Related papers: The IBEX Knowledge-Base: Achieving more together w…
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the…
High content imaging is needed to catalogue the variety of cellular phenotypes and multi-cellular ecosystems present in metazoan tissues. We recently developed Iterative Bleaching Extends multi-pleXity (IBEX), an iterative immunolabeling…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
Three-dimensional generative models increasingly drive structure-based drug discovery, yet it remains constrained by the scarce publicly available protein-ligand complexes. Under such data scarcity, almost all existing pipelines struggle to…
Distinguishing visually similar objects like forged/authentic bills and healthy/unhealthy plants is beyond the capabilities of even the most sophisticated classifiers. We propose the use of multiplexed illumination to extend the range of…
We have demonstrated the capability of spectral multiplexing in multi-distance diffractive imaging, enabling the reconstruction of samples with diverse spectral responses. While previous methods like ptychography utilize redundancy in…
A key goal of environmental health research is to assess the risk posed by mixtures of pollutants. As epidemiologic studies of mixtures can be expensive to conduct, it behooves researchers to incorporate prior knowledge about mixtures into…
This paper introduces MIX, a multi-task deep learning approach to solve open-ended question-answering. First, we design our system as a multi-stage pipeline of 3 building blocks: a BM25-based Retriever to reduce the search space, a…
This paper presents Deep Integrated Explanations (DIX) - a universal method for explaining vision models. DIX generates explanation maps by integrating information from the intermediate representations of the model, coupled with their…
Research collaborations are continuously emerging catalyzed by online platforms, where people can share their codes, calculations, data and results. These virtual research platforms are innovative, community oriented, flexible and secure as…
We introduce Interactive Bayesian Distributional Robustness (IBDR), a novel Bayesian inference framework that allows modeling the interactions between particles, thereby enhancing ensemble quality through increased particle diversity. IBDR…
Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…
Reflective ptychography is a promising lensless imaging technique with a wide field of view, offering significant potential for applications in semiconductor manufacturing and detection. However, many semiconductor materials are coated with…
Background, enhancing interoperability of bioinformatics knowledge bases is a high priority requirement to maximize data reusability, and thus increase their utility such as the return on investment for biomedical research. A knowledge base…
Gene expression is a complex phenomenon involving numerous interlinked variables, and studying these variables to control expression is essential in bioengineering and biomanufacturing. While cloning techniques for achieving plasmid…
Post-hoc explanation methods are gaining popularity for interpreting, understanding, and debugging neural networks. Most analyses using such methods explain decisions in response to inputs drawn from the test set. However, the test set may…
Replicability in machine learning (ML) research is increasingly concerning due to the utilization of complex non-deterministic algorithms and the dependence on numerous hyper-parameter choices, such as model architecture and training…
One strategy to scale up ML-driven science is to increase wet lab experiments' information density. We present a method based on a neural extension of compressed sensing to function space. We measure the activity of multiple different…
A new class of implicit-explicit (IMEX) methods combined with a p-adaptive mixed finite element formulation is proposed to simulate the diffusion of reacting species. Hierarchical polynomial functions are used to construct an…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…