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Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a…
Generalization to novel compound tasks under distribution shift is important for deploying transformer-based language models (LMs). This work investigates Chain-of-Thought (CoT) reasoning as a means to enhance OOD generalization. Through…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Code translation across multiple programming languages is essential yet challenging due to two vital obstacles: scarcity of parallel data paired with executable test oracles, and optimization imbalance when handling diverse language pairs.…
We present a unifying framework for type systems for process calculi. The core of the system provides an accurate correspondence between essentially functional processes and linear logic proofs; fragments of this system correspond to…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
Kohn-Sham density functional theory is the base of modern computational approaches to electronic structures. Their accuracy vitally relies on the exchange-correlation energy functional, which encapsulates electron-electron interaction…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
Surgical procedures unfold in complex environments demanding coordination between surgical teams, tools, imaging and increasingly, intelligent robotic systems. Ensuring safety and efficiency in ORs of the future requires intelligent…
We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
While Chain-of-Thought (CoT) prompting enhances the reasoning capabilities of large language models, the faithfulness of the generated rationales remains an open problem for model interpretability. We propose a novel theoretical lens for…
Program synthesis with Genetic Programming searches for a correct program that satisfies the input specification, which is usually provided as input-output examples. One particular challenge is how to effectively handle loops and recursion…
Designing quantum processors is a complex task that demands advanced verification methods to ensure their correct functionality. However, traditional methods of comprehensively verifying quantum devices, such as quantum process tomography,…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Quantum computers promise to perform certain computations exponentially faster than any classical device. Precise control over their physical implementation and proper shielding from unwanted interactions with the environment become more…
DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules,…
This paper addresses the problem of giving conditions for transcriptional systems to be globally entrained to external periodic inputs. By using contraction theory, a powerful tool from dynamical systems theory, it is shown that certain…
We present Korali, an open-source framework for large-scale Bayesian uncertainty quantification and stochastic optimization. The framework relies on non-intrusive sampling of complex multiphysics models and enables their exploitation for…