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We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting,…
Image-based species identification could help scaling biodiversity monitoring to a global scale. Many challenges still need to be solved in order to implement these systems in real-world applications. A reliable image-based monitoring…
In this paper, we propose a novel Explanation Neural Network (XNN) to explain the predictions made by a deep network. The XNN works by learning a nonlinear embedding of a high-dimensional activation vector of a deep network layer into a…
Recently several deep learning models have been used for DNA sequence based classification tasks. Often such tasks require long and variable length DNA sequences in the input. In this work, we use a sequence-to-sequence autoencoder model to…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical cross-linking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments…
Higher-order graph clustering aims to partition the graph using frequently occurring subgraphs. Motif conductance is one of the most promising higher-order graph clustering models due to its strong interpretability. However, existing motif…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
Detecting slender, overlapping structures remains a challenge in computational microscopy. While recent coordinate-based approaches improve detection, they often produce less accurate splines than pixel-based methods. We introduce a…
Many constraint satisfaction and optimisation problems can be solved effectively by encoding them as instances of the Boolean Satisfiability problem (SAT). However, even the simplest types of constraints have many encodings in the…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
Background: The inception of next generations sequencing technologies have exponentially increased the volume of biological sequence data. Protein sequences, being quoted as the `language of life', has been analyzed for a multitude of…
Modern language models (LMs) are trained in an autoregressive manner, conditioned only on the prefix. In contrast, sequence labeling (SL) tasks assign labels to each individual input token, naturally benefiting from bidirectional context.…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into…
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in the biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers…
In this work, we modify the superparamagnetic clustering algorithm (SPC) by adding an extra weight to the interaction formula that considers which genes are regulated by the same transcription factor. With this modified algorithm that we…