Agents build RAG pipelines, semantic search and recommendation retrieval every day, but they cannot see the embedding space they are searching. When retrieval goes wrong it rarely looks like a bug. It looks like "the same three chunks come back for everything", "every score is 0.8-something", "top-k is full of copies", or "brute force finds it and HNSW does not".

Each of those failures has a known, deterministic diagnostic in the literature. vecscope turns them into one command and one JSON: measurements, ok / warn / fail verdicts, and an explanation an agent can act on. It runs locally on NumPy, needs no model or network, and reports the same numbers every time.

vecscope diagnoses the vector search implementation: the geometry the model produced, the hygiene of the corpus, the distance metric, the index and the query pipeline. It does not measure relevance. Whether the right documents come back for a question needs labeled queries, and a clean audit is evidence that search is not sabotaging retrieval, not proof that retrieval is good.

Quick start

1. Install

pip install vecscope

2. Get a file of embeddings

vecscope reads a file with one embedding vector per row: the (n, dim) array a model's encode returns, saved as .npy, .parquet, .jsonl, .json or .csv (all formats).

import numpy as np
embeddings = model.encode(texts)          # shape (n, dim), e.g. (3000, 128)
np.save("embeddings.npy", embeddings)

No embeddings at hand? Generate three synthetic matrices (healthy, anisotropic, collapsed):

python -c "import urllib.request as u; u.urlretrieve('https://raw.githubusercontent.com/076923/vecscope/main/examples/make_examples.py', 'make_examples.py')"
python make_examples.py

3. Run the audit

vecscope audit embeddings.npy

vecscope 0.3.0  n=3000 dim=128 k=10  verdict=FAIL
  [ok  ] hubness          skewness=1.1661  (ok < 2, warn >= 2, fail >= 4)
                         k-occurrence skewness 1.17; top 1% of items take 3.9% of all neighbor slots (max N_k=51, expected 10).
  [WARN] antihubs         antihub_excess=0.0523  (ok < 0.05, warn >= 0.05, fail >= 0.2)
                         5.2% of items are never anyone's neighbor (random data at k=10 would give 0.0%); the excess is unreachable through k-NN retrieval.
                         try: inspect a sample of never-retrieved items; drop empty inputs, then apply the hubness fix
  [FAIL] anisotropy       mean_random_cosine=0.8734  (ok < 0.5, warn >= 0.5, fail >= 0.85)
                         random pairs have mean cosine 0.873 (isotropic ~0); mean unit vector has norm 0.93; centering would bring the cosine to -0.001.
                         try: subtract the corpus mean vector and re-normalize, applying the same transform to queries; details.mean_random_cosine_after_centering shows the expected result
  [ok  ] effective_rank   effective_rank_ratio=0.5407  (ok >= 0.1, warn < 0.1, fail < 0.05)
                         effective rank 69.2 of 128 dims (54.1%); low values mean most dimensions carry nothing.
  [ok  ] collapse         near_duplicate_ratio=0.0000  (ok < 0.02, warn >= 0.02, fail >= 0.1)
                         0.0% of items have a neighbor with cosine >= 0.99 (exact duplicates 0.0%); no row has a near-duplicate.
  [ok  ] rogue_dimensions top1_dim_variance_ratio=1.3070  (ok < 10, warn >= 10, fail >= 50)
                         dimension 94 alone holds 1.0% of variance, 1.3x the uniform share of 0.78%; top 3 dims hold 3.0%. Rogue dimensions dominate cosine.
  [ok  ] norms            norm_cv=0.0000  (ok < 0.1, warn >= 0.1, fail >= 0.3)
                         vector norms vary with CV 0.000 (median 1.000, range 1.000-1.000); 0.00% are zero vectors. Unequal norms bias inner-product search toward long vectors.
  [ok  ] metric_mismatch  topk_overlap=1.0000  (ok >= 0.9, warn < 0.9, fail < 0.7)
                         cosine and inner-product top-10 share 100.0% of neighbors; 100.0% of items get identical lists. Low overlap means the index metric changes the results.
  [ok  ] distance_concentration contrast_over_noise=2.2753  (ok >= 1.4, warn < 1.4, fail < 1.1)
                         a random item is 3.27x farther than the nearest neighbor (median NN distance 0.039, random 0.127); isotropic noise at 128-d would give 1.44x, so the contrast is 2.28x that of noise. Near 1.0 means distances carry no signal.
  [ok  ] outliers         outlier_ratio=0.0030  (ok < 0.01, warn >= 0.01, fail >= 0.05)
                         0.30% of items have no neighbor within cosine distance 0.050 (median 0.039); see details.sample_ids. Typically junk, empty or foreign-language content.
  [ok  ] connectivity     island_ratio=0.0000  (ok < 0.01, warn >= 0.01, fail >= 0.1)
                         0.00% of items sit in 0 small island(s) of the k-NN graph (fewer than 15 items; 60 components in total). Graph-based ANN (HNSW) attaches islands to the wrong region or never reaches them.

4. Read the result

• The first line gives the overall verdict: the worst verdict among the findings.
• Each finding shows the measured value, the range that would be ok, and a sentence saying what the number means for retrieval. Findings that are not ok add a try: line with the smallest change to test first.
• The exit code is 1 on FAIL, so the same command works as a CI gate.
• Add --json to get the same evidence as JSON for an agent or a script.

What vecscope measures

Every finding in the JSON carries its healthy_range, warn_at and fail_at, plus a details block with the raw numbers. For anisotropy that block includes the cosine the same vectors would have after centering, so the agent can see whether centering alone fixes the problem. ann_recall appears only when you pass an ANN neighbor file with --ann; ood_queries and query_hubness only when you pass query embeddings with --queries.

Each finding also carries likely_causes, suggested_action and verify_by. They are hypotheses, not prescriptions: apply the smallest change, re-audit, and compare retrieval on real queries before adopting it. The agent skill spells out that loop.

Thresholds are defaults calibrated on eight public models; they are a starting point for diagnosis, not a universal quality bar. Embedding spaces differ by model, language, domain and dimensionality, so a warn on a good model is normal and a clean audit does not guarantee good search. Override any pair per run:

vecscope audit vectors.npy --thresholds my_thresholds.json
# my_thresholds.json: {"anisotropy.mean_random_cosine": [0.4, 0.7], "hubness.skewness": [2.5, 5]}

The keys are listed in src/vecscope/evidence.py (THRESHOLDS) and echoed in every JSON result under thresholds.

Queries and clusters

Pass the query embeddings too and vecscope checks whether queries live where the corpus lives. Asymmetric models used without their query prefix, a different model on the query side, or questions about topics the corpus does not cover all show up as ood_queries; the same few chunks answering everything shows up as query_hubness.

vecscope audit corpus.npy --queries queries.npy

Add --clusters 10 to append a per-cluster map: size, tightness, near-duplicate share, how much of the hub traffic each cluster takes, and sample ids the agent can look up. It carries no verdicts; it tells the agent where a problem lives.

  clusters (3):
     id   size  share  cos2ctr  neardup  hubshare  sample_ids
      1   1014  33.8%    0.111     0.0%     34.5%  [1533, 2934, 800, 1585, 824]
      2   1001  33.4%    0.109     0.0%     33.4%  [2550, 1171, 4, 1496, 668]
      0    985  32.8%    0.111     0.0%     32.0%  [1910, 2516, 2859, 124, 2392]

Index sweep

vecscope sweep builds HNSW and IVF indexes with a small parameter grid and reports, for each setting, recall@k against exact k-NN, build time and queries per second on this corpus. It then recommends the fastest setting that reaches the target recall (default 0.95) and reports its margin over the target. A margin under 0.02 marks the recommendation tight and names the fastest setting with real headroom, because recall at fixed parameters falls as the corpus grows: a setting that just clears the target on a 50k-row sample usually misses it on the full corpus. It needs the faiss-cpu extra.

pip install "vecscope[index]"
vecscope sweep embeddings.npy -k 10 --target-recall 0.95

  index params                                       recall  build s       qps
 *hnsw  M=8, ef_construction=100, ef_search=16        0.988     0.49    588131
 *hnsw  M=16, ef_construction=100, ef_search=32       1.000     0.48    238146
 *ivf   nlist=76, nprobe=16                           1.000     0.14    182966
  recommendation: hnsw (M=8, ef_construction=100, ef_search=16)  recall=0.988  qps=588131  margin=+0.038  (fastest configuration with recall@10 >= 0.95)
  note: recall is measured on 1000 queries drawn from the corpus itself; real query traffic can differ, pass it as queries when available
  note: recall at fixed parameters falls as the corpus grows; a sweep on a sample is optimistic for the full corpus, re-run at production size before fixing parameters
  note: queries_per_second is the median of 3 runs on this machine with one query batch; it ranks settings against each other and is not a serving throughput

Queries default to a seeded sample of the corpus; pass --queries to time real queries. Each setting is timed three times and the median kept (--timing-repeats); the notes at the end are part of the JSON as caveats. The MCP tool is sweep_index.

With a GPU build of faiss (pip install faiss-gpu-cu12 on Linux) the IVF index and the exact baseline run on the GPU automatically; the output header names the device. HNSW has no GPU implementation in faiss and stays on the CPU. Force a device with --device cpu|gpu.

Compare two embeddings

When two models embedded the same items, or one model did before and after a change, vecscope compare tells how far the two spaces agree on who is near whom. It reports how often the nearest neighbor and the top-k lists coincide, the near-duplicate share in each space and in both, whether both spaces pick the same duplicate partner, and the rows that disagree most. It carries no verdicts. Its job is to separate item problems from model problems: a 10% collapse that both spaces flag with the same partners is a property of the items (the same image under several ids, say); duplicates that only one space flags point at that model.

vecscope compare clip.npy lens.npy -k 10          # rows must be the same items in the same order

vecscope 0.3.0  compare  n=3000 dim=128/128 k=10
  nn1_agreement=0.7050  topk_overlap=0.8537  topk_overlap_p10=0.7000  rows_with_no_overlap=0.0000
  near_dup A=0.0400  B=0.0400  both=0.0400  only_A=0.0000  only_B=0.0000  same_nearest_among_both=1.0000
    the two spaces share the nearest neighbor for 70.5% of rows and 85.4% of their top-10 lists
    on average (0.0% of rows share nothing). Near-duplicates: 4.0% in A, 4.0% in B, 4.0% in both,
    and 100.0% of those agree on the partner. Duplicates flagged by both spaces with the same
    partner are a property of the items; duplicates flagged by one space only point at that model.
  largest disagreements (row: nearest in A / nearest in B, top-k overlap):
    1769: 1340 / 1340  0.50
    1810: 1229 / 1229  0.50

The MCP tool is compare_embeddings.

Use with an agent

vecscope ships an MCP server with four read-only tools: audit_embeddings, sweep_index, compare_embeddings and describe_findings. Register it with any MCP client (Claude Code, Cursor, Codex, ...):

pip install "vecscope[mcp]"

{ "mcpServers": { "vecscope": { "command": "vecscope-mcp" } } }

Then ask:

Audit the embeddings in data/chunks.npy before we tune the retriever, and tell me
which finding to fix first.

The agent skill in .agents/skills/vecscope/SKILL.md tells the agent when to run the audit and what to do about each verdict: center or swap the model, deduplicate, re-rank, or rebuild the index. The server also carries those instructions, so an agent that only has the MCP connection follows the same loop. sweep_index runs the index sweep, compare_embeddings the comparison; describe_findings lists every finding with its thresholds, causes and actions. Responses start with a one-line summary; pass verbose=false to drop details for findings that are ok. Agents without MCP can run the CLI with --json and read the same evidence.

If the server stops connecting ("vecscope-mcp not found"), the Python environment it was installed into has usually been replaced; this happens on hosted notebooks and clusters that rebuild their environment. Check with pip show vecscope in the interpreter the client uses, reinstall there, and prefer registering the server through that interpreter so the error names the right environment:

{ "mcpServers": { "vecscope": { "command": "/path/to/env/bin/python", "args": ["-m", "vecscope.mcp_server"] } } }

Use as a library

import numpy as np
from vecscope import audit

embeddings = np.load("embeddings.npy")    # any (n, dim) float array

ev = audit(embeddings, k=10)
ev.verdict                                # "ok" | "warn" | "fail"
ev.findings[0].value                      # measured value of the first finding
ev.to_dict()                              # the full evidence, same as --json

CLI options

vecscope audit vectors.npy -k 20                       # neighbors per item (default 10)
vecscope audit vectors.parquet --json                  # JSON evidence
vecscope audit vectors.npy --ann hnsw_neighbors.npy    # score ANN recall against exact k-NN
vecscope audit vectors.npy --queries queries.npy       # add query-side findings
vecscope audit vectors.npy --clusters 10               # append a per-cluster report
vecscope audit vectors.npy --thresholds th.json         # override (warn, fail) pairs
vecscope audit vectors.npy --fail-on warn              # exit 1 on WARN as well
vecscope audit vectors.npy --near-dup 0.98             # cosine threshold for near-duplicates
vecscope audit vectors.npy --sample 0                  # audit every row (default samples 100k)
vecscope audit vectors.npy --sample-repeats 3          # re-audit 3 samples; report value ranges and verdict stability
vecscope sweep vectors.npy --target-recall 0.95        # HNSW/IVF parameter sweep (faiss extra)
vecscope sweep vectors.npy --device gpu                # IVF on the GPU (faiss GPU build)
vecscope sweep vectors.npy --margin 0.05               # headroom under which the pick is marked tight (default 0.02)
vecscope compare a.npy b.npy -k 10                     # agreement between two embeddings of the same rows

Input formats

The embedding file holds one vector per row. Every format is converted to a 2-D float32 array of shape (n, dim) before the audit. In the examples embeddings is that array, for instance the output of a model's encode:

embeddings = model.encode(texts)        # shape (n, dim), e.g. (3000, 128)
embeddings[0]                           # the vector of the first item
# array([ 0.0312, -0.1187,  0.0459, ...], dtype=float32)

The optional --ann file (or ann_path in MCP) is an integer array of shape (n, k): row i holds the ids of the k neighbors an ANN index returned for item i, in the same row order as the embedding file. Any of the formats above works. Ids refer to row positions, so the file must come from an index built on exactly these rows, so --ann requires --sample 0 (the audit refuses to combine the two). Ids that point at the item itself are ignored, so an index that returns self first should be queried with k + 1.

The optional --queries file (queries_path in MCP) holds query embeddings in any of the same formats, with the same dim as the corpus.

Performance

Exact k-NN is quadratic in the number of rows, so the full audit (--sample 0) costs this on a 6-core laptop (Intel i7-8750H, NumPy only, single process). Memory is the peak tracked by Python for the audit itself; the process needs the input matrix on top of that.

The default 100k-row sample keeps any corpus inside the last row. Doubling the rows roughly quadruples the time; --queries adds one more pass over the corpus per query batch, and metric_mismatch adds a second k-NN pass only when vector norms vary. A sampled audit is a statement about the sample: use --sample 0 when you need every island and outlier counted.

How vecscope works

vecscope computes exact k-NN once over the matrix and derives every diagnostic from it: the k-occurrence distribution gives hubness and anti-hubs, nearest-neighbor cosines give collapse, outliers and distance concentration, the k-NN graph gives connectivity, random pairs and the covariance spectrum give anisotropy, effective rank and rogue dimensions, vector norms give the norm spread, a second inner-product pass (skipped when norms are uniform) gives metric mismatch, and the ANN neighbor file, if present, is compared against the exact neighbors for recall. Query embeddings, if present, get their own exact search against the corpus for the query-side findings.

Everything is deterministic: fixed seeds, exact neighbors, no learned components, no network. Two runs on the same file give the same JSON. Exact k-NN is quadratic in the number of rows, so inputs above 100,000 rows are audited on a seeded random sample unless you pass --sample 0.

Real embeddings

Thresholds are calibrated on public, pre-computed embeddings from eight models: OpenAI ada-002 and text-embedding-3-large, Cohere embed-v3, all-MiniLM-L6-v2, bge-m3, mxbai-embed-large-v1 and gte-base-en-v1.5. The table shows the measured value for the first 40k rows of each dataset; cells without a label are ok. python examples/real_models.py reproduces it, no model download needed.

ada-002's well-known anisotropy is the only warn besides hubness: its mean unit vector has norm 0.83, so unrelated documents start from a cosine floor near 0.7. Its successor is isotropic on the same corpus (norm 0.29). Centering brings every model here to a random-pair cosine of 0.00, which is why the finding reports that number. Hubness skewness of 1.2 to 1.9 is the normal range for text embeddings, so the warn threshold sits at 2.0; gte-base on arXiv abstracts sits just above it. The anisotropy thresholds (0.5, 0.85) come from the retrieval-quality study below, where the best models sit between 0.58 and 0.81.

Do the findings predict retrieval quality?

Partly, and in a specific way. docs/retrieval_quality.md measures every finding against nDCG@10 on two labeled BEIR datasets (SciFact, NFCorpus) with exact cosine search, for eight public models and for controlled defects injected into the best one. python examples/retrieval_quality.py reproduces it.

• Within one pipeline the findings track damage. Injecting a rogue dimension, cutting the rank, adding noise or duplicating rows moves the watched finding from ok to fail while nDCG@10 falls, and the drop is monotone in the defect level. Queries embedded with the wrong model score ood_queries = 1.0.
• Across good models the geometry findings do not rank the models. The best models on both datasets (gte-base, bge, e5) have the highest anisotropy (0.58 to 0.81) and ordinary effective rank. What does separate the weak models is norms with metric_mismatch (unnormalized outputs) and hubness, each at Spearman |rho| of 0.5 to 0.8 with nDCG@10.
• Anisotropy alone does not hurt ranking. Adding a shared offset until the random-pair cosine reaches 0.98 leaves nDCG@10 unchanged. It compresses scores, so absolute cosine thresholds and score calibration break; distance_concentration is the finding that moves when the signal itself is lost.

The anisotropy and distance_concentration thresholds were recalibrated from this study.

FAQ

Documentation

• Agent skill: when to run the audit and what to do with each verdict
• Retrieval-quality study: every finding against nDCG@10 on labeled data
• Examples: synthetic matrices, the calibration script and the retrieval-quality study
• Changelog

Contributing

Issues and pull requests are welcome. See CONTRIBUTING.md for how to run the tests and what a good change looks like. Security reports go through SECURITY.md.

License

MIT