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Punctuation is a strong indicator of syntactic structure, and parsers trained on text with punctuation often rely heavily on this signal. Punctuation is a diversion, however, since human language processing does not rely on punctuation to…
Automatic evaluation metrics are central to the development of machine translation systems, yet their robustness under domain shift remains unclear. Most metrics are developed on the Workshop on Machine Translation (WMT) benchmarks, raising…
Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…
Recent wireless testbed implementations have proven that full-duplex communication is in fact possible and can outperform half-duplex systems. Many of these implementations modify existing half-duplex systems to operate in full-duplex. To…
Both genomic stability and sustenance of day-to-day life rely on efficient and accurate readout of the genetic code. Single-molecule experiments show that transcription and replication are highly stochastic and irregular processes, with the…
High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are…
Distantly supervised (DS) relation extraction (RE) has attracted much attention in the past few years as it can utilize large-scale auto-labeled data. However, its evaluation has long been a problem: previous works either took costly and…
Large language models (LLMs) often exhibit gender bias, posing challenges for their safe deployment. Existing methods to mitigate bias lack a comprehensive understanding of its mechanisms or compromise the model's core capabilities. To…
Stories generated with neural language models have shown promise in grammatical and stylistic consistency. However, the generated stories are still lacking in common sense reasoning, e.g., they often contain sentences deprived of world…
Recent papers in explainable AI have made a compelling case for counterfactual modes of explanation. While counterfactual explanations appear to be extremely effective in some instances, they are formally equivalent to adversarial examples.…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Background: MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human…
Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the…
In recent years there has been a burgeoning interest in the use of computational methods to distinguish between elicited speech samples produced by patients with dementia, and those from healthy controls. The difference between perplexity…
For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using a pseudo-energy framework developed for 2'-OH…
We consider the problem of learning regression functions from pairwise data when there exists prior knowledge that the relation to be learned is symmetric or anti-symmetric. Such prior knowledge is commonly enforced by symmetrizing or…
Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crick pairs guanine-cytosine and adenine-thymine. Such mismatches bear adverse consequences for human health. We utilize molecular dynamics and metadynamics computer…
Inferring commonsense knowledge is a key challenge in natural language processing, but due to the sparsity of training data, previous work has shown that supervised methods for commonsense knowledge mining underperform when evaluated on…
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…
In the wake of responsible AI, interpretability methods, which attempt to provide an explanation for the predictions of neural models have seen rapid progress. In this work, we are concerned with explanations that are applicable to natural…