Related papers: The IBEX Knowledge-Base: Achieving more together w…
Energy dispersive X-ray (EDX) spectrum imaging yields compositional information with a spatial resolution down to the atomic level. However, experimental limitations often produce extremely sparse and noisy EDX spectra. Under such…
Global overlay maps of science use base maps that are overlaid by specific data (from single researchers, institutions, or countries) for visualizing scientific performance such as field-specific paper output. A procedure to create global…
We introduce MixtureKit, a modular open-source framework for constructing, training, and analyzing Mixture-of-Experts (MoE) models from arbitrary pre-trained or fine-tuned models. MixtureKit currently supports three complementary methods:…
We introduce Ibex, a pan-immunoglobulin structure prediction model that achieves state-of-the-art accuracy in modeling the variable domains of antibodies, nanobodies, and T-cell receptors. Unlike previous approaches, Ibex explicitly…
The Information Bottleneck (IB) method is an information theoretical framework to design a parsimonious and tunable feature-extraction mechanism, such that the extracted features are maximally relevant to a specific learning or inference…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…
Scopus and the Web of Science have been the foundation for research in the science of science even though these traditional databases systematically underrepresent certain disciplines and world regions. In response, new inclusive databases,…
The work is devoted to the study of the correlation technique of formation of laser beams under conditions of the interaction of coherent fields spatially periodic in the transverse direction.\,\,It is aimed at the application of this…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
The discovery and optimization of materials for specific applications is hampered by the practically infinite number of possible elemental combinations and associated properties, also known as the `combinatorial explosion'. By nature of the…
Information extraction from chemistry literature is vital for constructing up-to-date reaction databases for data-driven chemistry. Complete extraction requires combining information across text, tables, and figures, whereas prior work has…
In this study, a novel computer aided diagnosis (CADx) framework is devised to investigate interpretability for classifying breast masses. Recently, a deep learning technology has been successfully applied to medical image analysis…
The Information Bottleneck (IB) framework is a general characterization of optimal representations obtained using a principled approach for balancing accuracy and complexity. Here we present a new framework, the Dual Information Bottleneck…
eXplanation Based Learning (XBL) is a form of Interactive Machine Learning (IML) that provides a model refining approach via user feedback collected on model explanations. Although the interactivity of XBL promotes model transparency, XBL…
We present a novel approach that combines machine learning based interactive image segmentation using supervoxels with a clustering method for the automated identification of similarly colored images in large data sets which enables a…
Fluorescence microscopy allows for a detailed inspection of cells, cellular networks, and anatomical landmarks by staining with a variety of carefully-selected markers visualized as color channels. Quantitative characterization of…
Reflectometry is a technique that uses the light reflected by a sample to determine properties of the sample. Interferometric reflectometry uses interference between two beams, one of which is incident on ---and reflected back by--- a…
With the wide adoption of black-box models, instance-based \emph{post hoc} explanation tools, such as LIME and SHAP became increasingly popular. These tools produce explanations, pinpointing contributions of key features associated with a…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…