Related papers: A Novel P-bit-based Probabilistic Computing Approa…
Probabilistic bit (p-bit)-based compute engines utilize the unique capability of a p-bit to probabilistically switch between two states to solve computationally challenging problems. However, when solving problems that require more than two…
With the advent of high-throughput wet lab technologies the amount of protein interaction data available publicly has increased substantially, in turn spurring a plethora of computational methods for in silico knowledge discovery from this…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
We study a variant of the median problem for a collection of point sets in high dimensions. This generalizes the geometric median as well as the (probabilistic) smallest enclosing ball (pSEB) problems. Our main objective and motivation is…
Ising machines -- special-purpose hardware for heuristically solving Ising optimization problems -- based on probabilistic bits (p-bits) have been established as a promising alternative to heuristic optimization algorithms run on…
In VLSI physical design, many algorithms require the solution of difficult combinatorial optimization problems such as max/min-cut, max-flow problems etc. Due to the vast number of elements typically found in this problem domain, these…
Image segmentation is a popular area of research in computer vision that has many applications in automated image processing. A recent technique called piecewise flat embeddings (PFE) has been proposed for use in image segmentation; PFE…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
Computational workloads are growing exponentially, driving power consumption to unsustainable levels. Efficiently distributing large-scale networks is an NP-Complete problem equivalent to Boolean satisfiability (SAT), making it one of the…
The photonic Ising machine is a new paradigm of optical computing that takes advantage of the unique properties of light wave propagation, parallel processing, and low-loss transmission. Thus, the process of solving combinatorial…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…
Probability Density Estimation (PDE) is a multivariate discrimination technique based on sampling signal and background densities defined by event samples from data or Monte-Carlo (MC) simulations in a multi-dimensional phase space. In this…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology. The problem of protein structure prediction is about predicting the native conformation of a protein, while its sequence of amino acids is…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
Ongoing semiconductor scaling challenges and the rise of neuromorphic computing have sparked interest in exploring novel computing schemes to achieve higher power efficiency and computational capabilities. Probabilistic computing is one…
We provide Ising formulations for many NP-complete and NP-hard problems, including all of Karp's 21 NP-complete problems. This collects and extends mappings to the Ising model from partitioning, covering and satisfiability. In each case,…