Question about the position encoding of 'pe = 0.' code

[lishensuo]

https://github.com/OmicsML/CellPLM/blob/b59ee7688b1bd2a745856a610248b46f15019a22/CellPLM/embedder/omics.py#L88C1-L101C17

In the last forwrd part of CellPLM/CellPLM/embedder/omics.py, I notice that the pe variable is always initialized as 0 and it seems that pe not related the coordinate encoding. Does it mean that x only includes the expression embed and batch embed? Could you explain the reasons? Thanks.

    def forward(self, x_dict, input_gene_list=None):
        x = self.feat_enc(x_dict, input_gene_list)#self.act(self.feat_enc(x_dict, input_gene_list))
        if self.pe_enc is not None:
            pe_input = x_dict[self.pe_enc.pe_key]
            pe = 0.#self.pe_enc(pe_input)
            if self.inject_covariate:
                pe = pe + self.cov_enc(x_dict['batch'])
            if self.cat_pe:
                x = torch.cat([x, pe], 1)
            else:
                x = x + pe
        x = self.extra_linear(x)
        # x = self.norm0(self.dropout(x))
        return x

[wehos]

Sorry for the late response. This is a bug for sure and I'm very sad that I didn't see this issue until today. This comment should definitely be removed in order to facilitate spatial transcriptomics. I'll fix it in an update soon.

Thank you very much for this good catch!