Python torch.tril_indices() Examples

def deprecate_task_noise_corr(state_dict, prefix, local_metadata, strict, missing_keys, unexpected_keys, error_msgs):
    if prefix + "task_noise_corr_factor" in state_dict:
        # Remove after 1.0
        warnings.warn(
            "Loading a deprecated parameterization of _MultitaskGaussianLikelihoodBase. Consider re-saving your model.",
            OldVersionWarning,
        )
        # construct the task correlation matrix from the factors using the old parameterization
        corr_factor = state_dict.pop(prefix + "task_noise_corr_factor").squeeze(0)
        corr_diag = state_dict.pop(prefix + "task_noise_corr_diag").squeeze(0)
        num_tasks, rank = corr_factor.shape[-2:]
        M = corr_factor.matmul(corr_factor.transpose(-1, -2))
        idx = torch.arange(M.shape[-1], dtype=torch.long, device=M.device)
        M[..., idx, idx] += corr_diag
        sem_inv = 1 / torch.diagonal(M, dim1=-2, dim2=-1).sqrt().unsqueeze(-1)
        C = M * sem_inv.matmul(sem_inv.transpose(-1, -2))
        # perform a Cholesky decomposition and extract the required entries
        L = torch.cholesky(C)
        tidcs = torch.tril_indices(num_tasks, rank)[:, 1:]
        task_noise_corr = L[..., tidcs[0], tidcs[1]]
        state_dict[prefix + "task_noise_corr"] = task_noise_corr 

def get_modified_adj(self, ori_adj):

        if self.complementary is None:
            self.complementary = (torch.ones_like(ori_adj) - torch.eye(self.nnodes).to(self.device) - ori_adj) - ori_adj

        m = torch.zeros((self.nnodes, self.nnodes)).to(self.device)
        tril_indices = torch.tril_indices(row=self.nnodes-1, col=self.nnodes-1, offset=0)
        m[tril_indices[0], tril_indices[1]] = self.adj_changes
        # m += m.t()
        m = m + m.t()
        modified_adj = self.complementary * m + ori_adj

        return modified_adj 

def interact_features(self, x, ly):
        if self.arch_interaction_op == "dot":
            # concatenate dense and sparse features
            (batch_size, d) = x.shape
            T = torch.cat([x] + ly, dim=1).view((batch_size, -1, d))
            # perform a dot product
            Z = torch.bmm(T, torch.transpose(T, 1, 2))
            # append dense feature with the interactions (into a row vector)
            # approach 1: all
            # Zflat = Z.view((batch_size, -1))
            # approach 2: unique
            _, ni, nj = Z.shape
            # approach 1: tril_indices
            # offset = 0 if self.arch_interaction_itself else -1
            # li, lj = torch.tril_indices(ni, nj, offset=offset)
            # approach 2: custom
            offset = 1 if self.arch_interaction_itself else 0
            li = torch.tensor([i for i in range(ni) for j in range(i + offset)])
            lj = torch.tensor([j for i in range(nj) for j in range(i + offset)])
            Zflat = Z[:, li, lj]
            # concatenate dense features and interactions
            R = torch.cat([x] + [Zflat], dim=1)
        elif self.arch_interaction_op == "cat":
            # concatenation features (into a row vector)
            R = torch.cat([x] + ly, dim=1)
        else:
            sys.exit(
                "ERROR: --arch-interaction-op="
                + self.arch_interaction_op
                + " is not supported"
            )

        return R 

def interact_features(self, x, ly):
        if self.arch_interaction_op == "dot":
            # concatenate dense and sparse features
            (batch_size, d) = x.shape
            T = torch.cat([x] + ly, dim=1).view((batch_size, -1, d))
            # perform a dot product
            Z = torch.bmm(T, torch.transpose(T, 1, 2))
            # append dense feature with the interactions (into a row vector)
            # approach 1: all
            # Zflat = Z.view((batch_size, -1))
            # approach 2: unique
            _, ni, nj = Z.shape
            # approach 1: tril_indices
            # offset = 0 if self.arch_interaction_itself else -1
            # li, lj = torch.tril_indices(ni, nj, offset=offset)
            # approach 2: custom
            offset = 1 if self.arch_interaction_itself else 0
            li = torch.tensor([i for i in range(ni) for j in range(i + offset)])
            lj = torch.tensor([j for i in range(nj) for j in range(i + offset)])
            Zflat = Z[:, li, lj]
            # concatenate dense features and interactions
            R = torch.cat([x] + [Zflat], dim=1)
        elif self.arch_interaction_op == "cat":
            # concatenation features (into a row vector)
            R = torch.cat([x] + ly, dim=1)
        else:
            sys.exit(
                "ERROR: --arch-interaction-op="
                + self.arch_interaction_op
                + " is not supported"
            )

        return R 

def _triangular_form(v):
    b_size = v.shape[0]
    N = v.shape[1]
    # TODO; assert shape
    M = int((np.sqrt(1 + 8 * N) - 1) / 2)
    tril_matrix = torch.zeros((b_size, M, M))
    tril_indices = torch.tril_indices(row=M, col=M, offset=0)
    tril_matrix[:, tril_indices[0], tril_indices[1]] = v
    return tril_matrix 

def __init__(self, num_tasks, noise_covar, rank=0, task_correlation_prior=None, batch_shape=torch.Size()):
        """
        Args:
            num_tasks (int):
                Number of tasks.
            noise_covar (:obj:`gpytorch.module.Module`):
                A model for the noise covariance. This can be a simple homoskedastic noise model, or a GP
                that is to be fitted on the observed measurement errors.
            rank (int):
                The rank of the task noise covariance matrix to fit. If `rank` is set to 0, then a diagonal covariance
                matrix is fit.
            task_correlation_prior (:obj:`gpytorch.priors.Prior`):
                Prior to use over the task noise correlation matrix. Only used when `rank` > 0.
            batch_shape (torch.Size):
                Number of batches.
        """
        super().__init__(noise_covar=noise_covar)
        if rank != 0:
            if rank > num_tasks:
                raise ValueError(f"Cannot have rank ({rank}) greater than num_tasks ({num_tasks})")
            tidcs = torch.tril_indices(num_tasks, rank, dtype=torch.long)
            self.tidcs = tidcs[:, 1:]  # (1, 1) must be 1.0, no need to parameterize this
            task_noise_corr = torch.randn(*batch_shape, self.tidcs.size(-1))
            self.register_parameter("task_noise_corr", torch.nn.Parameter(task_noise_corr))
            if task_correlation_prior is not None:
                self.register_prior(
                    "MultitaskErrorCorrelationPrior", task_correlation_prior, lambda: self._eval_corr_matrix
                )
        elif task_correlation_prior is not None:
            raise ValueError("Can only specify task_correlation_prior if rank>0")
        self.num_tasks = num_tasks
        self.rank = rank
        # Handle deprecation of parameterization - TODO: Remove in future release
        self._register_load_state_dict_pre_hook(deprecate_task_noise_corr) 

def triple_by_molecule(atom_index12: Tensor) -> Tuple[Tensor, Tensor, Tensor]:
    """Input: indices for pairs of atoms that are close to each other.
    each pair only appear once, i.e. only one of the pairs (1, 2) and
    (2, 1) exists.

    Output: indices for all central atoms and it pairs of neighbors. For
    example, if input has pair (0, 1), (0, 2), (0, 3), (0, 4), (1, 2),
    (1, 3), (1, 4), (2, 3), (2, 4), (3, 4), then the output would have
    central atom 0, 1, 2, 3, 4 and for cental atom 0, its pairs of neighbors
    are (1, 2), (1, 3), (1, 4), (2, 3), (2, 4), (3, 4)
    """
    # convert representation from pair to central-others
    ai1 = atom_index12.view(-1)
    sorted_ai1, rev_indices = ai1.sort()

    # sort and compute unique key
    uniqued_central_atom_index, counts = torch.unique_consecutive(sorted_ai1, return_inverse=False, return_counts=True)

    # compute central_atom_index
    pair_sizes = counts * (counts - 1) // 2
    pair_indices = torch.repeat_interleave(pair_sizes)
    central_atom_index = uniqued_central_atom_index.index_select(0, pair_indices)

    # do local combinations within unique key, assuming sorted
    m = counts.max().item() if counts.numel() > 0 else 0
    n = pair_sizes.shape[0]
    intra_pair_indices = torch.tril_indices(m, m, -1, device=ai1.device).unsqueeze(1).expand(-1, n, -1)
    mask = (torch.arange(intra_pair_indices.shape[2], device=ai1.device) < pair_sizes.unsqueeze(1)).flatten()
    sorted_local_index12 = intra_pair_indices.flatten(1, 2)[:, mask]
    sorted_local_index12 += cumsum_from_zero(counts).index_select(0, pair_indices)

    # unsort result from last part
    local_index12 = rev_indices[sorted_local_index12]

    # compute mapping between representation of central-other to pair
    n = atom_index12.shape[1]
    sign12 = ((local_index12 < n).to(torch.int8) * 2) - 1
    return central_atom_index, local_index12 % n, sign12