Computing with many encoded logical qubits beyond break-even

High-rate quantum error correcting (QEC) codes encode many logical qubits in a given number of physical qubits, making them promising candidates for quantum computation. Implementing high-rate codes at a scale that both frustrates classical computing and improves performance by encoding requires both high fidelity gates and long-range qubit connectivity -- both of which are offered by trapped-ion quantum computers. Here, we demonstrate computations that outperform their unencoded counterparts in the high-rate $[[ k+2,\, k,\, 2 ]]$ iceberg quantum error detecting (QED) and $[[ (k_2 + 2)(k_1 + 2),\, k_2k_1,\, 4 ]]$ two-level concatenated iceberg QEC codes, using the 98-qubit Quantinuum Helios trapped-ion quantum processor. Utilizing new gadgets for encoded operations, we realize this "beyond break-even" performance with reasonable postselection rates across a range of fault-tolerant (FT) and partially-fault-tolerant (pFT) component and application benchmarks with between $48$ and $94$ logical qubits. These benchmarks include FT state preparation and measurement, QEC cycle benchmarking, logical gate benchmarking, GHZ state preparation, and a pFT quantum simulation of the three-dimensional $XY$ model of quantum magnetism. Additionally, we illustrate that postselection rates can be suppressed by increasing the code distance via concatenation. Our results represent state-of-the-art logical component and state fidelities and provide evidence that high-rate QED/QEC codes are viable on contemporary quantum computers for near-term beyond-classical-scale computation.