As the volume of publicly available data continues to grow, researchers face the challenge of limited diversity in benchmarking machine learning tasks. Although thousands of datasets are available in public repositories, the sheer abundance often complicates the search for suitable data, leaving many valuable datasets underexplored. This situation is further amplified by the fact that, despite longstanding advocacy for improving data curation quality, current solutions remain prohibitively time-consuming and resource-intensive. In this paper, we propose a novel approach that combines intelligent agents with retrieval augmented generation to automate data analysis, dataset curation and indexing at scale. Our system leverages multiple agents to analyze raw, unstructured data across public repositories, generating dataset reports and interactive visual indexes that can be easily explored. We demonstrate that our approach results in more detailed dataset descriptions, higher hit rates and greater diversity in dataset retrieval tasks. Additionally, we show that the dataset reports generated by our method can be leveraged by other machine learning models to improve the performance on specific tasks, such as improving the accuracy and realism of synthetic data generation. By streamlining the process of transforming raw data into machine-learning-ready datasets, our approach enables researchers to better utilize existing data resources.

This white paper, developed through close collaboration between IBM Research and UIUC researchers within the IIDAI Institute, envisions transforming hybrid cloud systems to meet the growing complexity of AI workloads through innovative, full-stack co-design approaches, emphasizing usability, manageability, affordability, adaptability, efficiency, and scalability. By integrating cutting-edge technologies such as generative and agentic AI, cross-layer automation and optimization, unified control plane, and composable and adaptive system architecture, the proposed framework addresses critical challenges in energy efficiency, performance, and cost-effectiveness. Incorporating quantum computing as it matures will enable quantum-accelerated simulations for materials science, climate modeling, and other high-impact domains. Collaborative efforts between academia and industry are central to this vision, driving advancements in foundation models for material design and climate solutions, scalable multimodal data processing, and enhanced physics-based AI emulators for applications like weather forecasting and carbon sequestration. Research priorities include advancing AI agentic systems, LLM as an Abstraction (LLMaaA), AI model optimization and unified abstractions across heterogeneous infrastructure, end-to-end edge-cloud transformation, efficient programming model, middleware and platform, secure infrastructure, application-adaptive cloud systems, and new quantum-classical collaborative workflows. These ideas and solutions encompass both theoretical and practical research questions, requiring coordinated input and support from the research community. This joint initiative aims to establish hybrid clouds as secure, efficient, and sustainable platforms, fostering breakthroughs in AI-driven applications and scientific discovery across academia, industry, and society.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains. Our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

Existing deep learning models applied to reaction prediction in organic chemistry can reach high levels of accuracy (> 90% for Natural Language Processing-based ones). With no chemical knowledge embedded than the information learnt from reaction data, the quality of the data sets plays a crucial role in the performance of the prediction models. While human curation is prohibitively expensive, the need for unaided approaches to remove chemically incorrect entries from existing data sets is essential to improve artificial intelligence models' performance in synthetic chemistry tasks. Here we propose a machine learning-based, unassisted approach to remove chemically wrong entries from chemical reaction collections. We applied this method to the collection of chemical reactions Pistachio and to an open data set, both extracted from USPTO (United States Patent Office) patents. Our results show an improved prediction quality for models trained on the cleaned and balanced data sets. For the retrosynthetic models, the round-trip accuracy metric grows by 13 percentage points and the value of the cumulative Jensen Shannon divergence decreases by 30% compared to its original record. The coverage remains high with 97%, and the value of the class-diversity is not affected by the cleaning. The proposed strategy is the first unassisted rule-free technique to address automatic noise reduction in chemical data sets.

Biochemical methods that measure affinity and biophysical methods that describe the interaction in atomistic level detail have provided valuable information toward a mechanistic explanation for bimolecular recognition [1]. However, more often than not, compounds with drug potential are discovered serendipitously or by phenotypic drug discovery [2] since this highly specific interaction is still difficult to predict [3]. Protein structure based computational strategies such as docking [4], ultra-large library docking for discovering new chemotypes [5], and molecular dynamics simulations [4] or ligand based strategies such as quantitative structure-activity relationship (QSAR) [6, 7], and molecular similarity [8] have been powerful at narrowing down the list of compounds to be tested experimentally. With the increase in available data, machine learning and deep learning architectures are also starting to play a significant role in cheminformatics and drug discovery [9]. These approaches often require extensive computational resources or they are limited by the availability of 3D information. On the other hand, text based representations of biochemical entities are more readily available as evidenced by the 19,588 biomolecular complexes (3D structures) in PDB-Bind [10] (accessed on Nov 13, 2019) compared with 561,356 (manually annotated and reviewed) protein sequences in Uniprot [11] (accessed on Nov 13, 2019) or 97 million compounds in Pubchem [12] (accessed on Nov 13, 2019). The advances in natural language processing (NLP) methodologies make processing of text based representations of biomolecules an area of intense research interest. The discipline of natural language processing (NLP) comprises a variety of methods that explore a large amount of textual data in order to bring unstructured, latent (or hidden) knowledge to the fore [13]. Advances in this field are beneficial for tasks that use language (textual data) to build insight.

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce new metrics (coverage, class diversity, round-trip accuracy and Jensen-Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is constructed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and academic exams. Overall, the frameworks has a very good performance with few weaknesses due to the bias induced during the training process. The use of the newly introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks through focusing on the performance of the single-step model only.

There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a novel way of tokenization, which is arbitrarily extensible with reaction information. With this approach, we demonstrate results superior to the state-of-the-art solution by a significant margin on the top-1 accuracy. Specifically, our approach achieves an accuracy of 80.1% without relying on auxiliary knowledge such as reaction templates. Also, 66.4% accuracy is reached on a larger and noisier dataset.