RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with $650$ million parameters pre-trained on $36$ million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

Improving Explainable Object-induced Model through Uncertainty for Automated Vehicles

The rapid evolution of automated vehicles (AVs) has the potential to provide safer, more efficient, and comfortable travel options. However, these systems face challenges regarding reliability in complex driving scenarios. Recent explainable AV architectures neglect crucial information related to inherent uncertainties while providing explanations for actions. To overcome such challenges, our study builds upon the "object-induced" model approach that prioritizes the role of objects in scenes for decision-making and integrates uncertainty assessment into the decision-making process using an evidential deep learning paradigm with a Beta prior. Additionally, we explore several advanced training strategies guided by uncertainty, including uncertainty-guided data reweighting and augmentation. Leveraging the BDD-OIA dataset, our findings underscore that the model, through these enhancements, not only offers a clearer comprehension of AV decisions and their underlying reasoning but also surpasses existing baselines across a broad range of scenarios.

From molecules to scaffolds to functional groups: building context-dependent molecular representation via multi-channel learning

Reliable molecular property prediction is essential for various scientific endeavors and industrial applications, such as drug discovery. However, the scarcity of data, combined with the highly non-linear causal relationships between physicochemical and biological properties and conventional molecular featurization schemes, complicates the development of robust molecular machine learning models. Self-supervised learning (SSL) has emerged as a popular solution, utilizing large-scale, unannotated molecular data to learn a foundational representation of chemical space that might be advantageous for downstream tasks. Yet, existing molecular SSL methods largely overlook domain-specific knowledge, such as molecular similarity and scaffold importance, as well as the context of the target application when operating over the large chemical space. This paper introduces a novel learning framework that leverages the knowledge of structural hierarchies within molecular structures, embeds them through separate pre-training tasks over distinct channels, and employs a task-specific channel selection to compose a context-dependent representation. Our approach demonstrates competitive performance across various molecular property benchmarks and establishes some state-of-the-art results. It further offers unprecedented advantages in particularly challenging yet ubiquitous scenarios like activity cliffs with enhanced robustness and generalizability compared to other baselines.

Retroformer: Pushing the Limits of Interpretable End-to-end Retrosynthesis Transformer

Retrosynthesis prediction is one of the fundamental challenges in organic synthesis. The task is to predict the reactants given a core product. With the advancement of machine learning, computer-aided synthesis planning has gained increasing interest. Numerous methods were proposed to solve this problem with different levels of dependency on additional chemical knowledge. In this paper, we propose Retroformer, a novel Transformer-based architecture for retrosynthesis prediction without relying on any cheminformatics tools for molecule editing. Via the proposed local attention head, the model can jointly encode the molecular sequence and graph, and efficiently exchange information between the local reactive region and the global reaction context. Retroformer reaches the new state-of-the-art accuracy for the end-to-end template-free retrosynthesis, and improves over many strong baselines on better molecule and reaction validity. In addition, its generative procedure is highly interpretable and controllable. Overall, Retroformer pushes the limits of the reaction reasoning ability of deep generative models.