Related papers: A quick guide for student-driven community genome …
Cytometry enables precise single-cell phenotyping within heterogeneous populations. These cell types are traditionally annotated via manual gating, but this method suffers from a lack of reproducibility and sensitivity to batch-effect.…
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
The language used by US courtroom actors in criminal trials has long been studied for biases. However, systematic studies for bias in high-stakes court trials have been difficult, due to the nuanced nature of bias and the legal expertise…
This position paper argues that the machine learning community should prioritize early-stage quality assurance in annotation pipelines over the prevailing practice of late-stage validation. Data quality bottlenecks increasingly limit…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
An annotation consists of a portion of information that is associated with a piece of content in order to explain something about the content or to add more information. The use of annotations as a tool in the educational field has positive…
Certain forms of linguistic annotation, like part of speech and semantic tagging, can be automated with high accuracy. However, manual annotation is still necessary for complex pragmatic and discursive features that lack a direct mapping to…
Text generation is increasingly common but often requires manual post-editing where high precision is critical to end users. However, manual editing is expensive so we want to ensure this effort is focused on high-value tasks. And we want…
Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in…
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 microscopy, the time burden and cost of acquiring and annotating large datasets that many deep learning models take as a prerequisite, often appears to make these methods impractical. Can this requirement for annotated data be relaxed?…
Automated cellular instance segmentation is a process utilized for accelerating biological research for the past two decades, and recent advancements have produced higher quality results with less effort from the biologist. Most current…
Large language models (LLMs) can label data faster and cheaper than humans for various NLP tasks. Despite their prowess, LLMs may fall short in understanding of complex, sociocultural, or domain-specific context, potentially leading to…
The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the…
Deep-learning pipelines for microscopy image classification often require expensive, labor- and time-intensive expert annotation to produce high-quality ground truth for training. Recent work has shown that prompt tuning of vision-language…
Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
Modern computing students often rely on both natural-language prompting and manual code editing to solve programming tasks. Yet we still lack a clear understanding of how these two modes are combined in practice, and how their usage varies…
State-of-the-art question answering (QA) relies upon large amounts of training data for which labeling is time consuming and thus expensive. For this reason, customizing QA systems is challenging. As a remedy, we propose a novel framework…
Personalized community detection aims to generate communities associated with user need on graphs, which benefits many downstream tasks such as node recommendation and link prediction for users, etc. It is of great importance but lack of…