tinygnn 0.1.5

TinyGNN — A zero-dependency C++17 inference engine for Sparse Graph Neural Networks with Python bindings

TinyGNN

A dependency-free C++ inference engine optimized for Sparse Graph Neural Networks.

TinyGNN pivots from a dense-only deep learning runtime to a sparse-native architecture, demonstrating low-level systems programming, memory architecture optimizations, and parallel computing -- with zero external dependencies.

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Project Roadmap

Phase	Title	Status
1	Hybrid Tensor Core	Complete
2	Graph Data Loader	Complete
3	Dense Compute Kernels (GEMM)	Complete
4	Sparse Compute Kernels (SpMM)	Complete
5	Activations & Utilities	Complete
6	Multi-Architecture Layer Assembly	Complete
7	Multi-Model End-to-End Pipeline & Reference Matching	Complete
8	Python Bridge (pybind11)	Complete
9	Software-Level Parallelism (OpenMP & AVX2)	Complete
10	Operator Fusion (GAT & GraphSAGE)	Complete
11	Packaging, CI/CD & Documentation	Complete

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Project Structure

TinyGNN/
├── CMakeLists.txt
├── setup.py                    # pybind11 Python extension build
├── pyproject.toml              # Phase 11: PEP 517/518 packaging metadata (PyPI)
├── MANIFEST.in                 # Phase 11: source distribution manifest
├── LICENSE                     # Phase 11: MIT license
├── CITATION.cff                # Phase 11: JOSS/JMLR citation metadata
├── CONTRIBUTING.md             # Phase 11: contributor guidelines
├── Doxyfile                    # Phase 11: Doxygen C++ documentation config
├── .github/
│   └── workflows/
│       └── ci.yml              # Phase 11: GitHub Actions CI/CD pipeline
├── docs/                       # Phase 11: Sphinx documentation
│   ├── conf.py                 # Sphinx configuration
│   ├── index.rst               # Documentation home page
│   ├── installation.rst        # Installation guide
│   ├── quickstart.rst          # Quick start tutorial
│   ├── python_api.rst          # Python API reference
│   ├── cpp_api.rst             # C++ API reference (Breathe + Doxygen)
│   ├── benchmarks.rst          # Benchmark results
│   └── Makefile                # Sphinx build helper
├── benchmarks/
│   ├── bench_parallel.cpp      # Phase 9: OpenMP + AVX2 thread-scaling benchmark
│   ├── bench_fusion.cpp        # Phase 10: fused vs. unfused GAT/SAGE runtime + memory
│   ├── massif_gat_fused.cpp    # Phase 10: Massif profiling (fused GAT heap)
│   ├── massif_gat_unfused.cpp  # Phase 10: Massif profiling (unfused GAT heap)
│   └── thread_scaling.png      # Phase 9: generated thread-scaling chart
├── include/
│   └── tinygnn/
│       ├── tensor.hpp          # StorageFormat enum + Tensor struct
│       ├── graph_loader.hpp    # GraphData + GraphLoader (CSV -> CSR pipeline)
│       ├── ops.hpp             # compute kernels + activations: matmul, spmm, relu, softmax, etc.
│       ├── layers.hpp          # GCN, GraphSAGE, GAT layer structs + helpers
│       └── model.hpp           # Model execution graph + binary weight/graph loaders
├── src/
│   ├── tensor.cpp
│   ├── graph_loader.cpp        # CSV parser + edge-list-to-CSR conversion
│   ├── ops.cpp                 # matmul, spmm, relu, leaky_relu, elu, sigmoid, tanh, gelu, softmax, log_softmax, add_bias
│   ├── layers.cpp              # add_self_loops, gcn_norm, GCNLayer, SAGELayer, GATLayer, edge_softmax
│   └── model.cpp               # Model::forward(), load_cora_binary(), load_weight_file()
├── python/
│   ├── tinygnn_ext.cpp         # Phase 8: pybind11 C++ bindings (280+ lines)
│   └── tinygnn/
│       └── __init__.py         # Phase 8: Python package re-exports
├── tests/
│   ├── test_tensor.cpp         # Phase 1 -- 104 assertions
│   ├── test_graph_loader.cpp   # Phase 2 -- 269 assertions
│   ├── test_matmul.cpp         # Phase 3 -- 268 assertions
│   ├── test_spmm.cpp           # Phase 4 -- 306 assertions
│   ├── test_activations.cpp    # Phase 5 -- 266 assertions
│   ├── test_gcn.cpp            # Phase 6a -- 764 assertions
│   ├── test_graphsage.cpp      # Phase 6b -- 1,011 assertions
│   ├── test_gat.cpp            # Phase 6c -- 1,284 assertions
│   ├── test_e2e.cpp            # Phase 7  -- 13,862 assertions (end-to-end pipeline)
│   └── test_python_bindings.py # Phase 8  -- 49 pytest tests (Python bridge)
├── datasets/                   # downloaded via scripts/fetch_datasets.py
│   ├── cora/                   # 2,708 nodes, 5,429 edges, 1,433 features
│   └── reddit/                 # 232,965 nodes, 114,615,892 edges, 602 features
├── weights/                    # exported by train_cora.py (gitignored)
│   ├── cora_graph.bin          # Cora graph in binary (features, labels, masks, edges)
│   ├── gcn_cora.bin            # GCN trained weights (~78% test accuracy)
│   ├── sage_cora.bin           # GraphSAGE trained weights (~81% test accuracy)
│   └── gat_cora.bin            # GAT trained weights (~80% test accuracy)
└── scripts/
    ├── install_wsl_tools.sh    # one-time WSL tooling setup
    ├── fetch_datasets.py       # download Cora + Reddit, convert to CSV
    ├── train_cora.py           # PyG training: GCN/SAGE/GAT → binary weight export
    ├── validate_cora.py        # PyG ↔ TinyGNN logit-level comparison
    ├── plot_scaling.py         # thread-scaling chart generator (matplotlib)
    ├── run_massif_phase9.sh    # Massif memory profiling (fused vs unfused)
    ├── build_python.py         # build Python extension + run tests
    ├── sanitizers.sh           # ASan + UBSan (27 configs, all phases)
    └── valgrind_all.sh         # Memcheck + Helgrind + Callgrind (all phases)

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Installation

Option 1 — PyPI (Python users)

pip install tinygnn

Installs the pre-built Python extension wheel (_tinygnn_core) plus the tinygnn Python package. Supports Python 3.8–3.13 on Linux, macOS, and Windows (x86-64).

Development install from source

git clone https://github.com/AnubhavChoudhery/TinyGNN.git
cd TinyGNN
pip install -e ".[dev]"    # builds the C++ extension in-place + installs dev deps

Verify the install

python -c "import tinygnn; print(tinygnn.__version__)"    # → 0.1.5
python -m pytest tests/test_python_bindings.py -v         # 49 tests
python scripts/validate_cora.py --logit-check             # PyG logit comparison

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Option 3 — Build from source (C++ only)

Prerequisites

• C++17-capable compiler: GCC 8+, Clang 7+, MSVC 2019+
• CMake 3.16+ (optional — g++ directly also works)
• OpenMP (bundled with GCC; for macOS use brew install libomp)
• CPU with AVX2 + FMA (Intel Haswell+ / AMD Zen+; scalar fallback always available)

With CMake

cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build --config Release --parallel
ctest --test-dir build -C Release --output-on-failure

CMake options:

Option	Default	Description
TINYGNN_BUILD_TESTS	ON	Build test executables
TINYGNN_BUILD_BENCHMARKS	ON	Build C++ benchmark executables

Directly with g++ (single test example)

g++ -std=c++17 -O2 -fopenmp -mavx2 -mfma -Wall -Wextra -I include \
    src/tensor.cpp src/graph_loader.cpp src/ops.cpp src/layers.cpp src/model.cpp \
    tests/test_tensor.cpp -o build/test_tensor && ./build/test_tensor

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Python SDK Reference

Install: pip install tinygnn

Tensor

import tinygnn
import numpy as np
from scipy.sparse import csr_matrix

# Dense tensors from NumPy (float32)
arr = np.random.randn(10, 16).astype(np.float32)
X = tinygnn.Tensor.from_numpy(arr)
print(X.rows, X.cols)           # 10, 16
out = X.to_numpy()              # → np.ndarray shape (10, 16)

# 1-D arrays (bias vectors) → (1 × N) Tensor
b = tinygnn.Tensor.from_numpy_1d(np.zeros(16, dtype=np.float32))

# Sparse CSR from SciPy
mat = csr_matrix(...)
A = tinygnn.Tensor.from_scipy_csr(mat)

# Sparse CSR from PyG edge_index
import torch
ei = torch.randint(0, 100, (2, 500))
A = tinygnn.Tensor.from_edge_index(ei, num_nodes=100)

# Inspect CSR internals
rp = A.row_ptr_numpy()    # → np.ndarray int32
ci = A.col_ind_numpy()    # → np.ndarray int32

Ops

# Dense GEMM
C = tinygnn.matmul(A, B)   # Dense A (M×K), Dense B (K×N) → Dense C (M×N)

# Sparse-Dense SpMM
C = tinygnn.spmm(A, B)     # SparseCSR A (M×K), Dense B (K×N) → Dense C (M×N)

# In-place activations
tinygnn.relu_inplace(X)
tinygnn.leaky_relu_inplace(X, alpha=0.01)
tinygnn.elu_inplace(X, alpha=1.0)
tinygnn.sigmoid_inplace(X)
tinygnn.tanh_inplace(X)
tinygnn.gelu_inplace(X)
tinygnn.softmax_inplace(X)        # row-wise, numerically stable
tinygnn.log_softmax_inplace(X)    # row-wise log-softmax

# Bias broadcast  (X[i][j] += bias[0][j])
tinygnn.add_bias(X, bias)

Graph utilities

A_sl   = tinygnn.add_self_loops(A)      # insert identity self-loops
A_norm = tinygnn.gcn_norm(A)            # D̃^(-1/2)(A+I)D̃^(-1/2), adds self-loops
alpha  = tinygnn.edge_softmax(attn_csr) # sparse row-wise softmax
agg    = tinygnn.sage_max_aggregate(A, H)  # CSR neighborhood max-pool

Layers

import tinygnn

# GCN layer  (A must be gcn_norm output)
gcn = tinygnn.GCNLayer(F_in=64, F_out=32, bias=True,
                        activation=tinygnn.Activation.RELU)
gcn.set_weight(tinygnn.Tensor.from_numpy(W))     # Dense (F_in × F_out)
gcn.set_bias(tinygnn.Tensor.from_numpy_1d(b))
H2 = gcn.forward(A_norm, H)

# GraphSAGE layer
sage = tinygnn.SAGELayer(F_in=64, F_out=32,
                          aggregator=tinygnn.SAGELayer.Aggregator.Mean,
                          bias=True,
                          activation=tinygnn.Activation.RELU)
# Aggregator.Mean | Aggregator.Max
sage.set_weight_neigh(tinygnn.Tensor.from_numpy(Wn))
sage.set_weight_self(tinygnn.Tensor.from_numpy(Ws))
sage.set_bias(tinygnn.Tensor.from_numpy_1d(b))
H2 = sage.forward(A, H)    # A is raw adjacency (no gcn_norm)

# GAT layer  (A must include self-loops via add_self_loops)
gat = tinygnn.GATLayer(F_in=64, F_out=32, negative_slope=0.2,
                        bias=True, activation=tinygnn.Activation.NONE)
gat.set_weight(tinygnn.Tensor.from_numpy(W))
gat.set_attn_left(tinygnn.Tensor.from_numpy(al))
gat.set_attn_right(tinygnn.Tensor.from_numpy(ar))
gat.set_bias(tinygnn.Tensor.from_numpy_1d(b))
H2 = gat.forward(A_sl, H)

End-to-end: two-layer GCN on Cora

import tinygnn
import numpy as np

# Load pre-trained weights (produced by scripts/train_cora.py)
cora = tinygnn.load_cora_binary("weights/cora_graph.bin")

model = tinygnn.Model()
model.add_gcn_layer(1433, 64, bias=True, activation=tinygnn.Activation.RELU)
model.add_gcn_layer(64,   7,  bias=True, activation=tinygnn.Activation.NONE)
model.load_weights("weights/gcn_cora.bin")

logits      = model.forward(cora.adjacency, cora.features)  # Dense (2708 × 7)
predictions = logits.to_numpy().argmax(axis=1)               # (2708,) int

test_mask   = np.array(cora.test_mask)
labels      = np.array(cora.labels)
accuracy    = (predictions[test_mask] == labels[test_mask]).mean()
print(f"Test accuracy: {accuracy:.1%}")   # → ~78%

Enumerations

tinygnn.StorageFormat.Dense        # 0
tinygnn.StorageFormat.SparseCSR    # 1

tinygnn.Activation.NONE
tinygnn.Activation.RELU
tinygnn.Activation.ELU
tinygnn.Activation.SIGMOID
tinygnn.Activation.TANH
tinygnn.Activation.LEAKY_RELU
tinygnn.Activation.GELU
tinygnn.Activation.SOFTMAX
tinygnn.Activation.LOG_SOFTMAX

tinygnn.SAGELayer.Aggregator.Mean
tinygnn.SAGELayer.Aggregator.Max

GraphLoader (Python)

from tinygnn import GraphLoader

# Parse CSVs directly in Python
edges = GraphLoader.parse_edges("datasets/cora/edges.csv")
feats = GraphLoader.parse_features("datasets/cora/features.csv")
adj   = GraphLoader.edge_list_to_csr(edges, num_nodes=2708)

# Or use the full pipeline
data = GraphLoader.load("datasets/cora/edges.csv",
                        "datasets/cora/features.csv")

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SDK Reference (C++ API)

Include the top-level headers — all APIs are in the global namespace:

#include "tinygnn/tensor.hpp"       // Tensor, StorageFormat
#include "tinygnn/graph_loader.hpp" // GraphLoader, GraphData
#include "tinygnn/ops.hpp"          // matmul, spmm, activations, utilities
#include "tinygnn/layers.hpp"       // GCNLayer, SAGELayer, GATLayer
#include "tinygnn/model.hpp"        // Model, load_cora_binary, load_weight_file

Link with tinygnn::tinygnn_core (CMake) or compile with all .cpp files under src/.

Tensor

// --- Construction (Dense) ---
Tensor t(rows, cols);                         // zero-initialized row-major float32
Tensor t(rows, cols, {v00, v01, ...});        // from initializer list

// --- Construction (SparseCSR) ---
Tensor t(rows, cols,
         std::vector<float>   values,
         std::vector<int32_t> row_ptr,        // size rows+1
         std::vector<int32_t> col_ind);

// --- Inspection ---
t.rows();                   // number of rows
t.cols();                   // number of columns
t.nnz();                    // non-zeros (SparseCSR only)
t.format();                 // StorageFormat::Dense | SparseCSR
t.memory_footprint_bytes(); // exact byte count including all arrays

// --- Element access (Dense only) ---
float v = t.at(i, j);      // bounds-checked read
t.set(i, j, value);        // bounds-checked write
float* p = t.data_ptr();   // raw pointer (row-major)

// --- CSR accessors (SparseCSR only) ---
const float*   t.csr_values();
const int32_t* t.csr_row_ptr();
const int32_t* t.csr_col_ind();

Graph Utilities

#include "tinygnn/ops.hpp"

// Add identity self-loops (modifies CSR structure)
Tensor A_sl = add_self_loops(A);

// Symmetric GCN normalization:  D̃^(-1/2) (A+I) D̃^(-1/2)
// (implicitly adds self-loops; pass raw adjacency, not add_self_loops output)
Tensor A_norm = gcn_norm(A);

// Sparse row-wise softmax over CSR non-zeros (attention weights)
Tensor alpha = edge_softmax(attention_csr);

// CSR neighborhood max-pooling: max_{j in N(i)} H[j]  per row
Tensor agg = sage_max_aggregate(A, H);

Graph I/O

#include "tinygnn/graph_loader.hpp"

// Load Cora binary (produced by scripts/train_cora.py)
GraphData data = load_cora_binary("weights/cora_graph.bin");
// data.adjacency  → SparseCSR Tensor  (N × N)
// data.features   → Dense Tensor      (N × F)
// data.labels     → std::vector<int>
// data.train_mask, val_mask, test_mask → std::vector<bool>

// Parse arbitrary CSV graphs
auto edges    = GraphLoader::parse_edges("edges.csv");
Tensor feats  = GraphLoader::parse_features("features.csv");
Tensor adj    = GraphLoader::edge_list_to_csr(edges, num_nodes);

// Full pipeline shortcut
GraphData gd  = GraphLoader::load("edges.csv", "features.csv");

Layers

All layers implement Tensor forward(const Tensor& A, const Tensor& H).

#include "tinygnn/layers.hpp"

// --- GCN (Kipf & Welling, ICLR 2017) ---
// A must be pre-normalized: A_norm = gcn_norm(raw_adj)
GCNLayer gcn(F_in, F_out, /*bias=*/true, Activation::ReLU);
gcn.set_weight(W);    // Dense Tensor F_in × F_out
gcn.set_bias(b);      // Dense Tensor 1 × F_out
Tensor H2 = gcn.forward(A_norm, H);

// --- GraphSAGE (Hamilton et al., NeurIPS 2017) ---
// A is raw (un-normalized) adjacency; module handles degree normalization
SAGELayer sage(F_in, F_out, SAGELayer::Aggregator::Mean, /*bias=*/true, Activation::ReLU);
// SAGELayer::Aggregator::Mean | Max
sage.set_weight_neigh(Wn);    // F_in × F_out
sage.set_weight_self(Ws);     // F_in × F_out
sage.set_bias(b);
Tensor H2 = sage.forward(A, H);

// --- GAT (Veličković et al., ICLR 2018) ---
// A must include self-loops: A_sl = add_self_loops(raw_adj)
GATLayer gat(F_in, F_out, /*negative_slope=*/0.2f, /*bias=*/true, Activation::None);
gat.set_weight(W);          // F_in × F_out
gat.set_attn_left(al);      // 1 × F_out  (destination attention)
gat.set_attn_right(ar);     // 1 × F_out  (source attention)
gat.set_bias(b);
Tensor H2 = gat.forward(A_sl, H);

Model (multi-layer execution graph)

#include "tinygnn/model.hpp"

Model model;

// Add layers in forward order
model.add_gcn_layer(1433, 64, /*bias=*/true, Activation::ReLU);
model.add_gcn_layer(64, 7,    /*bias=*/true, Activation::None);

// Load PyG-exported weights (TGNN binary format)
model.load_weights("weights/gcn_cora.bin");

// Run inference
GraphData cora = load_cora_binary("weights/cora_graph.bin");
Tensor logits  = model.forward(cora.adjacency, cora.features);
// → Dense Tensor (N × num_classes), call log_softmax_inplace for probabilities

Compute Ops

#include "tinygnn/ops.hpp"

// Dense GEMM:  C = A × B    (A: M×K Dense, B: K×N Dense → C: M×N Dense)
Tensor C = matmul(A, B);

// Sparse-Dense SpMM:  C = A × B    (A: M×K SparseCSR, B: K×N Dense → C: M×N Dense)
Tensor C = spmm(A, B);

// In-place activations (Dense only)
relu_inplace(X);
leaky_relu_inplace(X, /*alpha=*/0.01f);
elu_inplace(X, /*alpha=*/1.0f);
sigmoid_inplace(X);
tanh_inplace(X);
gelu_inplace(X);
softmax_inplace(X);       // row-wise; with max-subtraction stability
log_softmax_inplace(X);   // row-wise; numerically stable

// Bias broadcast  X[i][j] += bias[0][j]  for all i
add_bias(X, bias);        // bias: Dense 1 × F

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CLI Reference (Python Scripts)

All scripts live under scripts/. Run with the active Python environment.

Fetch datasets

python scripts/fetch_datasets.py               # Cora + Reddit
python scripts/fetch_datasets.py --cora-only   # Cora only (~170 KB)

Writes to datasets/cora/ and datasets/reddit/ (gitignored).

Train & export Cora weights

# Prerequisite: pip install torch torch_geometric
python scripts/train_cora.py

Trains GCN, GraphSAGE (Mean), and GAT on Cora; exports weights/gcn_cora.bin, weights/sage_cora.bin, weights/gat_cora.bin, and weights/cora_graph.bin.

Validate logit-level agreement

python scripts/validate_cora.py               # weight-file accuracy check
python scripts/validate_cora.py --logit-check # fresh PyG train → logit diff

Run GNN benchmarks

python scripts/bench_gnn.py                   # 8 reps (default)
python scripts/bench_gnn.py --reps 20         # smoother medians
python scripts/bench_gnn.py --no-bench        # accuracy checks only
python scripts/bench_gnn.py --no-accuracy     # timing only
python scripts/bench_gnn.py --csv path/out.csv  # custom CSV prefix

Writes benchmarks/gnn_bench_results_timing.csv and benchmarks/gnn_bench_results_accuracy.csv.

Generate benchmark charts

python scripts/plot_gnn_bench.py    # produces 5 PNGs in benchmarks/

Output file	Contents
gnn_runtime_comparison.png	Wall-time per layer & graph size
gnn_memory_comparison.png	Working-set memory (analytical, log scale)
gnn_speedup.png	TinyGNN-NT vs TinyGNN-1T and vs PyG
gnn_scaling.png	Runtime scaling with graph size
gnn_accuracy.png	TinyGNN vs PyG max absolute logit diff

Thread-scaling and operator-fusion benchmarks

cmake --build build --target bench_parallel
./build/bench_parallel                        # OpenMP thread-scaling report

cmake --build build --target bench_fusion
OMP_NUM_THREADS=8 ./build/bench_fusion        # fused vs unfused GAT/SAGE

python scripts/plot_scaling.py                # → benchmarks/thread_scaling.png

Memory safety (Linux / WSL)

bash scripts/sanitizers.sh       # ASan + UBSan, 27 configs across all phases
bash scripts/valgrind_all.sh     # Memcheck + Helgrind + Callgrind

Documentation

doxygen Doxyfile                              # C++ API → docs/doxygen/html/
pip install sphinx sphinx-rtd-theme breathe
cd docs && make html                          # Python API → docs/_build/html/

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GNN Benchmark Results

Machine-dependent results — all numbers vary with CPU core count, NUMA topology, memory bandwidth, and OS scheduler behaviour. Results from two different hardware environments are shown below. On machines with fewer cores, TinyGNN-MT may be slower than TinyGNN-1T for very small graphs (thread-launch overhead dominates). Run python scripts/bench_gnn.py --reps 8 && python scripts/plot_gnn_bench.py to reproduce on your own hardware.

Accuracy (TinyGNN vs PyTorch Geometric)

Synthetic graphs: N=30, F_in=8, F_out=4 — numerically identical weights fed to both engines.

Layer	max|diff|	mean|diff|	Pass
GCNLayer	2.38e-07	4.32e-08	✅
SAGELayer-Mean	4.77e-07	7.74e-08	✅
SAGELayer-Max	4.77e-07	1.25e-07	✅
GATLayer	1.79e-07	4.90e-08	✅

All differences are well within float32 rounding tolerance (< 5×10⁻⁷).

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Wall-time — Jai Ansh's machine (Intel i7-12650H · 16T · Dell G15 5520)

Hardware: Intel Core i7-12650H @ 2.30 GHz (10 cores / 16 threads), 16 GB DDR5-4800, NVIDIA RTX 3060 6 GB, Windows 11, GCC 13.3 (MinGW-UCRT64), Python 3.12. 8 timed repetitions, median reported.

Graph configs: small (N=1K, deg=5, F_in=64→32), medium (N=10K, deg=10, F_in=128→64), large (N=100K, deg=5, F_in=256→128).

Graph	Layer	TinyGNN-1T	TinyGNN-16T	PyG	16T vs 1T	16T vs PyG
small-1K	GCN	0.29 ms	0.58 ms	2.05 ms	0.49× ¹	3.51×
small-1K	SAGE-Mean	0.38 ms	0.60 ms	1.65 ms	0.64× ¹	2.77×
small-1K	SAGE-Max	0.47 ms	0.78 ms	2.20 ms	0.61× ¹	2.83×
small-1K	GAT	0.46 ms	0.85 ms	2.17 ms	0.54× ¹	2.55×
medium-10K	GCN	9.74 ms	3.67 ms	33.10 ms	2.65×	9.02×
medium-10K	SAGE-Mean	15.50 ms	3.17 ms	54.16 ms	4.90×	17.11×
medium-10K	SAGE-Max	19.67 ms	3.63 ms	72.93 ms	5.42×	20.09×
medium-10K	GAT	9.56 ms	3.98 ms	36.55 ms	2.40×	9.18×
large-100K	GCN	262.59 ms	74.15 ms	597.18 ms	3.54×	8.05×
large-100K	SAGE-Mean	490.37 ms	120.10 ms	594.53 ms	4.08×	4.95×
large-100K	SAGE-Max	519.41 ms	89.52 ms	1010.78 ms	5.80×	11.29×
large-100K	GAT	274.30 ms	73.70 ms	510.89 ms	3.72×	6.93×

¹ Small-graph thread overhead: spawning 16 threads costs more than the actual computation for N=1K graphs. Single-threaded is faster at this scale — see the speedup chart.

The charts below were generated from this hardware run:

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Wall-time — Anubhav's machine (Intel Core 9 270H · 20T)

Hardware: Intel Core Ultra 9 270H (20 logical threads), GCC 13.3, Python 3.11, Windows 11 + WSL2. 10 timed repetitions, median reported.

Graph	Layer	TinyGNN-1T	TinyGNN-20T	PyG	20T vs 1T	20T vs PyG
small-1K	GCN	0.42 ms	0.84 ms	1.29 ms	0.49× ¹	1.54×
small-1K	SAGE-Mean	0.50 ms	0.73 ms	1.14 ms	0.68× ¹	1.55×
small-1K	SAGE-Max	0.46 ms	0.75 ms	1.61 ms	0.62× ¹	2.15×
small-1K	GAT	0.56 ms	1.20 ms	1.67 ms	0.47× ¹	1.39×
medium-10K	GCN	8.07 ms	3.67 ms	14.93 ms	2.20×	4.07×
medium-10K	SAGE-Mean	14.23 ms	6.20 ms	24.03 ms	2.29×	3.87×
medium-10K	SAGE-Max	11.70 ms	5.23 ms	35.29 ms	2.24×	6.74×
medium-10K	GAT	8.62 ms	3.64 ms	18.31 ms	2.37×	5.04×
large-100K	GCN	211.51 ms	55.99 ms	208.67 ms	3.78×	3.73×
large-100K	SAGE-Mean	390.21 ms	82.47 ms	258.09 ms	4.73×	3.13×
large-100K	SAGE-Max	390.84 ms	71.53 ms	393.57 ms	5.46×	5.50×
large-100K	GAT	281.61 ms	79.85 ms	253.06 ms	3.53×	3.17×

¹ Small-graph thread overhead: on a 20-core CPU, spawning 20 threads costs more than the computation for N=1K. Single-threaded is faster at this scale.

(Important note the links and png s below are from Anubhav's system)

(Important note the links and png s below are from Jai Ansh's system)

Working-set memory (analytical estimate)

Memory is computed analytically from tensor dimensions rather than measured at runtime (C++ heap is invisible to Python memory profilers):

Graph	Layer	TinyGNN	PyG estimate	PyG / TinyGNN
small-1K	GCN	0.58 MB	1.11 MB	1.93×
medium-10K	GCN	11.36 MB	22.02 MB	1.94×
large-100K	GCN	203.45 MB	403.03 MB	1.98×

TinyGNN uses roughly 2× less working-set memory than PyG across all tested scales, reflecting the absence of PyTorch tensor metadata, autograd buffers, and COO→CSR conversion overhead.

---

CI/CD

Every push to main and every pull request automatically triggers GitHub Actions:

• C++ build + test on Linux (GCC + Clang), macOS, and Windows (MSVC)
• Python build + test on Linux, macOS, Windows (Python 3.10 + 3.12)
• ASan + UBSan sanitizer checks on Linux
• Documentation build (Doxygen + Sphinx)

Valgrind Memcheck + Helgrind can be run locally via bash scripts/valgrind_all.sh (excluded from CI due to runtime overhead on large graph tests).

---

Datasets

TinyGNN tests against two real-world graph datasets. Download them with the included Python script:

# Cora only (no extra Python deps, ~170 KB download)
python3 scripts/fetch_datasets.py --cora-only

# Both Cora and Reddit (needs numpy + scipy, ~200 MB download)
pip install numpy scipy
python3 scripts/fetch_datasets.py

Dataset	Source	Nodes	Edges	Features	CSV size
Cora	LINQS (McCallum et al. 2000)	2,708	5,429	1,433 (binary bag-of-words)	7.5 MB
Reddit	DGL / GraphSAGE (Hamilton et al. 2017)	232,965	114,615,892	602 (GloVe embeddings)	2.7 GB

Files are placed in datasets/cora/ and datasets/reddit/ (gitignored). Tests that require actual datasets skip gracefully when the files are not present.

---

Phase 1 -- Hybrid Tensor Core

Goal

Establish the fundamental data structure by expanding a contiguous memory design to support both dense and sparse graph layouts, without any third-party libraries.

Design

StorageFormat enum

enum class StorageFormat : uint8_t {
    Dense     = 0,   // Row-major contiguous storage
    SparseCSR = 1    // Compressed Sparse Row
};

Tensor struct layout

Dense:
  data_    -> [v00, v01, ..., v(R-1)(C-1)]   rows*cols floats, row-major
  strides_ -> {cols, 1}

SparseCSR:
  row_ptr_ -> size (rows+1)   row_ptr[i]..row_ptr[i+1] = col indices of row i
  col_ind_ -> size nnz        column index of each non-zero
  data_    -> size nnz        value of each non-zero

Memory footprint

Format	Formula	1000x1000 example
Dense	rows * cols * 4 bytes	4,000,000 bytes (3.8 MB)
SparseCSR	nnz4 + nnz4 + (rows+1)*4 bytes	44,004 bytes with 5000 edges (43 KB)

Sparse uses ~1.1% of the memory of the equivalent dense matrix in this benchmark.

Results

Dense  1000x1000 memory          = 4,000,000 bytes
Sparse 1000x1000 (5000 nnz)      =    44,004 bytes
Memory ratio (sparse / dense)    =      1.10%
Very sparse (10 nnz in 10k x10k) =      0.01%

Test suite -- 104 assertions, 18 test functions, 0 failures

Category	Functions
Dense construction and mutation	3
Memory footprint validation	2
Memory comparison / reduction ratios	2
Edge cases (empty, 1x1, 0-nnz, degenerate shapes, CSR data integrity)	6
Error handling (invalid args, out-of-bounds, wrong format access)	4
Utility (repr, enum values)	1

Total : 104
Passed: 104
Failed: 0

---

Phase 2 -- Graph Data Loader

Goal

Load irregular graph structures from CSV files and convert them to hardware-friendly sorted CSR format, ready for GNN inference.

Design

GraphLoader class

class GraphLoader {
public:
    // Edge-list CSV  ->  vector of (src, dst) pairs
    static std::vector<std::pair<int32_t, int32_t>>
        parse_edges(const std::string& path);

    // Feature CSV  ->  Dense tensor (num_nodes x num_features)
    static Tensor parse_features(const std::string& path);

    // Raw edge list  ->  sorted SparseCSR adjacency tensor
    static Tensor edge_list_to_csr(
        const std::vector<std::pair<int32_t, int32_t>>& edges,
        std::size_t num_nodes);

    // Full pipeline: CSV files  ->  GraphData (adjacency + features)
    static GraphData load(const std::string& edges_path,
                          const std::string& features_path);
};

CSR conversion algorithm -- O(E + V + E*log(E/V))

Step 1: Count out-degree per node         O(E)
Step 2: Build row_ptr via prefix sum      O(V)
Step 3: Fill col_ind via offset cursors   O(E)
Step 4: Sort col_ind within each row      O(E*log(E/V)) amortised

CSV format support

• Automatic header row detection (skips non-numeric first lines)
• Both LF and CRLF line endings
• Whitespace-tolerant parsing
• Out-of-order node IDs with gap zero-filling in feature tensor

Results (Cora-scale synthetic benchmark)

Nodes:     2,708
Edges:     10,556
Features:  1,433 per node

Adjacency: Tensor(2708x2708, SparseCSR, 95,284 bytes)
Features:  Tensor(2708x1433, Dense, 15,522,256 bytes)

Results (Reddit-scale synthetic benchmark)

Reddit (Hamilton et al. 2017, GraphSAGE paper): 232,965 nodes, 114,615,892 directed edges, 602 features. Generated synthetically with a fixed seed; full file pipeline writes ~1.4 GB edge CSV + ~282 MB feature CSV.

Nodes:     232,965
Edges:     114,615,892
Features:  602 per node

Adjacency: Tensor(232965x232965, SparseCSR, 917,859,000 bytes)  (~875 MB)
Features:  Tensor(232965x602,   Dense,      560,979,720 bytes)  (~535 MB)

In-memory CSR algorithm test:
  Edge generation (114M pairs):   1,350 ms
  CSR construction + sort:        5,591 ms
  Total:                          6,979 ms

Full file-pipeline test:
  Edge file write (1.4 GB):      25,491 ms
  Feature file write (282 MB):    3,748 ms
  GraphLoader::load():          119,047 ms
  Total:                        148,286 ms

Node 0 neighbors: 455 (CSR traversal matches raw CSV exactly)

Results (actual Cora dataset)

The real Cora citation network (McCallum et al. 2000): 2,708 papers linked by 5,429 directed citations, with 1,433 binary bag-of-words features per paper.

Nodes:     2,708
Edges:     5,429
Features:  1,433 per node (binary)

Adjacency: Tensor(2708x2708, SparseCSR, 54,268 bytes)     (~53 KB)
Features:  Tensor(2708x1433, Dense,     15,522,256 bytes)  (~14.8 MB)

Feature density: 49,216 / 3,880,564 entries are 1  (1.27%)
Node 0 neighbors: 3 (CSR traversal matches raw CSV exactly)

Results (actual Reddit dataset)

The real Reddit post network (Hamilton et al. 2017, GraphSAGE): 232,965 posts linked by 114,615,892 directed edges, with 602-dimensional GloVe word embeddings per post.

Nodes:     232,965
Edges:     114,615,892
Features:  602 per node (GloVe float)

Adjacency: Tensor(232965x232965, SparseCSR, 917,859,000 bytes)  (~875 MB)
Features:  Tensor(232965x602,   Dense,      560,979,720 bytes)  (~535 MB)

GraphLoader::load() time: 157 s  (WSL, Ubuntu 24.04, GCC 13.3)
Node 0 neighbors: 2,204

Test suite -- 269 assertions, 49 test functions, 0 failures

Category	Functions	Covers
Edge CSV parsing	6	header, no-header, CRLF, self-loops, trailing blanks
Feature CSV parsing	6	ordered, unordered, sparse IDs, negative values
CSR conversion	8	exact arrays, sort invariant, empty rows, memory footprint
Full load pipeline	4	node-0 neighbors, all-nodes verify, feature zero-expansion
Cora-scale validation	3	2708 nodes / 10556 edges / 1433 features / row_ptr invariants
Reddit-scale validation	4	232,965 nodes / 114,615,892 edges / in-memory CSR + full pipeline + node-0 match
Actual Cora dataset	4	2,708 nodes / 5,429 real citation edges / binary features / node-0 match
Actual Reddit dataset	4	232,965 nodes / 114,615,892 real edges / GloVe features / CSR invariants
Error handling	10	file-not-found, malformed lines, negative IDs, out-of-range

Total : 269
Passed: 269
Failed: 0

---

Phase 3 -- Dense Compute Kernels (GEMM)

Goal

Implement the baseline dense matrix multiplication needed for the GNN feature transformation H' = H x W, where H is the node feature matrix and W is the learned weight matrix.

Design

matmul function

// C = A x B
// A: Dense (M x K)   B: Dense (K x N)   C: Dense (M x N), newly allocated
Tensor matmul(const Tensor& A, const Tensor& B);

Loop order -- (i, k, j)

The implementation uses the (i, k, j) traversal order rather than the naive (i, j, k):

for i in [0, M):           // row of A and C
  for k in [0, K):         // shared dimension
    a_ik = A[i][k]         // hoisted into scalar register
    for j in [0, N):       // row of B, column of C
      C[i][j] += a_ik * B[k][j]

Why (i, k, j): A[i][k] is loop-invariant across the inner j-loop and lives in a register. B[k][j] is accessed row-sequentially (cache-friendly). The compiler can auto-vectorise the inner j-loop because the scalar a_ik eliminates a load dependency. __restrict__ pointers are used to communicate the no-aliasing guarantee to the compiler.

Complexity

Metric	Value
Time complexity	O(M * K * N)
FLOPs	2 * M * K * N (1 multiply + 1 add per A element)
Output allocation	M * N * 4 bytes

Preconditions enforced

• Both operands must be StorageFormat::Dense (sparse-dense SpMM is Phase 4)
• A.cols() must equal B.rows() -- throws std::invalid_argument with both dimensions in the message
• Zero-dimension tensors produce a valid zero-filled output

Results

matmul(128x128, 128x128)         =    1 ms
matmul(1024x32, 32x256)          =    4 ms  (output = 1024 KB)
matmul(256x256, I_256)           spot checks: 8/8 pass
matmul(5x8, 8x6) footprint       = 120 bytes (5*6*4)

GNN feature transform (H x W, one-hot nodes selecting rows of W):

H (3x4)  x  W (4x2)  ->  H' (3x2)
Node 0: [1, 2]   Node 1: [3, 4]   Node 2: [5, 6]

4x4 hardcoded result (spec required):

A = reshape([1..16], 4, 4)    B = reshape([17..32], 4, 4)

C = A x B:
  [  250,  260,  270,  280 ]
  [  618,  644,  670,  696 ]
  [  986, 1028, 1070, 1112 ]
  [ 1354, 1412, 1470, 1528 ]

Test suite -- 268 assertions, 30 test functions, 0 failures

Category	Functions	Covers
4x4 hardcoded result (spec)	3	full matrix, element spot-checks, 2x2 sub-block cross-check
Non-square shapes	3	(2x3)x(3x4), matrix x column-vector, row-vector x matrix
Identity and zero properties	4	AI=A, IA=A, non-square identity, zero matrix output
GNN feature transform	1	H x W with one-hot nodes verifying row selection from W
Algebraic properties	3	non-commutativity, associativity, scalar distributivity
Output tensor properties	3	format=Dense, shape MxN, footprint = MN4 bytes
Stress / scale	3	128x128 all-ones, 1024x32x256 rectangle, 256x256 identity
Dimension mismatch errors	5	basic throw, message content, 4 bad-shape combos, degenerate 0-dim
Sparse input errors	2	sparse A throws, sparse B throws (SparseCSR in message)
Edge / degenerate cases	3	1x1 scalar, all-zeros output, GNN layer chain (AB)C = A(BC)

Total : 268
Passed: 268
Failed: 0

---

Phase 4 -- Sparse Compute Kernels (SpMM)

Goal

Implement the sparse-dense matrix multiplication kernel that is the heart of GNN message-passing: H_agg = Adj × H, aggregating each node's neighbor features via the sparse adjacency matrix.

Design

spmm function

// C = A × B
// A: SparseCSR (M × K)   B: Dense (K × N)   C: Dense (M × N), newly allocated
Tensor spmm(const Tensor& A, const Tensor& B);

Algorithm -- CSR-SpMM

for i in [0, M):                        // row of A (node)
  for nz in [row_ptr[i], row_ptr[i+1]): // non-zeros in row i (neighbors)
    k = col_ind[nz]                     // column (neighbor node ID)
    a_val = data[nz]                    // edge weight (1.0 for unweighted)
    for j in [0, N):                    // feature dimension
      C[i][j] += a_val * B[k][j]       // accumulate neighbor's features

Why CSR-SpMM: The outer loop walks rows (nodes). The middle loop walks non-zero columns (graph neighbors) — this is the message-passing. The inner loop accumulates dense features — cache-friendly because B[k][j] is contiguous in memory and the compiler can auto-vectorise with the scalar a_val hoisted to a register.

Complexity

Metric	Value
Time complexity	O(nnz × N) — proportional to edges × features
FLOPs	2 × nnz × N (1 multiply + 1 add per edge per feature)
Output allocation	M × N × 4 bytes

Preconditions enforced

• A must be StorageFormat::SparseCSR (Dense A → "use matmul() instead")
• B must be StorageFormat::Dense (Sparse B → "Sparse × Sparse not supported")
• A.cols() must equal B.rows() — throws std::invalid_argument with dimensions in message
• Early exit for degenerate cases (M=0, N=0, or nnz=0) producing valid zero-filled output

Results

3×3 hand-calculated SpMM (spec required):

A (SparseCSR):                   B (Dense):
  [1 1 0]  row_ptr=[0,2,3,5]      [1 2]
  [0 1 0]  col_ind=[0,1,1,0,2]    [3 4]
  [1 0 1]  values =[1,1,1,1,1]    [5 6]

C = spmm(A, B):
  [4, 6]   ← 1·[1,2] + 1·[3,4]
  [3, 4]   ← 1·[3,4]
  [6, 8]   ← 1·[1,2] + 1·[5,6]

4×4 weighted hand-calculated:

A (SparseCSR):                B (Dense):
  [2 0 0 0]  values=[2,3,     [1  0  2]
  [0 3 1 0]   1,1,2,1,1]      [0  1  0]
  [1 0 0 2]                    [3  0  1]
  [0 1 1 0]                    [0  2  0]

C = spmm(A, B):
  [2, 0, 4]  [3, 3, 1]  [1, 4, 2]  [3, 1, 1]

GNN message-passing (star graph, 5 nodes):

H_agg = spmm(Adj_star, H)
  Hub (node 0): sum of all features = [10, 40]
  Leaf i:       H[0] + H[i]  (receives from hub + self)

Equivalence with dense matmul verified for:

• 32×32 sparse (~9% density) × 32×16 dense
• Cora-scale: 2,708×2,708 sparse (3 nnz/row) × 2,708×32 dense

Test suite -- 306 assertions, 35 test functions, 0 failures

Category	Functions	Covers
3×3 hand-calculated (spec)	3	full matrix, element checks, column vector
4×4 weighted CSR	2	full result, element derivations
Non-square shapes	3	(5×3)×(3×4), (2×5)×(5×1), (1×4)×(4×3)
Identity & zero properties	4	sparse I × B = B, 64×64, zero-nnz, all-ones
GNN message-passing	3	triangle (fully connected), star graph, two-hop path chain
Dense matmul equivalence	2	small 3×3, medium 32×32 deterministic sparse
Output tensor properties	3	format=Dense, shape M×N, memory footprint
Stress / scale	3	512×512 identity, 2708-node Cora-scale, 1024×128
Wrong format errors	4	dense A throws, message check, sparse B throws, message check
Dimension mismatch	3	basic throw, message "dimension mismatch", multiple combos
Edge / degenerate cases	5	single nnz, empty rows, diagonal/self-loops, negative weights, 1×1

Total : 306
Passed: 306
Failed: 0

---

Phase 5 -- Activations & Utilities

Goal

Implement the element-wise activation functions and utilities needed between GNN layers: H' = Activation(Adj × H × W + b). These operate in-place on Dense tensors for zero-copy efficiency.

Design

Activation functions

Function	Formula	GNN Use Case
relu_inplace(X)	max(0, x)	GCN, GraphSAGE, GIN — standard hidden layer activation
leaky_relu_inplace(X, α)	x if x≥0, else αx (default α=0.01)	GAT attention coefficients (α=0.2)
elu_inplace(X, α)	x if x≥0, else α(eˣ−1) (default α=1.0)	EGNN, PNA — smooth negative region
sigmoid_inplace(X)	1/(1+e⁻ˣ)	GGNN gating, link prediction, binary classification
tanh_inplace(X)	tanh(x)	GRU/LSTM graph networks (GGNN, MPNN)
gelu_inplace(X)	x·Φ(x) ≈ 0.5x(1+tanh(√(2/π)(x+0.044715x³)))	GPS, Graphormer, TokenGT — transformer GNNs
softmax_inplace(X)	row-wise softmax with max-subtraction stability	GAT attention normalization, classification output
log_softmax_inplace(X)	row-wise log-softmax (numerically stable)	NLL loss for node classification

Utility functions

Function	Operation	GNN Use Case
add_bias(X, bias)	X[i][j] += bias[0][j] — broadcast (1×N) across M rows	Linear layer bias: H' = AHW + b

Common properties

• All activations modify the tensor in-place (O(1) extra memory)
• All validate Dense format and throw std::invalid_argument on SparseCSR
• Softmax / log-softmax use the max-subtraction trick for numerical stability
• Sigmoid uses a two-branch implementation (x≥0 vs x<0) to prevent overflow
• GELU uses the tanh approximation (same as PyTorch F.gelu(approximate='tanh'))

Complexity

Function	Time	Extra Memory
relu, leaky_relu, sigmoid, tanh	O(M × N)	O(1)
elu, gelu	O(M × N) with exp/tanh on subset	O(1)
softmax, log_softmax	O(M × N) — 3 passes per row	O(1)
add_bias	O(M × N)	O(1)

Results

GCN layer pipeline (identity Adj, 3 nodes, 2 features):

H' = ReLU(Adj × H × W + b)
  Node 0: [1.5, 0.0]   (relu clamps negative bias-shifted value)
  Node 1: [2.5, 0.0]
  Node 2: [3.5, 0.0]

GAT-style attention (LeakyReLU + Softmax):

Scores:  [0.5, -0.3, 1.2]
LeakyReLU(α=0.2): [0.5, -0.06, 1.2]
Softmax: attention weights sum to 1.0, largest score gets most weight

Node classification (Log-Softmax for NLL loss):

3 nodes × 4 classes
All log-probabilities ≤ 0, exp(row) sums to 1.0
Argmax preserved through log-softmax

Numerical stability verified:

softmax([1000, 1001])     — no NaN/Inf, correct probabilities
log_softmax([1000, 1001, 999]) — no NaN/Inf, exp sums to 1.0

Test suite -- 266 assertions, 70 test functions, 0 failures

Category	Functions	Covers
ReLU	5	basic, 2D matrix, all-positive, all-negative, zero preservation
Leaky ReLU	5	default α=0.01, GAT α=0.2, 2D, α=0→ReLU, α=1→identity
ELU	4	basic, custom α=2.0, saturation at −α, 2D mixed signs
Sigmoid	5	basic values, σ(x)+σ(−x)=1 symmetry, bounds (0,1), hand-calculated, 2D
Tanh	5	basic, odd symmetry, bounds (−1,1), hand-calculated, 2D
GELU	4	basic (0→0, large→x, neg→0), hand-calculated vs reference, zero symmetry, 2D
Softmax	7	row sums=1, bounds [0,1], uniform dist, hand-calculated, multi-row, numerical stability, argmax preserved
Log-Softmax	6	exp sums=1, all ≤ 0, consistent with softmax, uniform, numerical stability, multi-row
Add bias	6	basic broadcasting, zero bias, negative bias, single-row, wrong-rows throw, wrong-cols throw
GNN pipeline integration	3	full GCN layer, GAT attention, node classification
Error handling (SparseCSR)	10	all 9 activations + add_bias reject sparse input
Stress / scale	5	relu 1024×256, softmax 1024×128, sigmoid 512×512, bias 2708×32, gelu 256×256
Edge / degenerate	5	1×1 through all activations, zero-cols rejected, zero-rows no-op, double-apply idempotency

Total : 266
Passed: 266
Failed: 0

---

Phase 6 -- Multi-Architecture Layer Assembly

Goal

Assemble complete GNN layer architectures from the tensor primitives built in Phases 1–5, implementing the three canonical propagation strategies: GCN (spectral normalization), GraphSAGE (inductive mean/max aggregation), and GAT (attention-based message passing).

Design

Helper functions

// Â = A + I  — insert identity self-loops into CSR (two-pass: detect diag, rebuild)
Tensor add_self_loops(const Tensor& A);

// D̃^(-1/2) Â D̃^(-1/2)  — symmetric GCN normalization
Tensor gcn_norm(const Tensor& A);

// Row-wise sparse softmax over CSR non-zeros only (max-subtract, two-pass)
Tensor edge_softmax(const Tensor& A);

// Element-wise max pooling over CSR neighborhoods
Tensor sage_max_aggregate(const Tensor& A, const Tensor& H);

GCN Layer (GCNLayer)

Kipf & Welling, ICLR 2017

H' = σ( Â_norm · (H · W) + b )

  ̂   precomputed by gcn_norm():  D̃^(-1/2) (A+I) D̃^(-1/2)
A = precomputed
Forward:
  Step 1: HW  = matmul(H, W)       [N × F_in] × [F_in × F_out] → [N × F_out]
  Step 2: out = spmm(Â_norm, HW)  sparse message-passing
  Step 3: add_bias(out, b)           optional
  Step 4: σ(out)                     ReLU or None

GraphSAGE Layer (SAGELayer)

Hamilton, Ying & Leskovec, NeurIPS 2017

h_v' = σ( W_neigh · AGG({h_u : u ∈ N(v)}) + W_self · h_v + b )

AGG variants:
  Mean: spmm(A, H) / degree[v]             (normalized neighbor sum)
  Max:  element-wise max over CSR row       (sage_max_aggregate)

Forward:
  Step 1: agg    = Mean-spmm or sage_max_aggregate
  Step 2: h_neigh = matmul(agg, W_neigh)
  Step 3: h_self  = matmul(H,   W_self)
  Step 4: out    = h_neigh + h_self        (element-wise add)
  Step 5: add_bias(out, b)                 optional
  Step 6: σ(out)                            ReLU or None

GAT Layer (GATLayer)

Veličković et al., ICLR 2018

Forward (single attention head):
  Step 1: Wh          = matmul(H, W)                     [N × F_out]
  Step 2: src[i]      = a_l · Wh[i],  dst[j] = a_r · Wh[j]   per node
  Step 3: e_ij        = LeakyReLU(src[i] + dst[j])       SpSDDMM — one value per CSR edge
  Step 4: α           = edge_softmax(e_csr)               sparse softmax per row
  Step 5: out         = spmm(α, Wh) + b                  attention-weighted aggregation
  Step 6: σ(out)

Weights: W (F_in×F_out), a_l (1×F_out), a_r (1×F_out), b (1×F_out)
A must include self-loops (use add_self_loops before forward).

Phase 6a: GCN Layer

Test suite -- 764 assertions, 68 test functions, 0 failures

Category	Tests	Covers
add_self_loops	7	basic, already-has-diagonal, empty
gcn_norm	7	hand-verified D̃^(-1/2) Â D̃^(-1/2) values
GCNLayer construction + weight management	8	shape checks, wrong-format, wrong-shape throws
GCNLayer forward — 3-node hand-computed	6	row-by-row numerical verification
GCNLayer forward — no bias, no activation	5	identity propagation
Two-layer GCN stacking	4	output shape and feature composition
10-node ring graph — full pipeline	11	symmetry, degree normalization, activation
Error handling	12	wrong formats, dimension mismatches, error messages
Edge / degenerate cases	8	single node, isolated nodes, identity adjacency

Total : 764
Passed: 764
Failed: 0

Phase 6b: GraphSAGE Layer

Test suite -- 1,011 assertions, 60 test functions, 0 failures

Category	Tests	Covers
sage_max_aggregate	8	basic, empty graph, single node
SAGELayer construction + weight management	9	shape checks, aggregator type, wrong-format throws
SAGELayer Mean forward — 3-node hand-computed	7	degree normalization, W_neigh/W_self combination
SAGELayer Max forward — 3-node hand-computed	7	max pooling, W_neigh/W_self combination
Multi-layer GraphSAGE	4	two-layer composition, feature dimension flow
10-node graph tests	7	mean vs max comparison, scale, bias/activation
Error handling	10	dense A, sparse H, dimension mismatches, messages
Edge / degenerate cases	8	isolated nodes get zero aggregation

Total : 1011
Passed: 1011
Failed: 0

Phase 6c: GAT Layer

Test suite -- 1,284 assertions, 60 test functions, 0 failures

Category	Tests	Covers
edge_softmax	10	row sums = 1, uniform input, single-entry rows, numerical stability
GATLayer construction + weight management	12	shape checks, wrong-format, wrong-shape throws
GATLayer forward — 3-node hand-computed	10	attention score computation, softmax, weighted SpMM
GATLayer forward — bias and activation	8	bias add, ReLU gate
Multi-layer GAT + mixed layer stacking	6	GAT→GAT, GCN→GAT, SAGEMax→GAT compositions
Larger graph tests (10-node, 100-node)	8	scale, output shape, attention normalization
Error handling	10	wrong formats, dimension mismatches, negative slope validation
Edge / degenerate cases	6	self-loop-only, single node, all-zero attention

Total : 1284
Passed: 1284
Failed: 0

---

Phase 7 -- Multi-Model End-to-End Pipeline & Reference Matching

Goal

Close the loop from training to inference: train three GNN architectures (GCN, GraphSAGE, GAT) on the standard Cora citation dataset using PyTorch Geometric, export their FP32 weights to a custom binary format, and validate that TinyGNN's C++ inference engine reproduces the same classification accuracy.

Architecture

Python Training Pipeline (scripts/train_cora.py)

• Loads Cora from PyG's Planetoid dataset (2,708 nodes, 10,556 directed edges, 1,433 features, 7 classes)
• Trains three models with early stopping on validation accuracy:
  • GCN: 2-layer, 1433 → 64 → 7, ReLU, dropout 0.5
  • GraphSAGE: 2-layer Mean aggregation, 1433 → 64 → 7, ReLU, dropout 0.5
  • GAT: 2-layer, 8 heads × 8 features (concat) → 7 (single head), ELU, dropout 0.6
• Exports binary graph data and per-model weight files

Binary Format

Graph data (cora_graph.bin):

num_nodes, num_features, num_classes, num_edges  (4 × uint32)
features   (N × F × float32, row-major)
labels     (N × int32)
train_mask, val_mask, test_mask  (N × uint8 each)
edge_src, edge_dst  (E × int32 each)

Weight files ({gcn,sage,gat}_cora.bin):

Magic "TGNN"  (4 bytes)
Version       (uint32 = 1)
TestAccuracy  (float32)
NumTensors    (uint32)
─ per tensor ─
NameLen (uint32) | Name (bytes) | Rows (uint32) | Cols (uint32) | Data (float32[])

C++ Model Class (model.hpp / model.cpp)

The Model class implements a dynamic execution graph that chains heterogeneous GNN layers:

Model model;
model.add_gcn_layer(1433, 64, true, Activation::ReLU);
model.add_gcn_layer(64, 7, true, Activation::None);
model.load_weights("weights/gcn_cora.bin");
Tensor logits = model.forward(adjacency, features);

Key features:

• Heterogeneous layer support: GCN, SAGE, and GAT layers can be freely mixed in a single execution graph
• Multi-head GAT: multiple independent GATLayer instances per logical layer, with concat or average aggregation
• Automatic adjacency preprocessing: gcn_norm() for GCN layers, raw adjacency for SAGE, add_self_loops() for GAT — computed once and cached
• Inter-layer activations: ELU, ReLU, or None applied between layers (separate from each layer's internal activation)

Weight Mapping (PyG → TinyGNN)

PyG Parameter	TinyGNN Parameter	Transform
GCNConv.lin.weight (out×in)	GCNLayer.weight (in×out)	Transpose
GCNConv.bias (out)	GCNLayer.bias (1×out)	Reshape
SAGEConv.lin_l.weight (out×in)	SAGELayer.weight_neigh (in×out)	Transpose
SAGEConv.lin_r.weight (out×in)	SAGELayer.weight_self (in×out)	Transpose
GATConv.lin.weight[h*F:(h+1)*F]	GATLayer.weight per head (in×F)	Slice + Transpose
GATConv.att_src[0,h,:]	GATLayer.attn_left (1×F)	Extract head
GATConv.att_dst[0,h,:]	GATLayer.attn_right (1×F)	Extract head

Accuracy Results

Model	PyG Accuracy	C++ Accuracy	Match
GCN (2-layer, 64 hidden)	78.3%	78.3%	Exact
GraphSAGE (2-layer, Mean, 64 hidden)	80.6%	80.6%	Exact
GAT (8-head + 1-head, ELU)	80.3%	79.3%	±1% (FP rounding)

Test Suite -- 13,862 assertions, 26 test functions, 0 failures

Category	Tests	Covers
Data loading	3	Binary graph loader, weight file loader, data integrity
Weight shape validation	3	GCN/SAGE/GAT tensor shapes match architecture
Model API	5	Layer addition, empty model throws, missing weight throws
Small graph forward pass	4	GCN/SAGE/GAT on 3-node graph, multi-head concat
Logit sanity	4	All outputs finite, log-softmax sums to 1
Prediction distribution	3	All 7 classes present in predictions
End-to-end accuracy	4	GCN/SAGE/GAT match PyG ±5%, train accuracy ≥ 85%

Tests run:    26
Assertions:   13862
Passed:       13862
Failed:       0

---

Phase 8 -- Python Bridge (pybind11)

Goal

Expose the entire TinyGNN C++ inference engine to Python via pybind11, enabling researchers to import tinygnn and run GNN inference from Python with NumPy/SciPy/PyTorch interoperability.

Architecture

pybind11 Bindings (python/tinygnn_ext.cpp)

A single C++ source wrapping the full TinyGNN API:

• Tensor — zero-copy NumPy interop via from_numpy(), to_numpy(), SciPy CSR via from_scipy_csr(), PyG edge_index via from_edge_index()
• Ops — all 8 activations, matmul, spmm, add_bias (in-place semantics preserved)
• Graph utilities — add_self_loops, gcn_norm, edge_softmax, sage_max_aggregate
• Layers — GCNLayer, SAGELayer (Mean/Max), GATLayer with full weight management
• Model — dynamic execution graph with weight loading from TGNN binary files
• I/O — load_cora_binary, load_weight_file, GraphLoader

Build System (setup.py)

• Uses setuptools + pybind11 C++ extension
• MinGW cross-compilation with static GCC runtime linking (no DLL dependencies)
• Produces _tinygnn_core.cp312-win_amd64.pyd (~558 KB)
• Clean pip install -e . or python setup.py build_ext --inplace

Python Package (python/tinygnn/)

import tinygnn
import numpy as np

# Create tensor from NumPy
X = tinygnn.Tensor.from_numpy(np.random.randn(10, 16).astype(np.float32))

# Build and run GCN model
model = tinygnn.Model()
model.add_gcn_layer(1433, 64, activation=tinygnn.Activation.RELU)
model.add_gcn_layer(64, 7, activation=tinygnn.Activation.NONE)
model.load_weights("weights/gcn_cora.bin")
logits = model.forward(adjacency, features)
result = logits.to_numpy()  # → NumPy array

Zero-Copy Interop

Method	Direction	Data Type
Tensor.from_numpy(arr)	NumPy → TinyGNN	2D float32/float64 array → Dense Tensor
Tensor.from_numpy_1d(arr)	NumPy → TinyGNN	1D array → (1×N) Dense Tensor (bias)
Tensor.to_numpy()	TinyGNN → NumPy	Dense Tensor → 2D float32 array
Tensor.from_scipy_csr(mat)	SciPy → TinyGNN	csr_matrix → SparseCSR Tensor
Tensor.from_edge_index(ei, N)	PyG → TinyGNN	(2×E) int32 COO → SparseCSR Tensor
Tensor.row_ptr_numpy()	TinyGNN → NumPy	CSR row_ptr as int32 array
Tensor.col_ind_numpy()	TinyGNN → NumPy	CSR col_ind as int32 array

Cora Validation (scripts/validate_cora.py)

Two validation modes:

Mode 1 — Weight File Validation: Loads pre-trained weights, runs TinyGNN inference, verifies test accuracy within 1% of expected.

Mode 2 — Logit-Level Comparison: Trains a fresh GCN in PyG, exports weights, runs both PyG and TinyGNN on identical inputs, asserts logits match:

Metric	Result
Max absolute logit diff	0.000002
Mean absolute logit diff	0.000000
Mean relative diff	0.000001
Prediction agreement	100.0%

Test Suite -- 49 pytest tests, 0 failures

Category	Tests	Covers
Dense Tensor	9	creation, from_numpy, to_numpy, roundtrip, repr, memory
Sparse CSR Tensor	5	creation, CSR accessors, from_scipy, from_edge_index, error
Ops (matmul/spmm)	4	identity, values, SpMM identity, SpMM aggregation
Activations	9	relu, leaky_relu, elu, sigmoid, tanh, gelu, softmax, log_softmax, add_bias
Graph utilities	4	add_self_loops, gcn_norm, edge_softmax, sage_max_aggregate
GCN Layer	3	construction, identity weight forward, ReLU forward
SAGE Layer	4	Mean/Max construction, Mean forward, Max forward
GAT Layer	2	construction, forward pass
Model	3	GCN model build+forward, SAGE model build+forward, weight file loading
Enums	3	StorageFormat, Activation, Aggregator
Error handling	3	wrong ndim, sparse-to-numpy, bad edge_index shape

Tests run:    49
Passed:       49
Failed:       0

---

Phase 9 -- Software-Level Parallelism (OpenMP & AVX2)

Goal

Maximize CPU throughput by adding thread-level parallelism (OpenMP) and data-level parallelism (AVX2 SIMD intrinsics) to the compute kernels, achieving near-linear speedup on multi-core CPUs.

Design

OpenMP Parallelism

All outer (row/node) loops are parallelized with OpenMP pragmas:

Kernel	Pragma	Schedule	Rationale
matmul	#pragma omp parallel for	dynamic	Rows are uniform, but dynamic handles cache-sharing effects
spmm	#pragma omp parallel for	dynamic	Power-law graphs have highly variable row lengths
softmax_inplace	#pragma omp parallel for	dynamic	Each row is independent (3 passes: max, exp+sum, normalize)
log_softmax_inplace	#pragma omp parallel for	dynamic	Same row-independent structure as softmax
relu/elu/sigmoid/tanh/gelu	#pragma omp parallel for	static	Element-wise ops with uniform work per iteration
add_bias	#pragma omp parallel for	static	Uniform row-based broadcasting

AVX2 + FMA Intrinsics

The inner feature-dimension loops of matmul and spmm use 256-bit SIMD (8 floats per cycle):

// Inner loop of spmm (8-wide FMA):
const __m256 va = _mm256_set1_ps(a_val);          // broadcast edge weight
__m256 vc = _mm256_loadu_ps(crow + j);             // load 8 output features
__m256 vb = _mm256_loadu_ps(brow + j);             // load 8 neighbor features
vc = _mm256_fmadd_ps(va, vb, vc);                  // fused multiply-add
_mm256_storeu_ps(crow + j, vc);                     // store 8 results

Scalar tail handles feature dimensions not divisible by 8. Code compiles cleanly without AVX2 via #ifdef __AVX2__ guards.

Build Flags

g++ -std=c++17 -O2 -fopenmp -mavx2 -mfma ...

CMake automatically detects OpenMP and AVX2/FMA support via find_package(OpenMP) and check_cxx_compiler_flag.

Benchmark Results

Machine-dependent results — numbers below measured on Intel Core 9 270H (20 logical threads), GCC 13.3, Ubuntu 24.04 (WSL2). Thread counts, memory bandwidth, and topology will produce different speedup figures on other hardware.

Tested on Intel Core 9 270H (20 threads), GCC 13.3, Ubuntu 24.04 (WSL2):

Cora-scale (2,708 nodes x 1,433 features, avg degree 3.9)

Threads	SpMM	Speedup	GEMM	Speedup	Softmax	Speedup
1	6.4 ms	1.00x	500 ms	1.00x	15.4 ms	1.00x
2	4.0 ms	1.58x	250 ms	2.00x	10.4 ms	1.48x
4	3.4 ms	1.85x	167 ms	2.99x	6.6 ms	2.35x
8	2.6 ms	2.49x	114 ms	4.38x	4.6 ms	3.35x

Large-scale (50,000 nodes x 256 features, avg degree 15)

Threads	SpMM	Speedup	Softmax	Speedup
1	152 ms	1.00x	69.0 ms	1.00x
2	81 ms	1.87x	65.0 ms	1.06x
4	57 ms	2.68x	56.7 ms	1.22x
8	68 ms	2.24x	48.0 ms	1.44x

Key observations:

• GEMM achieves super-linear scaling (4.38x on 8 threads) due to improved cache utilization when threads share L2/L3
• SpMM scales well (2.49x on 8 threads for Cora) despite irregular memory access patterns
• Softmax scales efficiently (3.35x on 8 threads) because rows are fully independent
• Large-scale SpMM saturates at 4 threads — memory bandwidth becomes the bottleneck

Thread-Scaling Chart

---

Phase 10 -- Operator Fusion (GAT & GraphSAGE)

Goal

Fuse multi-step GNN layer operations into single row-wise loops, eliminating intermediate tensor allocations and reducing peak memory consumption while improving runtime through better data locality.

Design

GAT Fusion: SpSDDMM + edge_softmax + SpMM

The unfused GAT forward pass allocates three nnz-sized intermediate tensors:

Step	Operation	Intermediate	Size
3	SpSDDMM	edge_logits vector	nnz × 4 bytes
3	Build CSR	attn_csr (rp + ci + vals copies)	(N+1)×4 + 2×nnz×4 bytes
4	edge_softmax	alpha CSR (another full copy)	(N+1)×4 + 2×nnz×4 bytes

The fused kernel replaces Steps 3–5 with a single row-wise loop:

for each node i:                                    // parallelized with OpenMP
    for j ∈ N(i):
        e_ij = LeakyReLU(src_score[i] + dst_score[j])   // SpSDDMM
    α = softmax(e_row)                                    // edge_softmax
    out[i] = Σ_j α_ij · Wh[j]                            // SpMM (AVX2 FMA)

This eliminates ~7 × nnz bytes of intermediate allocations, replacing them with a single per-row buffer of size max_degree × 4 bytes.

SAGE Fusion: Aggregation + Dual-Matmul

The unfused SAGE forward allocates:

Step	Operation	Intermediate	Size
1	spmm(A, H)	agg tensor	N × F_in × 4 bytes
2	matmul(agg, W_neigh)	h_neigh tensor	N × F_out × 4 bytes
3	matmul(H, W_self)	h_self tensor	N × F_out × 4 bytes

The fused kernel computes everything row-by-row:

for each node i:                                    // parallelized with OpenMP
    agg_row = mean({H[j] : j ∈ N(i)})                // AVX2 accumulate
    out[i] = agg_row · W_neigh + H[i] · W_self       // dual-matmul (AVX2 FMA)

This eliminates the N × F_in aggregation tensor and the N × F_out h_self tensor, needing only an F_in-sized per-row buffer.

Benchmark Results

Machine-dependent results — fused vs. unfused timings below are representative for AVX2 CPUs with multi-level caches. The crossover point (where fusion starts winning) shifts with L2/L3 cache size and memory bandwidth.

Tested on Intel Core 9 270H (8 threads), GCC 13.3, Ubuntu 24.04 (WSL2):

GAT: Fused SpSDDMM + edge_softmax + SpMM

Configuration	Unfused	Fused	Speedup	Memory Ratio
Cora-like (2708×1433→8, deg≈5)	4,867 µs	5,391 µs	0.90×	2.8×
Medium (5000×128→64, deg≈10)	4,211 µs	3,129 µs	1.35×	1.4×
Large (10000×64→32, deg≈20)	5,717 µs	3,534 µs	1.62×	2.6×
XL (20000×32→16, deg≈30)	12,323 µs	4,726 µs	2.61×	5.6×

SAGE: Fused Aggregation + Dual-Matmul

Configuration	Unfused	Fused	Speedup	Memory Ratio
Cora-like (2708×1433→128, deg≈5)	60,259 µs	20,209 µs	2.98×	13.1×
Medium (5000×128→64, deg≈10)	6,107 µs	1,858 µs	3.29×	4.0×
Large (10000×64→32, deg≈20)	5,631 µs	3,293 µs	1.71×	4.0×
XL (20000×128→64, deg≈30)	30,015 µs	18,246 µs	1.64×	4.0×

Key observations:

• GAT fusion scales with graph density — at deg≈30, the nnz-sized intermediates dominate and fusion saves 5.6× memory with 2.61× speedup
• SAGE fusion excels when F_in is large — Cora layer 1 (F_in=1433) shows 13.1× memory reduction and 2.98× speedup by avoiding the N×F_in aggregate tensor
• Cora-like GAT is slightly slower (0.90×) because the per-row softmax buffer allocation overhead dominates for very small neighborhoods (deg≈5)

Valgrind Massif Profiling

Massif heap profiling on GAT (N=10000, F_in=64, F_out=32, deg≈20, nnz≈210K):

Variant	Peak Heap	Savings
Unfused	10,857,004 bytes (10.35 MB)	—
Fused	7,420,824 bytes (7.08 MB)	3.44 MB (31.6%)

Run profiling: bash scripts/run_massif_phase9.sh

---

Phase 11 -- Packaging, CI/CD & Documentation

Goal

Make TinyGNN a "one-click install" package ready for JMLR MLOSS or JOSS submission, with professional CI/CD, comprehensive documentation, and PyPI packaging.

PyPI Packaging

TinyGNN ships as a standard Python package with a pybind11 C++ extension:

pip install tinygnn

Package structure:

• pyproject.toml — PEP 517/518 metadata (name, version, authors, classifiers, dependencies)
• setup.py — Extension build configuration (C++17 flags, OpenMP, AVX2, MinGW/MSVC/GCC support)
• MANIFEST.in — Source distribution manifest (ensures headers, sources, docs are included)
• LICENSE — MIT License
• CITATION.cff — Machine-readable citation metadata for JOSS/JMLR

Classifiers:

• Development Status :: 4 - Beta
• Topic :: Scientific/Engineering :: Artificial Intelligence
• License :: OSI Approved :: MIT License
• Python 3.8–3.13 support

CI/CD (GitHub Actions)

Every push to main and every PR triggers 5 parallel jobs:

Job	Platform	What it does
C++ Build + Test	Ubuntu (GCC + Clang), macOS, Windows (MSVC)	CMake build → CTest (18,000+ assertions)
Python Build + Test	Ubuntu (3.10, 3.12), macOS (3.12), Windows (3.12)	pip install → pytest (49 tests)
Sanitizers	Ubuntu (GCC)	ASan + UBSan + leak detection (-DCMAKE_EXE_LINKER_FLAGS)
Valgrind	Ubuntu (GCC)	Memcheck (0 errors, 0 leaks) + Helgrind (0 data races)
Documentation	Ubuntu	Doxygen (C++) + Sphinx (Python) → artifact upload

Documentation

C++ API (Doxygen):

• Configured via Doxyfile in project root
• Extracts from annotated headers in include/tinygnn/
• Generates HTML + XML (for Breathe cross-reference)
• Class diagrams, include graphs (via Graphviz)
• Build: doxygen Doxyfile → docs/doxygen/html/

Python API (Sphinx):

• Read the Docs theme (sphinx-rtd-theme)
• Cross-references C++ docs via Breathe bridge
• Pages: Installation, Quick Start, Python API, C++ API, Benchmarks, Contributing
• Build: cd docs && make html → docs/_build/html/

Authors

Jai Ansh Singh Bindra and Anubhav Choudhery (under JBAC EdTech)

---

Cumulative Test Statistics

Phase	Test file	Functions	Assertions	Result
1	test_tensor.cpp	18	104	104 / 104
2	test_graph_loader.cpp	49	269	269 / 269
3	test_matmul.cpp	30	268	268 / 268
4	test_spmm.cpp	35	306	306 / 306
5	test_activations.cpp	70	266	266 / 266
6a	test_gcn.cpp	68	764	764 / 764
6b	test_graphsage.cpp	60	1,011	1,011 / 1,011
6c	test_gat.cpp	60	1,284	1,284 / 1,284
7	test_e2e.cpp	26	13,862	13,862 / 13,862
8	test_python_bindings.py	49	49 (pytest)	49 / 49
Total		465	18,183	18,183 / 18,183

---

Memory Safety

All seven phases pass the full sanitizer matrix with zero errors:

Config	Tensor	Graph Loader	Matmul	SpMM	Activations	GCN	GraphSAGE	GAT	E2E
ASan + LSan	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass
UBSan	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass
ASan + UBSan combined	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass	Pass
Valgrind Memcheck	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks	0 errors, 0 leaks
Valgrind Helgrind	0 races	0 races	0 races	0 races	0 races	0 races	0 races	0 races	0 races

---

Design Principles

• Zero dependencies -- no Eigen, no BLAS, no Boost, no external libraries of any kind
• Exact memory accounting -- memory_footprint_bytes() returns precise byte counts for both storage formats
• Fail-fast validation -- CSR construction validates row_ptr monotonicity, column index bounds, and size consistency; matmul validates format and inner dimensions before allocating output
• Unified interface -- Dense and SparseCSR tensors share the same Tensor type; format is a runtime tag, not a separate class hierarchy
• Cache-aware loop ordering -- GEMM uses (i,k,j) order with a register-hoisted scalar to enable compiler auto-vectorisation on the inner loop
• Explicit SIMD -- AVX2 FMA intrinsics (_mm256_fmadd_ps) in matmul and SpMM inner loops give 8-wide float throughput with scalar fallback for portability
• Thread-level parallelism -- OpenMP parallel for on all outer loops (rows/nodes) with schedule(dynamic) for load-balanced graph kernels
• Sparse-native message passing -- SpMM walks the CSR structure directly (row_ptr → col_ind → accumulate), avoiding any sparse-to-dense conversion
• In-place activations -- all 8 activation functions modify tensors in-place with O(1) extra memory, avoiding unnecessary allocations in GNN inference pipelines
• Numerical stability -- softmax/log-softmax use the max-subtraction trick; sigmoid uses a two-branch formula to prevent overflow for extreme inputs
• Operator fusion -- GAT fuses SpSDDMM + edge_softmax + SpMM into a single row-wise loop (eliminating nnz-sized intermediate CSR tensors); SAGE fuses aggregation + dual-matmul (eliminating N×F_in intermediate)
• One-click install -- pip install tinygnn builds the C++ extension, links statically, and ships a clean Python package; GitHub Actions CI/CD validates every commit across 4 platforms