Related papers: Achieving DNA Labeling Capacity with Minimum Label…
The labor-intensive annotation process of semantic segmentation datasets is often prone to errors, since humans struggle to label every pixel correctly. We study algorithms to automatically detect such annotation errors, in particular…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
A distance labeling scheme is an assignment of bit-labels to the vertices of an undirected, unweighted graph such that the distance between any pair of vertices can be decoded solely from their labels. We propose a series of new labeling…
Large Deep Neural Networks (DNNs) are often data hungry and need high-quality labeled data in copious amounts for learning to converge. This is a challenge in the field of medicine since high quality labeled data is often scarce. Data…
Label propagation is a powerful and flexible semi-supervised learning technique on graphs. Neural networks, on the other hand, have proven track records in many supervised learning tasks. In this work, we propose a training framework with a…
We consider labeling nodes of a directed graph for reachability queries. A reachability labeling scheme for such a graph assigns a binary string, called a label, to each node. Then, given the labels of nodes $u$ and $v$ and no other…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…
Graph-based methods have been demonstrated as one of the most effective approaches for semi-supervised learning, as they can exploit the connectivity patterns between labeled and unlabeled data samples to improve learning performance.…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
Semantic labeling for numerical values is a task of assigning semantic labels to unknown numerical attributes. The semantic labels could be numerical properties in ontologies, instances in knowledge bases, or labeled data that are manually…
Is self-supervised deep learning (DL) for medical image analysis already a serious alternative to the de facto standard of end-to-end trained supervised DL? We tackle this question for medical image classification, with a particular focus…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
The learning of the deep networks largely relies on the data with human-annotated labels. In some label insufficient situations, the performance degrades on the decision boundary with high data density. A common solution is to directly…
Graph Neural Networks (GNNs) have achieved remarkable performance in modeling graphs for various applications. However, most existing GNNs assume the graphs exhibit strong homophily in node labels, i.e., nodes with similar labels are…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
Extreme multi-label learning (XML) or classification has been a practical and important problem since the boom of big data. The main challenge lies in the exponential label space which involves $2^L$ possible label sets especially when the…
Graph pattern matching is a routine process for a wide variety of applications such as social network analysis. It is typically defined in terms of subgraph isomorphism which is NP-Complete. To lower its complexity, many extensions of graph…
We propose a Label Propagation based algorithm for weakly supervised text classification. We construct a graph where each document is represented by a node and edge weights represent similarities among the documents. Additionally, we…