Related papers: Error probability amplification in cellular transl…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
A new approach to the problem of error correction in communication channels is proposed, in which the input sequence is transformed in such a way that the interdependence of symbols is significantly increased. Then, after the sequence is…
Recent research has generated hope that inference scaling, such as resampling solutions until they pass verifiers like unit tests, could allow weaker models to match stronger ones. Beyond inference, this approach also enables training…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
Societal accumulation of knowledge is a complex process. The correctness of new units of knowledge depends not only on the correctness of new reasoning, but also on the correctness of old units that the new one builds on. The errors in such…
In neural machine translation, cross entropy (CE) is the standard loss function in two training methods of auto-regressive models, i.e., teacher forcing and scheduled sampling. In this paper, we propose mixed cross entropy loss (mixed CE)…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
The performance of maximum-likelihood (ML) decoded binary linear block codes is addressed via the derivation of tightened upper bounds on their decoding error probability. The upper bounds on the block and bit error probabilities are valid…
Constancy of life vitally depends on the internalization of particles through biomembranes. Of particular interest, cellular uptake, including phagocytosis, receptor-mediated endocytosis, and membrane fusion, critically depends on the…
In probabilistic cloning with two auxiliary systems, we consider and compare three different protocols for the success probabilities of cloning. We show that, in certain circumstances, it may increase the success probability to add an…
Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Sensitive detection of low-abundance molecular targets is widely assumed to require enzymatic amplification, such as PCR, to achieve low detection limits. In amplification-free platforms, sensitivity is traditionally constrained by…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
Chiral effective field theory (EFT) predictions are necessarily truncated at some order in the EFT expansion, which induces an error that must be quantified for robust statistical comparisons to experiment. In previous work, a Bayesian…
We demonstrate that theoretical predictions using current resummation techniques for the lepton pair production (LPP) rapidity and $x_F$ distributions can be inconsistent with data in high rapidity and $x_F$ kinematic regions by observing…
Recent studies have revealed that neural networks learn interpretable algorithms for many simple problems. However, little is known about how these algorithms emerge during training. In this article, I study the training dynamics of a small…
We consider hard-decision iterative decoders for product codes over the erasure channel, which employ repeated rounds of decoding rows and columns alternatingly. We derive the exact asymptotic probability of decoding failure as a function…
The problem of channel coding with the erasure option is revisited for discrete memoryless channels. The interplay between the code rate, the undetected and total error probabilities is characterized. Using the information spectrum method,…