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For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…
Deep learning models in medical imaging are susceptible to shortcut learning, relying on confounding metadata (e.g., scanner model) that is often encoded in image embeddings. The crucial question is whether the model actively utilizes this…
The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…
Deep learning (DL) has been used in the automatic diagnosis of Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD) with brain imaging data. However, previous methods have not fully exploited the relation between brain image and…
Machine-learned potentials (MLPs) trained on ab initio data combine the computational efficiency of classical interatomic potentials with the accuracy and generality of the first-principles method used in the creation of the respective…
Proton therapy offers superior organ-at-risk sparing but is highly sensitive to anatomical changes, making accurate deformable image registration (DIR) across longitudinal CT scans essential. Conventional DIR methods are often too slow for…
Image deep features extracted by pre-trained networks are known to contain rich and informative representations. In this paper, we present Deep Degradation Response (DDR), a method to quantify changes in image deep features under varying…
Purpose: A new method for magnetic resonance (MR) imaging water-fat separation using a convolutional neural network (ConvNet) and deep learning (DL) is presented. Feasibility of the method with complex and magnitude images is demonstrated…
Modern cancer genomics datasets involve widely varying sizes and scales, measurement variables, and correlation structures. A fundamental analytical goal in these high-throughput studies is the development of general statistical techniques…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
Computed Tomography (CT) is widely used in healthcare for detailed imaging. However, Low-dose CT, despite reducing radiation exposure, often results in images with compromised quality due to increased noise. Traditional methods, including…
Image denoising is the process of removing noise from noisy images, which is an image domain transferring task, i.e., from a single or several noise level domains to a photo-realistic domain. In this paper, we propose an effective image…
It is important to quantify Damage Assessment (DA) for Human Assistance and Disaster Response (HADR) applications. In this paper, to achieve efficient and scalable DA in HADR, an image prior and posterior conditional probability (IP2CP) is…
Background and objective: Diabetes is a chronic pathology which is affecting more and more people over the years. It gives rise to a large number of deaths each year. Furthermore, many people living with the disease do not realize the…
Deep learning associated with neurological signals is poised to drive major advancements in diverse fields such as medical diagnostics, neurorehabilitation, and brain-computer interfaces. The challenge in harnessing the full potential of…
Risk stratification (characterization) of tumors from radiology images can be more accurate and faster with computer-aided diagnosis (CAD) tools. Tumor characterization through such tools can also enable non-invasive cancer staging,…
Photon-counting CT (PCCT) offers improved diagnostic performance through better spatial and energy resolution, but developing high-quality image reconstruction methods that can deal with these large datasets is challenging. Model-based…
Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only…
Learning interpretable disentangled representations is a crucial yet challenging task. In this paper, we propose a weakly semi-supervised method, termed as Dual Swap Disentangling (DSD), for disentangling using both labeled and unlabeled…
Inverse protein folding generates valid amino acid sequences that can fold into a desired protein structure, with recent deep-learning advances showing strong potential and competitive performance. However, challenges remain, such as…