Cirbo: A New Tool for Boolean Circuit Analysis and Synthesis

We present an open-source tool for manipulating Boolean circuits. It implements efficient algorithms, both existing and novel, for a rich variety of frequently used circuit tasks such as satisfiability, synthesis, and minimization. We tested the tool on a wide range of practically relevant circuits (computing, in particular, symmetric and arithmetic functions) that have been optimized intensively by the community for the last three years. The tool helped us to win the IWLS 2024 Programming Contest. In 2023, it was Google DeepMind who took the first place in the competition. We were able to reduce the size of the best circuits from 2023 by 12\% on average, whereas for some individual circuits, our size reduction was as large as 83\%.

CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data

Paired single-cell sequencing technologies enable the simultaneous measurement of complementary modalities of molecular data at single-cell resolution. Along with the advances in these technologies, many methods based on variational autoencoders have been developed to integrate these data. However, these methods do not explicitly incorporate prior biological relationships between the data modalities, which could significantly enhance modeling and interpretation. We propose a novel probabilistic learning framework that explicitly incorporates conditional independence relationships between multi-modal data as a directed acyclic graph using a generalized hierarchical variational autoencoder. We demonstrate the versatility of our framework across various applications pertinent to single-cell multi-omics data integration. These include the isolation of common and distinct information from different modalities, modality-specific differential analysis, and integrated cell clustering. We anticipate that the proposed framework can facilitate the construction of highly flexible graphical models that can capture the complexities of biological hypotheses and unravel the connections between different biological data types, such as different modalities of paired single-cell multi-omics data. The implementation of the proposed framework can be found in the repository https://github.com/kuijjerlab/CAVACHON.