相关论文: Biases in the Experimental Annotations of Protein …
In attempts to develop sample-efficient and interpretable algorithms, researcher have explored myriad mechanisms for collecting and exploiting feature feedback (or rationales) auxiliary annotations provided for training (but not test)…
Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Yet existing pipelines built on protein encoders do not model…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…
Clinical dataset labels are rarely certain as annotators disagree and confidence is not uniform across cases. Typical aggregation procedures, such as majority voting, obscure this variability. In simple experiments on medical imaging…
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry…
The effect of bias on hypothesis formation is characterized for an automated data-driven projection pursuit neural network to extract and select features for binary classification of data streams. This intelligent exploratory process…
Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…
Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Science is becoming increasingly more interdisciplinary, giving rise to more diversity in the areas of expertise within research labs and groups. This also have brought changes to the role researchers in scientific works. As a consequence,…
Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…
Neuroscience has traditionally relied on manually observing lab animals in controlled environments. Researchers usually record animals behaving in free or restrained manner and then annotate the data manually. The manual annotation is not…
In essence, embedding algorithms work by optimizing the distance between a word and its usual context in order to generate an embedding space that encodes the distributional representation of words. In addition to single words or word…
The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…
In large organisations, identifying experts on a given topic is crucial in leveraging the internal knowledge spread across teams and departments. So-called enterprise expert retrieval systems automatically discover and structure employees'…
Online experiments (A/B tests) are widely regarded as the gold standard for evaluating recommender system variants and guiding launch decisions. However, a variety of biases can distort the results of the experiment and mislead…