9 papers · ranked by Valyu relevance
Yiming Xue, Xiaojian Liu, Weimin Zhu, Shengfan Wang + 2 more
While protein-RNA interactions are fundamental to post-transcriptional processes, achieving a holistic understanding of their regulatory logic remains challenging. Current computational models often treat binding affinity, interface mapping, and RNA design as isolated tasks, thereby failing to provide a unified…
Alp Tartici, Mihajlo Stojkovic, Anru Tian, Michael C. Jewett + 2 more
Protein engineering has important implications in the bioeconomy, enabling applications in materials, medicine, and energy. A key challenge is designing protein sequences that have a specific form and function. Protein inverse folding seeks to address this challenge by identifying amino acid sequences compatible with a…
Hao Ding, Nannan Wu, Tianyi Qiu
DNA foundation models such as Evo2 7B adopt hybrid Hyena/attention architectures (Striped-Hyena2) whose single-stream autoregressive decoding is bounded by weight bandwidth at ∼45 tok/s. Speculative decoding on such hybrids faces a systems problem that prior SSM work solves only partially: after a draft is verified…
Kunyu Wang, Jon Paul Janet, Alessandro Tibo
Three-dimensional molecular generative models have emerged that produce de novo molecules both unconditionally and conditionally, e.g., within protein pockets. However, steering those models in a specific region of the chemical space that satisfies a set of desired properties remains challenging. In this study, we…
William JF Rieger, Sebastian Häussermann, Luca Herrmann, Zecheng Li + 8 more
Enzymes frequently exhibit promiscuous activity beyond their native roles, providing starting-points for new functions. Finding these promiscuous enzymes, especially for non-native chemical transformations, is challenging but highly valuable, as they promise novel, sustainable solutions for chemistry and biotechnology.…
Zichao Jin, Jiaoru Wang, Wenjiang Huang, Jingcheng Zhang + 2 more
Accurate, reliable, large-scale disease predictions are essential to ensure rice production. Existing disease prediction models often face a trade-off between interpretability and predictive capability, necessitating the integration of mechanistic knowledge and data-driven learning within a modelling framework.…
Xuebin Feng, Emma R. Master
Sequence similarity networks (SSNs) are graphical representations of sequence relationship frequently used for exploring protein sequence space. Conventional SSN workflows typically use BLAST to calculate sequence similarities and rely on external visualization tools to generate the final networks. Consequently, raw…
Manuel Treutlein, Pascal Bothe, Marc Schmidt, Roman Hahn + 4 more
The last mile of the distribution grid is crucial for a successful energy transition, as more low-carbon technology like photovoltaic systems, heat pumps, and electric vehicle chargers connect to the low-voltage grid. Despite considerable challenges in operation and planning, researchers often lack access to suitable…
Hadeer Kamal, Amira Y. Haikal, Mahmoud M. Saafan
Traffic collisions and congestion represent significant challenges within intelligent transportation systems (ITS). Consequently, a vehicular ad-hoc network (VANET) has been established. Numerous architectures have been incorporated into VANETs to manage the extensive data generated by vehicles. Collaboration with fog…