Related papers: Four small puzzles that Rosetta doesn't solve
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
The adsorption or adhesion of large particles (proteins, colloids, cells, >...) at the liquid-solid interface plays an important role in many diverse applications. Despite the apparent complexity of the process, two features are…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Neural networks have in recent years shown promise for helping software engineers write programs and even formally verify them. While semantic information plays a crucial part in these processes, it remains unclear to what degree popular…
Two questions regarding practitioners' use of patent embeddings arise: (i) Does one fine-tuning recipe suffice for all downstream applications? (ii) Is fine-tuning on one patent landscape sufficient for downstream application on other…
The constraint satisfaction problem (CSP) and its quantified extensions, whether without (QCSP) or with disjunction (QCSP_or), correspond naturally to the model checking problem for three increasingly stronger fragments of positive…
Large Language Models (LLMs), such as OpenAI's o1 and DeepSeek's R1, excel at advanced reasoning tasks like math and coding via Reinforcement Learning with Verifiable Rewards (RLVR), but still struggle with puzzles solvable by humans…
This work studies the Tensor Robust Principal Component Analysis (TRPCA) problem, which aims to exactly recover the low-rank and sparse components from their sum. Our model is motivated by the recently proposed linear transforms based…
Background. All-atom crystallographic refinement of proteins is a laborious manually driven procedure, as a result of which, alternative and multiconformer interpretations are not routinely investigated. Results. We describe efficient loop…
Despite the recent progress of automated program verification techniques, fully automated verification of programs manipulating recursive data structures remains a challenge. We introduce solvable tuple patterns (STPs) and conjunctive STPs…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Software reliability growth models (SRGM) enable failure data collected during testing. Specifically, nonhomogeneous Poisson process (NHPP) SRGM are the most commonly employed models. While software reliability growth models are important,…
Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion, from a relatively small number of components. Here we propose to identify the…
Despite nearly two scores of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. Researchers have proposed increasingly complex energy…
We propose a new benchmark evaluating the performance of multimodal large language models on rebus puzzles. The dataset covers 333 original examples of image-based wordplay, cluing 13 categories such as movies, composers, major cities, and…
As scientific knowledge grows at an unprecedented pace, evaluation benchmarks must evolve to reflect new discoveries and ensure language models are tested on current, diverse literature. We propose a scalable, modular framework for…
Four zero neutrino Yukawa textures in a specified weak basis, combined with $\mu\tau$ symmetry and type-I seesaw, yield a highly constrained and predictive scheme. Two alternately viable $3\times3$ light neutrino Majorana mass matrices…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…