Related papers: Diversity in immunogenomics: the value and the cha…
Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations…
University admissions offices face the significant challenge of managing high volumes of inquiries efficiently while maintaining response quality, which critically impacts prospective students' perceptions. This paper addresses the issues…
Information Retrieval (IR) is the task of obtaining pieces of data (such as documents) that are relevant to a particular query or need from a large repository of information. IR is a valuable component of several downstream Natural Language…
Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…
RNA-seq has become a de facto standard for measuring gene expression. Traditionally, RNA-seq experiments are mathematically averaged -- they sequence the mRNA of individuals from different treatment groups, hoping to correlate phenotype…
Biological datasets amenable to applied machine learning are more available today than ever before, yet they lack adequate representation in the Data-for-Good community. Here we present a work in progress case study performing analysis on…
As AI adoption expands across human society, the problem of aligning AI models to match human preferences remains a grand challenge. Currently, the AI alignment field is deeply divided between behavioral and representational approaches,…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Understanding the structure of the human T-cell receptor repertoire is a crucial precondition to understand the ability of the immune system to recognize and respond to antigens. T-cells are often compared via the complementarity…
T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We developed EAMil, a multi-instance deep…
Benchmarking the performance of information retrieval (IR) is mostly conducted with a fixed set of documents (static corpora). However, in realistic scenarios, this is rarely the case and the documents to be retrieved are constantly updated…
Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these…
The ways in which race, ethnicity, and ancestry are used and reported in human genomics research has wide-ranging implications for how research is translated into clinical care, incorporated into public understanding, and implemented in…
Here we present the first genome wide statistical test for recessive selection. This test uses explicitly non-equilibrium demographic differences between populations to infer the mode of selection. By analyzing the transient response to a…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Dendritic cells are antigen presenting cells that provide a vital link between the innate and adaptive immune system. Research into this family of cells has revealed that they perform the role of coordinating T-cell based immune responses,…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…
Artificial immune systems primarily mimic the adaptive nature of biological immune functions. Their ability to adapt to varying pathogens makes such systems a suitable choice for various robotic applications. Generally, AIS-based robotic…
One of the challenges in the design of confirmatory trials is to deal with uncertainties regarding the optimal target population for a novel drug. Adaptive enrichment designs (AED) which allow for a data-driven selection of one or more…