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This paper develops a nonlinear operator dynamic that progressively removes the influence of a prescribed feature subspace while retaining maximal structure elsewhere. The induced sequence of positive operators is monotone, admits an exact…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
We propose Seq2Edits, an open-vocabulary approach to sequence editing for natural language processing (NLP) tasks with a high degree of overlap between input and output texts. In this approach, each sequence-to-sequence transduction is…
Image registration is fundamental in medical imaging applications, such as disease progression analysis or radiation therapy planning. The primary objective of image registration is to precisely capture the deformation between two or more…
Image-guided drawing can compensate for the lack of skills but often requires a significant number of repetitive strokes to create textures. Existing automatic stroke synthesis methods are usually limited to predefined styles or require…
The pretraining-fine-tuning paradigm has been the de facto strategy for transfer learning in modern language modeling. With the understanding that task adaptation in LMs is often a function of parameters shared across tasks, we argue that a…
We propose a nested recurrent neural network (nested RNN) model for English spelling error correction and generate pseudo data based on phonetic similarity to train it. The model fuses orthographic information and context as a whole and is…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
Recently, it was shown that any theory of strings containing the string-replace function (even the most restricted version where pattern/replacement strings are both constant strings) becomes undecidable if we do not impose some kind of…
This paper proposes an algorithm (RMDA) for training neural networks (NNs) with a regularization term for promoting desired structures. RMDA does not incur computation additional to proximal SGD with momentum, and achieves variance…
Revision programming is a formalism to describe and enforce updates of belief sets and databases. That formalism was extended by Fitting who assigned annotations to revision atoms. Annotations provide a way to quantify the confidence…
Most existing sequence generation models produce outputs in one pass, usually left-to-right. However, this is in contrast with a more natural approach that humans use in generating content; iterative refinement and editing. Recent work has…
Regularization is one of the crucial ingredients of deep learning, yet the term regularization has various definitions, and regularization methods are often studied separately from each other. In our work we present a systematic, unifying…
Existing GAN inversion methods are stuck in a paradox that the inverted codes can either achieve high-fidelity reconstruction, or retain the editing capability. Having only one of them clearly cannot realize real image editing. In this…
The several algebraic approaches to graph transformation proposed in the literature all ensure that if an item is preserved by a rule, so are its connections with the context graph where it is embedded. But there are applications in which…
Regular expressions are pervasive in modern systems. Many real-world regular expressions are inefficient, sometimes to the extent that they are vulnerable to complexity-based attacks, and while much research has focused on detecting…
Graph-Rewriting Automata (GRA) are an extension of Cellular Automata to a dynamic structure using local graph-rewriting rules. This work introduces linear algebra based tools that allow for a practical investigation of their behavior in…
In this paper we give a criterion by which one can conclude that every reduction of a basic term to normal form has the same length. As a consequence, the number of steps to reach the normal form is independent of the chosen strategy. In…