Related papers: TCRTransBench: A Comprehensive Benchmark for Bidir…
Generative models coupled with reinforcement learning (RL), such as REINVENT and PepINVENT, have emerged as a powerful framework for de novo molecular design. During the ideation process these generative frameworks utilize various…
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus.…
This paper presents the Task-Parameter Nexus (TPN), a learning-based approach for online determination of the (near-)optimal control parameters of model-based controllers (MBCs) for tracking tasks. In TPN, a deep neural network is…
The diversity of T-cell receptor (TCR) repertoires is achieved by a combination of two intrinsically stochastic steps: random receptor generation by VDJ recombination, and selection based on the recognition of random self-peptides presented…
Text-to-video (T2V) generative models have advanced significantly, yet their ability to compose different objects, attributes, actions, and motions into a video remains unexplored. Previous text-to-video benchmarks also neglect this…
B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively…
Motivation: The analysis of antibodies and T-cell receptors (TCRs) concentrations in serum is a fundamental problem in immunoinformatics. Repertoire construction is a preliminary step of analysis of clonal lineages, understanding of immune…
T-cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical…
Tracking cells in time-lapse videos is an essential technique for monitoring cell population dynamics at a single-cell level. Current methods for cell tracking are developed on videos with mostly single, constant signals and do not detect…
Electrocardiogram (ECG) biometrics have emerged as a promising modality for continuous, liveness-aware authentication in wearable systems. However, many prior studies report overly optimistic results due to data leakage (e.g., random splits…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
Synthetic Time Series Generation (TSG) is crucial in a range of applications, including data augmentation, anomaly detection, and privacy preservation. Although significant strides have been made in this field, existing methods exhibit…
Transfer learning refers to the process of adapting a model trained on a source task to a target task. While kernel methods are conceptually and computationally simple machine learning models that are competitive on a variety of tasks, it…
Machine translation (MT) has become indispensable for cross-border communication in globalized industries like e-commerce, finance, and legal services, with recent advancements in large language models (LLMs) significantly enhancing…
Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on…
Computational and machine learning approaches to model the conformational landscape of macrocyclic peptides have the potential to enable rational design and optimization. However, accurate, fast, and scalable methods for modeling macrocycle…
Temporal Graph Clustering (TGC) is a new task with little attention, focusing on node clustering in temporal graphs. Compared with existing static graph clustering, it can find the balance between time requirement and space requirement…
The Transformer-Kernel (TK) model has demonstrated strong reranking performance on the TREC Deep Learning benchmark---and can be considered to be an efficient (but slightly less effective) alternative to BERT-based ranking models. In this…
It has been verified that only a small fraction of the neoantigens presented by MHC class I molecules on the cell surface can elicit T cells. The limitation can be attributed to the binding specificity of T cell receptor (TCR) to…
Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural…