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A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…
Preferential Bayesian optimization (PBO) learns latent utilities from pairwise comparisons, but most existing methods assume homoscedastic comparison noise. This is inadequate in human-in-the-loop settings, where a user may compare some…
Existing manifold learning methods are not appropriate for image retrieval task, because most of them are unable to process query image and they have much additional computational cost especially for large scale database. Therefore, we…
In the class of immersed boundary (IB) methods, the choice of the delta function plays a crucial role in transferring information between fluid and solid domains. Most prior work has used isotropic kernels that do not preserve the…
Plastid targeted proteins of diatoms and related algae can be predicted with high sensitivity and specificity using the ASAFind method published in 2015. ASAFind predictions rely on SignalP predictions of endoplasmic reticulum (ER)…
Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)$^{1-3}$ offer a computationally efficient alternative to density…
We propose the use of probability models for ranked data as a useful alternative to a quantitative data analysis to investigate the outcome of bioassay experiments, when the preliminary choice of an appropriate normalization method for the…
Accurate polyp delineation in colonoscopy is crucial for assisting in diagnosis, guiding interventions, and treatments. However, current deep-learning approaches fall short due to integrity deficiency, which often manifests as missing…
Embedding-based retrieval (EBR) methods are widely used in modern recommender systems thanks to its simplicity and effectiveness. However, along the journey of deploying and iterating on EBR in production, we still identify some fundamental…
The Epithelial Dysplasia (ED) is a tissue alteration commonly present in lesions preceding oral cancer, being its presence one of the most important factors in the progression toward carcinoma. This study proposes a method to design a low…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
Colorectal polyps are important precursors to colon cancer, a major health problem. Colon capsule endoscopy (CCE) is a safe and minimally invasive examination procedure, in which the images of the intestine are obtained via digital cameras…
Downsampling images and labels, often necessitated by limited resources or to expedite network training, leads to the loss of small objects and thin boundaries. This undermines the segmentation network's capacity to interpret images…
Biologists frequently desire protein inhibitors for a variety of reasons, including use as research tools for understanding biological processes and application to societal problems in agriculture, healthcare, etc. Immunotherapy, for…
Edge detection is widely and fundamental feature used in various algorithms in computer vision to determine the edges in an image. The edge detection algorithm is used to determine the edges in an image which are further used by various…
Semi-supervised learning by self-training heavily relies on pseudo-label selection (PLS). The selection often depends on the initial model fit on labeled data. Early overfitting might thus be propagated to the final model by selecting…
We describe an automated method for assigning the most likely physical parameters to the components of an eclipsing binary (EB), using only its photometric light curve and combined color. In traditional methods (e.g. WD and EBOP) one…
Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…
In medical image processing, the most important information is often located on small parts of the image. Patch-based approaches aim at using only the most relevant parts of the image. Finding ways to automatically select the patches is a…
Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the…