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Tomography has reached its practical limits in characterization of new quantum devices, and there is a need for a new means of characterizing and validating new technological advances in this field. We propose a different verification…

We present an approach for implementing a formally certified loop-invariant code motion optimization by composing an unrolling pass and a formally certified yet efficient global subexpression elimination.This approach is lightweight: each…

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our…

This paper presents the main features of a system that aims to transform regular expressions into shorter equivalent expressions. The system is also capable of computing other operations useful for simplification, such as checking the…

Processing large amounts of data fast, in constant and small space is the point of stream processing and the reason for its increasing use. Alas, the most performant, imperative processing code tends to be almost impossible to read, let…

Quantum process tomography (QPT) plays a central role in characterizing quantum gates and circuits, diagnosing quantum devices, calibrating hardware, and supporting quantum error correction. However, conventional QPT methods face challenges…

Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…

Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…

We describe algorithms for symbolic reasoning about executable models of type systems, supporting three queries intended for designers of type systems. First, we check for type soundness bugs and synthesize a counterexample program if such…

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…

Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…

In this paper, we reconsider the unfolding-based technique that we have introduced previously for detecting loops in standard term rewriting. We improve it by guiding the unfolding process, using distinguished positions in the rewrite…

Any quantum computing application, once encoded as a quantum circuit, must be compiled before being executable on a quantum computer. Similar to classical compilation, quantum compilation is a sequential process with many compilation steps…

We present a framework for using transformer networks as universal computers by programming them with specific weights and placing them in a loop. Our input sequence acts as a punchcard, consisting of instructions and memory for data…

The increasing complexity of large-scale language models has amplified concerns regarding their interpretability and reusability. While traditional embedding models like Word2Vec and GloVe offer scalability, they lack transparency and often…

Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce whole-cell expression decoding (WCED), where models…

Soft robots employing compliant materials and deformable structures offer great potential for wearable devices that are comfortable and safe for human interaction. However, achieving both structural integrity and compliance for comfort…

As immersive technologies evolve, immersive computational notebooks offer new opportunities for interacting with code, data, and outputs. However, scaling these environments remains a challenge, particularly when analysts manually arrange…

Synthetic Biology is an interdisciplinary field that utilizes well-established engineering principles, ranging from electrical, control and computer systems, for analyzing the biological systems, such as biological circuits, enzymes,…

Band structure unfolding is a key technique for analyzing and simplifying the electronic band structure of large, internally distorted supercells that break the primitive cell's translational symmetry. In this work, we present an efficient…