Related papers: Methods to Estimate Cryptic Sequence Complexity
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
Constructing good test cases is difficult and time-consuming, especially if the system under test is still under development and its exact behavior is not yet fixed. We propose a new approach to compute test strategies for reactive systems…
We construct a complexity-based morphospace to study systems-level properties of conscious & intelligent systems. The axes of this space label 3 complexity types: autonomous, cognitive & social. Given recent proposals to synthesize…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
In this work, we study diversity-aware clustering problems where the data points are associated with multiple attributes resulting in intersecting groups. A clustering solution needs to ensure that the number of chosen cluster centers from…
The concept of information has emerged as a language in its own right, bridging several disciplines that analyze natural phenomena and man-made systems. Integrated information has been introduced as a metric to quantify the amount of…
We derive and analyze a generic, recursive algorithm for estimating all splits in a finite cluster tree as well as the corresponding clusters. We further investigate statistical properties of this generic clustering algorithm when it…
In the rapidly evolving field of quantum computing, quantifying circuit complexity remains a critical challenge. This paper introduces Character Complexity, a novel measure that bridges Group-theoretic concepts with practical quantum…
In this paper we examine the concept of complexity as it applies to generative and evolutionary art and design. Complexity has many different, discipline specific definitions, such as complexity in physical systems (entropy), algorithmic…
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition…
Changepoint detection is commonly formulated by minimizing the sum of in-sample losses to quantify the model's overall fit. However, for flexible modeling procedures -- especially those involving high-dimensional parameter spaces or…
Validation is a key challenge in the search for safe autonomy. Simulations are often either too simple to provide robust validation, or too complex to tractably compute. Therefore, approximate validation methods are needed to tractably find…
Science and technology have a growing need for effective mechanisms that ensure reliable, controlled performance from black-box machine learning algorithms. These performance guarantees should ideally hold conditionally on the input-that is…
This work addresses challenges in evaluating adaptive artificial intelligence (AI) models for medical devices, where iterative updates to both models and evaluation datasets complicate performance assessment. We introduce a novel approach…
In this paper we examine the concept of complexity as it applies to generative art and design. Complexity has many different, discipline specific definitions, such as complexity in physical systems (entropy), algorithmic measures of…
Answer Set Programming (ASP) is a problem modeling and solving framework for several problems in KR with growing industrial applications. Also for studies of computational complexity and deeper insights into the hardness and its sources,…
Often a screening or selection experiment targets a cell or tissue, which presents many possible molecular targets and identifies a correspondingly large number of ligands. We describe a statistical method to extract an estimate of the…
The clusters of a distribution are often defined by the connected components of a density level set. However, this definition depends on the user-specified level. We address this issue by proposing a simple, generic algorithm, which uses an…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…