Simulations | Results are shown in Fig 4 and S2 Table, where warmer colors indicate higher ploidy estimation accuracy . |
Simulations | When using the naive error model, ConPADE achieved substantially lower ploidy estimation accuracy , especially for coverages of 10X and 15X at intermediate ploidy levels (Fig 4 and S2 Table). |
Simulations | Because a coverage level of 50X resulted in correct estimated ploidies and high dosage estimation accuracy in the previous simulation sets, while still being viable in practice for de novo genome assembly efforts, we chose this value for more detailed simulations regarding contig lengths, the results of which are shown in Fig 5 and S5 Table. |
Supporting Information | Ploidy estimation accuracy for varying contig lengths and coverage levels. |
Complex driving protocols and objectives | This improvement was the result of: (i) some parameters being estimated accurately by the voltage-clamp protocol and (ii) information on two, rather than a single, state variable putting more constraints on the parameter values [36]. |
Extending the protocol: Adding multi-step voltage clamp data | To improve parameter estimation accuracy , more improvement is typically gained from adding measurements of a different state variable than adding additional measurements of the same state variable [36]. |
Extending the protocol: Adding multi-step voltage clamp data | Therefore, to improve the parameter estimation accuracy , we added a multi-step voltage clamp protocol to the objective function. |
Comparing current and conductance-based inputs with simulated neurons | Since real synaptic currents are generated by changing conductances, it is possible that our detection results overestimated the detectability and estimation accuracy of synaptic weights from spikes. |
Current-based vs conductance-based synaptic input | As before, the postsynaptic firing rate has a large effect on detectability and estimation accuracy with higher rates resulting in faster detection of inputs. |
Current-based vs conductance-based synaptic input | Estimation accuracy for the current-based model, in this case, was R2 = 0.85 for 1Hz output, 0.93 for 5Hz output, and 0.96 for 10Hz output (for clarity only 5Hz condition is shown in Fig. |