We present mycelium-index, a streaming approximate nearest neighbor (ANN) index for high-dimensional vector spaces, inspired by the adaptive growth patterns of biological mycelium. The system continuously adapts its topology through myelial edge decay and reinforcement, a traffic-driven living hierarchy, and hybrid deletion combining O(1) bypass for cold nodes with O(k) beam-search repair for hub nodes. Experimental evaluation on SIFT-1M demonstrates that mycelium achieves 0.927 +/- 0.028 recall@5 under FreshDiskANN's 100%-turnover benchmark protocol -- within the measurement confidence interval of FreshDiskANN's ~0.95 -- while using 5.7x less RAM (88 MB vs. >500 MB) and achieving 4.7x higher QPS (2,795 vs. ~600). On the static index, at ef=192, mycelium matches HNSW M=16 recall (0.962 vs. 0.965) at 5.2x less RAM (163 MB vs. 854 MB). Performance optimizations including NEON SIMD distance computation, Vec-backed node storage, and bitset visited tracking yield a cumulative 2.7x QPS improvement. A systematic study of ten streaming repair mechanisms finds that geometric heuristics universally fail in high dimensions, while topological mechanisms succeed -- a principle we term the topological repair invariance of high-dimensional ANN graphs.
Figures & tables
Method
ef
Recall@10
QPS
RAM (MB)
Streaming
HNSW M=16
64
0.942
1,941
854
No
HNSW M=16
128
0.965
1,170
854
No
HNSW M=8
128
0.876
1,890
671
No
HNSW M=8
200
0.896
1,170
671
No
HNSW M=6
200
0.813
1,732
626
No
HNSW M=4
200
0.646
2,281
580
No
Table 1: Recall–throughput–memory comparison on SIFT-1M. RAM for HNSW: n×d×4+n×M×2×12 bytes. All benchmarks single-threaded.
Configuration
Recall@10
QPS
Base graph, random entry
0.774
843
+ Living hierarchy
0.938
843
+ Bypass reconnection
0.938
843
+ Hybrid deletion
0.938
843
Table 2: Component ablation on SIFT-1M at ef=128.
Optimization
QPS
Cumul.
Baseline (HashSet, HashMap, scalar)
742
1.0×
+ Remove .collect() + #[inline]
1,287
1.7×
+ Vec-backed NodeStore
1,414
1.9×
+ NEON SIMD + compact NodeMeta
2,006
2.7×
Table 3: Performance optimization progression, ef=128. Recall unchanged (0.938) across all steps.
Iter
Mycelium
Tombstone
Δ
Edge store
0
0.858
0.912
− 0.054
—
10
0.908
0.840
+0.068
—
50
0.838
0.640
+0.198
2.3 → 112 MB
100
0.704
0.608
+0.096
1.2 → 105 MB
150
0.608
0.526
+0.082
972 → 102 MB
200
0.684
0.442
+0.242
732 → 101 MB
Table 4: Streaming deletion comparison, 500K active vectors.
Size
Before ( μ s)
After ( μ s)
Speedup
100K
386
467
0.8×
200K
1,119
731
1.5×
500K
3,726
1,390
2.7×
1M
5,290
1,835
2.9×
Table 5: Mean query latency ( μ s) vs. dataset size.
#
Mechanism
Recall@5 (cycle 20)
Degree
Verdict
1
Baseline (no hierarchy refresh)
0.122
13.4
Hierarchy staleness
2
+ Per-cycle hierarchy refresh
0.738
13.4
Best—fixes navigation
3
+ Adaptive ef (auto-tuned beam)
0.682
13.3
Marginal improvement
4
+ Physarum flow-weighted bypass
0.020
13.2
Hot edges dominate beam
5
+ Naive anastomosis (edge sharing)
0.496
14.3
Geometrically wrong edges
6
+ Greedy multi-bypass (all neighbors)
0.280
15.8
More bad edges = worse
Table 6: Systematic evaluation of streaming repair mechanisms. SIFT-1M, 20-cycle FreshDiskANN protocol, 100% total turnover.
Cycle
Mycelium
FreshDiskANN
Gap
Hub%
RAM
0
0.966
∼ 0.95
+0.02
—
84
5
0.921
∼ 0.95
− 0.03
26%
92
10
0.926
∼ 0.95
− 0.02
29%
97
15
0.924
∼ 0.95
− 0.03
31%
101
20
0.927
∼ 0.95
−0.02
40%
88
Table 7: Final streaming recall trajectory ( ± 0.028 CI).
Constraint removed
Recall@5 (cycle 10)
Δ from unconstrained
Unconstrained (k=16, ef=200, O(k) all, f32, ∞ RAM)
0.988
—
k=8 (from 16)
0.975
− 0.013
+ ef=128 (from 200)
0.955
− 0.033
+ Hybrid delete (from O(k) all)
0.927
− 0.061
+ Scalar quantization (u8)
0.927
− 0.061
+ 163 MB RAM limit
0.927
− 0.061
Table 8: Constraint ablation on SIFT-1M, cycle 10. Starting from unconstrained recall (k=16, ef=200, O(k) all deletions, f32 vectors, unlimited RAM), constraints are added one by one.
Mycelium (streaming)
Mycelium (static)
FreshDiskANN
HNSW M=16
Recall@5 (100% turnover)
0.927±0.028
—
∼0.95
N/A
Recall@10 (static)
—
0.962
—
0.965
RAM
88 MB
163 MB
> 500 MB
854 MB
QPS
2,795
2,006
∼600
1,170
Delete cost
O(1) 90% / O(k) 10%
—
O(k) all
N/A
Streaming
Yes
—
Yes
No
Table 9: Unified comparison across systems and workloads.
Appendix figures & tables1 asset
Supplementary material from the paper’s appendix.
Appendix
Parameter
Value
Default
Sensitivity
Graph construction
k_grow
8
8
8–16; higher improves recall, costs memory
k_local
6
6
Subset of k_grow
k_long_range
2
2
Kleinberg shortcuts; 0 in streaming
long_range_alpha
2.0
2.0
Optimal for high-dim data
max_edges_per_node
64
64
Effectively unlimited
Appendix
Table 10: Full parameter table for SIFT-1M experiments.
Approximate Nearest-Neighbor Search (ANNS) pipelines for high-dimensional neural embeddings spend the bulk of their query time in candidate verification, making it the primary bottleneck in the search process. In this paper, we present PANORAMA, a state-of-the-art refinement technique that accelerates verification by exploiting the inherent spectral decay of these embeddings. Using PCA to compact signal energy, PANORAMA evaluates candidate distances incrementally, computing at each step a strict lower bound on the full-vector distance and dynamically pruning candidates the moment this bound exceeds the running k-th nearest neighbor distance. While PCA's concentration of variance facilitates pruning, it breaks the uniform-variance assumption required by Product Quantization (PQ); we resolve this with a variance-shaping step that redistributes energy across subvectors, rendering accretive refinement compatible with quantized indexes. Optimized for modern memory hierarchies via vectorized bulk-pruning and cache-conscious data layouts, PANORAMA has been upstreamed into the FAISS library across major index families (IVFPQ/Flat, HNSW, and Refine). PANORAMA achieves higher QPS at any target recall with a cost that provably scales inversely with dataset spectral decay, delivering end-to-end speedups of up to 28.9x and outperforming probabilistic methods across all recall bands.
Vansh Ramani, Alexis Schlomer, Akash Nayar +3
IIT Delhi & CMU & UCPH · Carnegie Mellon University · Indian Institute of Technology Delhi +1
We present HNTL (Hierarchical No-pointer Tangent-Local), the core vector indexing and candidate generation framework of the Aperon vector memory system. Proximity graphs (e.g., HNSW) incur a heavy pointer tax in memory overhead and induce irregular memory accesses that stall CPU pipelines. HNTL resolves this by partitioning the high-dimensional space into local, coherent grains, representing vectors as low-dimensional coordinates on local tangent spaces, and scanning them sequentially using a pointerless Block-SoA (Structure-of-Arrays) layout. On anisotropic manifold data (d=768, N=10,000), local PCA captures 96.3% of the variance, allowing HNTL to achieve a final Rerank Recall@10 of 1.0000 with a candidate pool size of only C=20 vectors. Hardware profiling via Apple kperf CPU Performance Monitoring Unit (PMU) counters demonstrates a 3.61x speedup (4.137 ns/vector vs. 14.951 ns/vector) for our NEON auto-vectorized C++ Block-SoA scan engine over standard pointer-chasing graph traversals, driven by a 3.59x IPC (Instructions Per Cycle) and near-zero L1/L2 data cache misses.
Approximate Nearest Neighbor Search (ANNS) is fundamental to modern AI applications. Most existing solutions optimize query efficiency but fail to align with the practical requirements of modern workloads. In this paper, we outline six critical demands of modern AI applications: high query efficiency, fast indexing, low memory footprint, scalability to high dimensionality, robustness across varying retrieval sizes, and support for online insertions. To satisfy all these demands, we introduce Projection-Augmented Graph (PAG), a new ANNS framework that integrates projection techniques into a graph index. PAG reduces unnecessary exact distance computations through asymmetric comparisons between exact and approximate distances as guided by projection-based statistical tests. Three key components are designed and integrated into the graph index to optimize indexing and searching. Experiments on six modern datasets demonstrate that PAG consistently achieves superior queries per second (QPS)-recall performance -- up to 5x faster than HNSW -- while offering fast indexing speed and moderate memory footprint. PAG remains robust as dimensionality and retrieval size increase and naturally supports online insertions.
Kejing Lu, Zhenpeng Pan, Jianbin Qin +2
University of Yamanashi · Beijing Institute of Technology, Zhuhai · Shenzhen University +2