significantly impacting biotechnology, diagnostics, and therapeutics. Although these advancements have enhanced therapeutic interventions, the integration of artificial intelligence (AI) is revolutionizing antibody design and optimization. This review explores recent AI advancements, including large language models (LLMs), diffusion models, and generative AI-based applications, which have transformed antibody discovery by accelerating de novo generation, enhancing immune response precision, and optimizing therapeutic efficacy. Through advanced data analysis, AI enables the prediction and design of antibody sequences, 3D structures, complementarity-determining regions (CDRs), paratopes, epitopes, and antigen-antibody interactions. These AI-powered innovations address longstanding challenges in antibody development, significantly improving speed, specificity, and accuracy in therapeutic design. By integrating computational advancements with biomedical applications, AI is driving next-generation cancer therapies, transforming precision medicine, and enhancing patient outcomes.

An automatic end-to-end chemical synthesis development platform powered by large language models

The rapid emergence of large language model (LLM) technology presents promising opportunities to facilitate the development of synthetic reactions. In this work, we leveraged the power of GPT-4 to build an LLM-based reaction development framework (LLM-RDF) to handle fundamental tasks involved throughout the chemical synthesis development. LLM-RDF comprises six specialized LLM-based agents, including Literature Scouter, Experiment Designer, Hardware Executor, Spectrum Analyzer, Separation Instructor, and Result Interpreter, which are pre-prompted to accomplish the designated tasks. A web application with LLM-RDF as the backend was built to allow chemist users to interact with automated experimental platforms and analyze results via natural language, thus, eliminating the need for coding skills and ensuring accessibility for all chemists. We demonstrated the capabilities of LLM-RDF in guiding the end-to-end synthesis development process for the copper/TEMPO catalyzed aerobic alcohol oxidation to aldehyde reaction, including literature search and information extraction, substrate scope and condition screening, reaction kinetics study, reaction condition optimization, reaction scale-up and product purification. Furthermore, LLM-RDF's broader applicability and versability was validated on various synthesis tasks of three distinct reactions (SNAr reaction, photoredox C-C cross-coupling reaction, and heterogeneous photoelectrochemical reaction).

Machine learning predicts upper secondary education dropout as early as the end of primary school

Education plays a pivotal role in alleviating poverty, driving economic growth, and empowering individuals, thereby significantly influencing societal and personal development. However, the persistent issue of school dropout poses a significant challenge, with its effects extending beyond the individual. While previous research has employed machine learning for dropout classification, these studies often suffer from a short-term focus, relying on data collected only a few years into the study period. This study expanded the modeling horizon by utilizing a 13-year longitudinal dataset, encompassing data from kindergarten to Grade 9. Our methodology incorporated a comprehensive range of parameters, including students' academic and cognitive skills, motivation, behavior, well-being, and officially recorded dropout data. The machine learning models developed in this study demonstrated notable classification ability, achieving a mean area under the curve (AUC) of 0.61 with data up to Grade 6 and an improved AUC of 0.65 with data up to Grade 9. Further data collection and independent correlational and causal analyses are crucial. In future iterations, such models may have the potential to proactively support educators' processes and existing protocols for identifying at-risk students, thereby potentially aiding in the reinvention of student retention and success strategies and ultimately contributing to improved educational outcomes.