Related papers: Paradigm shifts. Part I. Collagen. Confirming and …

The reverse transcription paradigm shift in RNA tumor virus research marked by the discovery of the reverse transcriptase in 1970 was traced using co-citation and title word frequency analysis. It is shown that this event is associated with…

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction…

Recent years in NLP have seen the continued development of domain-specific information extraction tools for scientific documents, alongside the release of increasingly multimodal pretrained transformer models. While the opportunity for…

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Over the last four decades, the way knowledge is created in academia has transformed dramatically: research teams have grown larger, scholars draw from ever-wider pools of prior work, and the most influential discoveries increasingly emerge…

Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose…

The mechanical properties of biological tissues are strongly correlated to the specific distribution of their collagen fibers. Monitoring the dynamic reorganization of the collagen network during mechanical stretching is however a technical…

Collaboration is a key driver of science and innovation. Mainly motivated by the need to leverage different capacities and expertise to solve a scientific problem, collaboration is also an excellent source of information about the future…

Proteolysis targeting chimeras (PROTACs) are small molecules that trigger the breakdown of traditionally ``undruggable'' proteins by binding simultaneously to their targets and degradation-associated proteins. A key challenge in their…

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional…

The central dogma of molecular biology, formulated more than five decades ago, compartmentalized information exchange in the cell into the DNA, RNA and protein domains. This formalization has served as an implicit thematic distinguisher for…

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…

Large language models (LLMs) have shown potential as tools for scientific discovery. This has engendered growing interest in their use in humanistic disciplines, such as historical linguistics and literary studies. These fields often…

This thesis investigates two key phenomena in large language models (LLMs): in-context learning (ICL) and model collapse. We study ICL in a linear transformer with tied weights trained on linear regression tasks, and show that minimising…

Language modeling has seen impressive progress over the last years, mainly prompted by the invention of the Transformer architecture, sparking a revolution in many fields of machine learning, with breakthroughs in chemistry and biology. In…

Collagen, a key structural component of the extracellular matrix, undergoes significant remodeling during carcinogenesis. However, the important role of collagen levels in breast cancer diagnostics still lacks effective in vivo detection…

A study released by the Google Scholar team found an apparently increasing fraction of citations to old articles from studies published in the last 24 years (1990-2013). To demonstrate this finding we conducted a complementary study using a…

We investigate the Coulomb phase shift, and derive and analyze new and more precise analytical formulae. We consider next to leading order terms to the Stirling approximation, and show that they are important at small values of the angular…

Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…

Collagen is a key component of the extracellular matrix and well-oriented domains of collagen are relevant for mimicking the local cell environment in vitro. While there has been significant attention directed towards the alignment of…