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examples/vibecast-7sense/docs/plans/research/intro.md
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examples/vibecast-7sense/docs/plans/research/intro.md
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## What Perch 2.0 changes for a RuVector pipeline
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Perch 2.0 is explicitly designed to produce embeddings that stay useful under domain shift and support workflows like nearest-neighbor retrieval, clustering, and linear probes on modest hardware. ([arXiv][1])
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Key technical facts that matter for engineering:
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* Input is **5 second mono audio at 32 kHz** (160,000 samples), with a log-mel frontend producing **500 frames x 128 mel bins (60 Hz to 16 kHz)**. ([arXiv][2])
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* Backbone is **EfficientNet-B3**, and the mean pooled embedding is **1536-D**. ([arXiv][2])
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* Training includes:
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* supervised species classification,
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* **prototype-learning classifier head** used for self-distillation,
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* and an auxiliary **source-prediction** objective. ([arXiv][2])
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* It is multi-taxa and reports SOTA on BirdSet and BEANS, plus strong marine transfer despite little marine training data. ([arXiv][1])
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* DeepMind describes this Perch release as an open model and points to Kaggle availability. ([Google DeepMind][3])
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Why this is a big deal for RuVector: once embeddings are “good enough,” HNSW stops being a storage trick and becomes a navigable map where neighborhoods are meaningful. RuVector’s whole value proposition is then unlocked: fast HNSW retrieval, plus a learnable GNN reranker and attention on top of the neighbor graph. ([GitHub][4])
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## RAB is the right framing for “interpretation” without hallucination
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Retrieval-Augmented Bioacoustics (RAB) is basically “RAG for animal sound,” with two design choices that align perfectly with a RuVector substrate:
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1. adapt retrieval depth based on signal quality
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2. cite the retrieved calls directly in the generated output for transparency
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That is exactly how you keep “translation” honest: you are not translating meaning, you are producing an evidence-guided structural interpretation.
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## Practical integration blueprint: Perch 2.0 + RuVector + RAB
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### 1) Ingestion schema in RuVector
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Model the world as both vectors and a graph:
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**Nodes**
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* `Recording {id, sensor_id, lat, lon, start_ts, habitat, weather, ...}`
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* `CallSegment {id, recording_id, t0_ms, t1_ms, snr, energy, ...}`
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* `Embedding {id, segment_id, model="perch2", dim=1536, ...}`
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* `Prototype {id, cluster_id, centroid_vec, exemplars[]}`
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* `Cluster {id, method, params, ...}`
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* optional: `Taxon {inat_id, scientific_name, common_name}`
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**Edges**
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* `(:Recording)-[:HAS_SEGMENT]->(:CallSegment)`
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* `(:CallSegment)-[:NEXT {dt_ms}]->(:CallSegment)` for sequences
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* `(:CallSegment)-[:SIMILAR {dist}]->(:CallSegment)` from HNSW neighbors
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* `(:Cluster)-[:HAS_PROTOTYPE]->(:Prototype)`
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* `(:CallSegment)-[:ASSIGNED_TO]->(:Cluster)` (after clustering)
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RuVector already supports storing embeddings and querying with Cypher-style graph queries, plus a GNN refinement layer that applies multi-head attention over neighbors. ([GitHub][4])
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### 2) Embedding in Rust, not Python
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You have two very practical Rust-first options:
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**Option A: ONNX Runtime**
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There are published Perch v2 ONNX conversions with concrete tensor shapes:
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* input: `['batch', 160000]`
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* outputs include: `embedding ['batch', 1536]`, plus spectrogram and logits ([Hugging Face][5])
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That gets you native Rust inference with `onnxruntime` bindings, and you can keep everything in the same process as RuVector.
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**Option B: Use an existing Rust crate that already supports Perch v2**
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There is a Rust library `birdnet-onnx` that supports Perch v2 inference (32kHz, 5s segments) and returns predictions. ([Docs.rs][6])
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Even if you do not keep it long-term, it is an excellent “verification harness” to de-risk the pipeline.
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### 3) The retrieval core: HNSW is your “acoustic cartography”
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For each `CallSegment`:
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1. embed with Perch 2.0 -> `Vec<f32>(1536)`
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2. insert vector into RuVector
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3. store metadata and computed features (snr, pitch stats, rhythm, spectral centroid)
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4. periodically (or continuously) rebuild neighbor edges `SIMILAR` from top-k
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Once you have this, you instantly get:
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* nearest-neighbor “find similar calls”
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* cluster discovery (call types, dialects, soundscape regimes)
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* anomaly detection (rare calls, new species, anthropogenic intrusions)
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### 4) Add the GNN and attention where it matters
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Use the graph as supervision:
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* acoustic edges from HNSW (similarity)
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* temporal edges from `NEXT` (syntax)
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* optional co-occurrence edges (same time window, same sensor neighborhood)
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Then train a lightweight GNN reranker whose job is not “classify species,” but:
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* re-rank neighbors for retrieval quality
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* increase cluster coherence
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* learn transition regularities
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This matches RuVector’s “HNSW retrieval then GNN enhancement” pattern. ([GitHub][4])
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### 5) RAB layer: evidence packs + constrained generation
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For any query (a segment, a time interval, a habitat), build an **Evidence Pack**:
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* top-k neighbors (IDs, distances)
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* k cluster exemplars (prototype calls)
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* top predicted taxa (if you choose to surface logits)
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* local sequence context (previous and next segments)
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* signal quality (snr, clipping, overlap score)
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* spectrogram thumbnails
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Then generation produces only these kinds of outputs:
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* monitoring summary
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* annotation suggestions
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* “this resembles X and Y exemplars, differs by Z”
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* hypothesis prompts for researchers
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And it must cite which retrieved calls informed each statement, matching the RAB proposal’s attribution emphasis.
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## Verification that the geometry is real
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Here is a verification stack that starts cheap and becomes rigorous.
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### Level 1: Mechanical correctness
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* audio is actually 32 kHz mono
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* 5s windows align with model expectations ([arXiv][2])
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* embedding norms are stable (no NaNs, no collapse)
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* duplicate audio -> near-identical embedding
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### Level 2: Retrieval sanity
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Pick 50 known calls (or manually curated exemplars):
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* do nearest-neighbor retrieval
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* manually check if top 10 are genuinely similar
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Perch’s own evaluation includes one-shot retrieval style tests using cosine distance as a proxy for clustering usefulness, which is exactly your use case. ([arXiv][7])
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### Level 3: Few-shot probes
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Train linear probes on small labeled subsets:
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* species
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* call type
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* habitat context
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* sensor ID (should be weak if embeddings are not overfitting device artifacts)
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Perch 2.0 is explicitly oriented toward strong linear probing and retrieval without full fine-tuning. ([arXiv][1])
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### Level 4: Sequence validity
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Check whether your transition graph produces:
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* stable motifs
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* repeated trajectories
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* entropy rates that differ by condition or location
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If you want “motif truth,” DTW can be your high-precision confirmation step for a small subset, not your global engine.
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## Visualization in Rust, end-to-end
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You can do a fully Rust-native viz loop now:
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1. Use RuVector to get kNN for each point (already computed by HNSW).
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2. Feed that kNN graph into a Rust UMAP implementation such as `umap-rs` (it expects precomputed neighbors). ([Docs.rs][8])
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3. Render interactive scatter plots using Rust bindings for Plotly, or export JSON for a web viewer. ([Crates.io][9])
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Bonus: Perch outputs spectrogram tensors in some exported forms, so you can attach “what the model saw” to each point and show it on hover or click. ([Hugging Face][5])
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## “Translation” that stays scientifically honest
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If you use the word “translation,” I would keep it scoped like this:
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* Translate a call into:
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* nearest exemplars
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* cluster membership
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* structural descriptors (pitch contour stats, rhythm intervals, spectral texture)
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* sequence role (often followed by X, often precedes Y)
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Not “the bird said danger,” but:
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* “This call sits in the same neighborhood as known alarm exemplars and appears in similar sequence positions during disturbance periods.”
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That is the RAB sweet spot: interpretable, evidence-backed, testable.
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## Practical to exotic: what becomes feasible now
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With Perch-grade embeddings, your ladder tightens:
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**Practical**
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* biodiversity indexing and monitoring summaries
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* fast search over million-hour corpora
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* sensor drift and anthropogenic anomaly alerts
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**Advanced**
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* few-shot adaptation for new sites with tiny labeled sets
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* call library curation via cluster prototypes
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* cross-taxa transfer experiments (insects vs birds vs amphibians)
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**Exotic but defensible**
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* closed-loop call-response experiments that probe structural sensitivity
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* synthetic prototype interpolation (generate “between-cluster” calls) with strict ethics and permitting
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* cross-species “structure maps” that compare signaling complexity without pretending semantics
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## Two next moves that will accelerate you immediately
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1. **Build the “call library + evidence pack” layer first.**
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It turns embeddings into a product and forces transparency.
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2. **Treat GNN as retrieval optimization, not a magic classifier.**
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Your win is better neighborhoods, cleaner motifs, and more stable trajectories.
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If you want, I can turn this into:
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* a concrete repo layout (`ruvector-bioacoustic/` crate + CLI + wasm viewer), or
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* a short “vision memo” you can share publicly that frames Perch 2.0 + RuVector + RAB as the start of navigable animal communication geometry.
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[1]: https://www.arxiv.org/pdf/2508.04665v2 "Perch 2.0: The Bittern Lesson for Bioacoustics"
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[2]: https://arxiv.org/html/2508.04665v1 "Perch 2.0: The Bittern Lesson for Bioacoustics"
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[3]: https://deepmind.google/blog/how-ai-is-helping-advance-the-science-of-bioacoustics-to-save-endangered-species/ "
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How AI is helping advance the science of bioacoustics to save endangered species -
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Google DeepMind
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"
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[4]: https://github.com/ruvnet/ruvector "GitHub - ruvnet/ruvector: A distributed vector database that learns. Store embeddings, query with Cypher, scale horizontally with Raft consensus, and let the index improve itself through Graph Neural Networks."
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[5]: https://huggingface.co/justinchuby/Perch-onnx?utm_source=chatgpt.com "justinchuby/Perch-onnx"
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[6]: https://docs.rs/birdnet-onnx?utm_source=chatgpt.com "birdnet_onnx - Rust"
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[7]: https://arxiv.org/html/2508.04665v1?utm_source=chatgpt.com "Perch 2.0: The Bittern Lesson for Bioacoustics"
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[8]: https://docs.rs/umap-rs?utm_source=chatgpt.com "umap_rs - Rust"
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[9]: https://crates.io/crates/plotly?utm_source=chatgpt.com "plotly - crates.io: Rust Package Registry"
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---
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