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Web AI agents such as ChatGPT Agent and GenSpark are increasingly used for routine web-based tasks, yet they still rely on text-based input prompts, lack proactive detection of user intent, and offer no support for interactive data analysis…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
In data stream applications, one of the critical issues is to estimate the frequency of each item in the specific multiset. The multiset means that each item in this set can appear multiple times. The data streams in many applications are…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
The proliferation of the web presents an unsolved problem of automatically analyzing billions of pages of natural language. We introduce a scalable algorithm that clusters hundreds of millions of web pages into hundreds of thousands of…
Databases are widespread, yet extracting relevant data can be difficult. Without substantial domain knowledge, multivariate search queries often return sparse or uninformative results. This paper introduces an approach for searching…
Large databases are often organized by hand-labeled metadata, or criteria, which are expensive to collect. We can use unsupervised learning to model database variation, but these models are often high dimensional, complex to parameterize,…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Identifying trendline visualizations with desired patterns is a common and fundamental data exploration task. Existing visual analytics tools offer limited flexibility and expressiveness for such tasks, especially when the pattern of…
We propose an approach to index raster images of dictionary pages which in turn would require very little manual effort to enable direct access to the appropriate pages of the dictionary for lookup. Accessibility is further improved by…
We present iSLAT (the Interactive Spectral-Line Analysis Tool), a python-based graphical tool that allows users to interactively explore and manually fit line emission observed in molecular spectra. iSLAT adopts a simple slab model that…
We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
Modern Search Engine Results Pages (SERPs) present complex layouts where multiple elements compete for visibility. Attention modelling is crucial for optimising web design and computational advertising, whereas attention metrics can inform…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Search queries are appropriate when users have explicit intent, but they perform poorly when the intent is difficult to express or if the user is simply looking to be inspired. Visual browsing systems allow e-commerce platforms to address…
Recent developments in support for constructing knowledge graphs have led to a rapid rise in their creation both on the Web and within organisations. Added to existing sources of data, including relational databases, APIs, etc., there is a…
Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it.…