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5 papers
Humanity's Last Exam
Long Phan, Alice Gatti, Ziwen Han +1144
Benchmarks are important tools for tracking the rapid advancements in large language model (LLM) capabilities. However, benchmarks are not keeping pace in difficulty: LLMs now achi…
Value-Compressed Sparse Column (VCSC): Sparse Matrix Storage for Redundant Data
Skyler Ruiter, Seth Wolfgang, Marc Tunnell +3
Compressed Sparse Column (CSC) and Coordinate (COO) are popular compression formats for sparse matrices. However, both CSC and COO are general purpose and cannot take advantage of…
Ten Quick Tips for Deep Learning in Biology
Benjamin D. Lee, Anthony Gitter, Casey S. Greene +17
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that…
A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4
Bradley M. Dickson, Parker W de Waal, Zachary H Ramjan +2
In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We…
-tempered metadynamics: Artifact independent convergence times for wide hills
Bradley M. Dickson
Recent analysis of well-tempered metadynamics (WTmetaD) showed that it converges without mollification artifacts in the bias potential. Here we explore how metadynamics heals molli…