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The accurate analysis of medical images is vital for diagnosing and predicting medical conditions. Traditional approaches relying on radiologists and clinicians suffer from inconsistencies and missed diagnoses. Computer-aided diagnosis…
Plants rarely occur in isolated systems. Bacteria can inhabit either the endosphere, the region inside the plant root, or the rhizosphere, the soil region just outside the plant root. Our goal is to understand if using genomic data and…
Graph Transformers have garnered significant attention for learning graph-structured data, thanks to their superb ability to capture long-range dependencies among nodes. However, the quadratic space and time complexity hinders the…
Image inpainting for completing complicated semantic environments and diverse hole patterns of corrupted images is challenging even for state-of-the-art learning-based inpainting methods trained on large-scale data. A reference image…
Background: Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning…
The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…
We introduce RatchetEHR, a novel transformer-based framework designed for the predictive analysis of electronic health records (EHR) data in intensive care unit (ICU) settings, with a specific focus on bloodstream infection (BSI)…
This paper proposes Transducers with Pronunciation-aware Embeddings (PET). Unlike conventional Transducers where the decoder embeddings for different tokens are trained independently, the PET model's decoder embedding incorporates shared…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
Currently, this paper is under review in IEEE. Transformers have intrigued the vision research community with their state-of-the-art performance in natural language processing. With their superior performance, transformers have found their…
Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the…
High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…
Transformers have recently gained increasing attention in computer vision. However, existing studies mostly use Transformers for feature representation learning, e.g. for image classification and dense predictions, and the generalizability…
In the manufacturing process, sensor data collected from equipment is crucial for building predictive models to manage processes and improve productivity. However, in the field, it is challenging to gather sufficient data to build robust…
Time-series data are critical in diverse applications, such as industrial monitoring, medical diagnostics, and climate research. However, effectively integrating these high-dimensional temporal signals with natural language for dynamic,…
DNA methylation datasets in cancer studies are comprised of measurements on a large number of genomic locations called cytosine-phosphate-guanine (CpG) sites with complex correlation structures. A fundamental goal of these studies is the…
This paper investigates the application of the transformer architecture in protein folding, as exemplified by DeepMind's AlphaFold project, and its implications for the understanding of so-called large language models. The prevailing…
Blind detection of the forged regions in digital images is an effective authentication means to counter the malicious use of local image editing techniques. Existing encoder-decoder forensic networks overlook the fact that detecting complex…
Current and upcoming generations of visible-shortwave infrared (VSWIR) imaging spectrometers promise unprecedented capacity to quantify Earth System processes across the globe. However, reliable cloud screening remains a fundamental…
Temporal expressions in text play a significant role in language understanding and correctly identifying them is fundamental to various retrieval and natural language processing systems. Previous works have slowly shifted from rule-based to…