Revealing the vectors of cellular identity with single-cell genomics

A Wagner, A Regev, N Yosef - Nature biotechnology, 2016 - nature.com
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …

Executable cancer models: successes and challenges

MA Clarke, J Fisher - Nature Reviews Cancer, 2020 - nature.com
Making decisions on how best to treat cancer patients requires the integration of different
data sets, including genomic profiles, tumour histopathology, radiological images, proteomic …

Flashmeta: A framework for inductive program synthesis

O Polozov, S Gulwani - Proceedings of the 2015 ACM SIGPLAN …, 2015 - dl.acm.org
Inductive synthesis, or programming-by-examples (PBE) is gaining prominence with
disruptive applications for automating repetitive tasks in end-user programming. However …

Decoding the regulatory network of early blood development from single-cell gene expression measurements

V Moignard, S Woodhouse, L Haghverdi, AJ Lilly… - Nature …, 2015 - nature.com
Reconstruction of the molecular pathways controlling organ development has been
hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a …

Inversecsg: Automatic conversion of 3d models to csg trees

T Du, JP Inala, Y Pu, A Spielberg, A Schulz… - ACM Transactions on …, 2018 - dl.acm.org
While computer-aided design is a major part of many modern manufacturing pipelines, the
design files typically generated describe raw geometry. Lost in this representation is the …

A lightweight symbolic virtual machine for solver-aided host languages

E Torlak, R Bodik - ACM SIGPLAN Notices, 2014 - dl.acm.org
Solver-aided domain-specific languages (SDSLs) are an emerging class of computer-aided
programming systems. They ease the construction of programs by using satisfiability solvers …

Optimizing synthesis with metasketches

J Bornholt, E Torlak, D Grossman, L Ceze - Proceedings of the 43rd …, 2016 - dl.acm.org
Many advanced programming tools---for both end-users and expert developers---rely on
program synthesis to automatically generate implementations from high-level specifications …

Precise parameter synthesis for stochastic biochemical systems

M Češka, F Dannenberg, N Paoletti, M Kwiatkowska… - Acta Informatica, 2017 - Springer
We consider the problem of synthesising rate parameters for stochastic biochemical
networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of …

Scalable verification of border gateway protocol configurations with an SMT solver

K Weitz, D Woos, E Torlak, MD Ernst… - Proceedings of the …, 2016 - dl.acm.org
Internet Service Providers (ISPs) use the Border Gateway Protocol (BGP) to announce and
exchange routes for de-livering packets through the internet. ISPs must carefully configure …

Neurosymbolic programming for science

JJ Sun, M Tjandrasuwita, A Sehgal… - arXiv preprint arXiv …, 2022 - arxiv.org
Neurosymbolic Programming (NP) techniques have the potential to accelerate scientific
discovery. These models combine neural and symbolic components to learn complex …