The linked model uses nn.Conv1d layers, which is why the 3-dimensional input is expected (it should have the shape [batch_size, channels, seq_len]).
If you want to use only two dimensions, you could change the layer type to e.g. linear layers and would need to experiment with the architecture (i.e. number of features etc.). Alternatively, you could also add an additional dimension (e.g. the channel or temporal dimension) and run some experiments with the current architecture.