Related papers: The Stanford RNA Mapping Database for sharing and …
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
Reaction diagram parsing is the task of extracting reaction schemes from a diagram in the chemistry literature. The reaction diagrams can be arbitrarily complex, thus robustly parsing them into structured data is an open challenge. In this…
Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved…
We describe the current state and future plans for a set of tools for scientific data management (SDM) designed to support scientific transparency and reproducible research. SDM has been in active use at our MRI Center for more than two…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
Existing RGB-D saliency detection models do not explicitly encourage RGB and depth to achieve effective multi-modal learning. In this paper, we introduce a novel multi-stage cascaded learning framework via mutual information minimization to…
Emerging high-throughput technologies have led to a deluge of putative non-coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology…
Residual connection has been extensively studied and widely applied at the model architecture level. However, its potential in the more challenging data-centric approaches remains unexplored. In this work, we introduce the concept of Data…
Retrieval-Augmented Generation (RAG) systems in chemistry heavily depend on accurate and relevant retrieval of chemical literature. However, general-purpose text embedding models frequently fail to adequately represent complex chemical…
Simulating trajectories of multi-particle systems on complex energy landscapes is a central task in molecular dynamics (MD) and drug discovery, but remains challenging at scale due to computationally expensive and long simulations. Previous…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
A new family of Intensional RDBs (IRDBs), introduced in [1], extends the traditional RDBs with the Big Data and flexible and 'Open schema' features, able to preserve the user-defined relational database schemas and all preexisting user's…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
Large Language Models (LLMs) and their multimodal variants (LVLMs) hold immense promise for scientific and engineering applications, particularly in processing visual information like scientific diagrams. However, their practical deployment…
Identifying novel functional materials with desired key properties is an important part of bridging the gap between fundamental research and technological advancement. In this context, high-throughput calculations combined with data-mining…
Large networks are becoming a widely used abstraction for studying complex systems in a broad set of disciplines, ranging from social network analysis to molecular biology and neuroscience. Despite an increasing need to analyze and…
Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be applied to a non-model organism without a reference genome,…
Branched molecules of deoxyribonucleic acid (DNA) can self-assemble into nanostructures through complementary cohesive strand base pairing. The production of DNA nanostructures is valuable in targeted drug delivery and biomolecular…
We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation and evaluation to address unique challenges…
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the major techniques in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size…