Integrated optics is an engineering solution proposed for exquisite control of photonic quantum information. Here we use silicon photonics and the linear combination of quantum operators scheme to realise a fully programmable two-qubit quantum processor. The device is fabricated with readily available CMOS based processing and comprises four nonlinear photon-sources, four filters, eighty-two beam splitters and fifty-eight individually addressable phase shifters. To demonstrate performance, we programmed the device to implement ninety-eight various two-qubit unitary operations (with average quantum process fidelity of 93.2$pm$4.5%), a two-qubit quantum approximate optimization algorithm and efficient simulation of Szegedy directed quantum walks. This fosters further use of the linear combination architecture with silicon photonics for future photonic quantum processors.
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