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Make all hub models available for conversion to ONNX format.

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MaziyarPanahi  authored a paper about 2 months ago
Arcee Trinity Large Technical Report
lewtun  submitted a paper about 2 months ago
Single-minus gluon tree amplitudes are nonzero
lewtun  submitted a paper about 2 months ago
Reasoning Cache: Continual Improvement Over Long Horizons via Short-Horizon RL
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MaziyarPanahi 
posted an update 12 days ago
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993
Training mRNA Language Models Across 25 Species for $165

We built an end-to-end protein AI pipeline covering structure prediction, sequence design, and codon optimization. After comparing multiple transformer architectures for codon-level language modeling, CodonRoBERTa-large-v2 emerged as the clear winner with a perplexity of 4.10 and a Spearman CAI correlation of 0.40, significantly outperforming ModernBERT. We then scaled to 25 species, trained 4 production models in 55 GPU-hours, and built a species-conditioned system that no other open-source project offers. Complete results, architectural decisions, and runnable code below.

https://huggingface.co/blog/OpenMed/training-mrna-models-25-species
MaziyarPanahi 
posted an update 19 days ago
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2198
We annotated 119K medical images with two frontier VLMs (Qwen 3.5, Kimi K2.5), cross-validated at 93% agreement, and produced 110K training records, all for under $500. Fine-tuning 3 small models (2-3B params) improved all benchmarks: best model reaches +15.0% average exact match.

Everything is open-sourced: datasets, adapters, and code.

https://huggingface.co/blog/OpenMed/synthvision
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Nymbo 
posted an update 28 days ago
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We should really have a release date range slider on the /models page. Tired of "trending/most downloaded" being the best way to sort and still seeing models from 2023 on the first page just because they're embedded in enterprise pipelines and get downloaded repeatedly. "Recently Created/Recently Updated" don't solve the discovery problem considering the amount of noise to sift through.

Slight caveat: Trending actually does have some recency bias, but it's not strong/precise enough.
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MaziyarPanahi 
posted an update about 1 month ago
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4806
DNA, mRNA, proteins, AI. I spent the last year going deep into computational biology as an ML engineer. This is Part I of what I found. 🧬

In 2024, AlphaFold won the Nobel Prize in Chemistry.

By 2026, the open-source community had built alternatives that outperform it.

That's the story I find most interesting about protein AI right now. Not just the science (which is incredible), but the speed at which open-source caught up. Multiple teams, independently, reproduced and then exceeded AlphaFold 3's accuracy with permissive licenses. The field went from prediction to generation: we're not just modeling known proteins anymore, we're designing new ones.

I spent months mapping this landscape for ML engineers. What the architectures actually are (spoiler: transformers and diffusion models), which tools to use for what, and which ones you can actually ship commercially.

New post on the Hugging Face blog: https://huggingface.co/blog/MaziyarPanahi/protein-ai-landscape

Hope you all enjoy! 🤗
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MaziyarPanahi 
authored a paper about 2 months ago
lewtun 
submitted 2 papers to Daily Papers about 2 months ago
MaziyarPanahi 
posted an update 2 months ago
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Announcing: OpenMed Multilingual PII Detection Models

Today I am releasing 105 open-source models for Personally Identifiable Information (PII) detection in French, German, and Italian.

All Apache 2.0 licensed. Free for commercial use. No restrictions.

Performance:

- French: 97.97% F1 (top model)
- German: 97.61% F1 (top model)
- Italian: 97.28% F1 (top model)

All top-10 models per language exceed 96% F1

Coverage:

55+ PII entity types per language
Native ID formats: NSS (French), Sozialversicherungsnummer (German), Codice Fiscale (Italian)
Language-specific address, phone, and name patterns

Training Data:

French: 49,580 samples
German: 42,250 samples
Italian: 40,944 samples

Why Multilingual?

European healthcare operates in European languages. Clinical notes, patient records, and medical documents are generated in French, German, Italian, and other languages.

Effective de-identification requires:

- Native language understanding — not translation
- Local ID format recognition — each country has unique patterns
- Cultural context awareness — names, addresses, and formats vary
- These models deliver production-ready accuracy without requiring data to leave your infrastructure or language.

HIPAA & GDPR Compliance
Built for US and European privacy regulations:

- On-premise deployment: Process data locally with zero external dependencies
- Data sovereignty: No API calls, no cloud services, no cross-border transfers
- Air-gapped capable: Deploy in fully isolated environments if required
- Regulatory-grade accuracy: Supporting Expert Determination standards
- HIPAA and GDPR compliance across languages, without compliance gaps.

Use Cases
- Hospital EHR systems: Automated patient record de-identification
- Clinical research: Multilingual dataset preparation for studies
- Insurance companies: Claims processing across

https://huggingface.co/collections/OpenMed/multilingual-pii-and-de-identification
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MaziyarPanahi 
posted an update 2 months ago
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From Golden Gate Bridge to Broken JSON: Why Anthropic's SAE Steering Fails for Structured Output

I ran 6 experiments trying to use Anthropic's SAE steering for JSON generation.

- Base model: 86.8% valid JSON
- Steering only: 24.4%
- Fine-tuned: 96.6%
- FSM constrained: 100%

Steering is for semantics, not syntax.

https://huggingface.co/blog/MaziyarPanahi/sae-steering-json
MaziyarPanahi 
posted an update 2 months ago
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🚨 Day 8/8: OpenMed Medical Reasoning Dataset Release - THE GRAND FINALE

Today I complete my 8-day release series with Medical-Reasoning-SFT-Mega.
The largest open medical reasoning dataset, combining 7 state-of-the-art AI models with fair distribution deduplication.

THE 7 SOURCE MODELS (Original Sample Counts):

1. Trinity-Mini: 810,284 samples
2. Qwen3-Next-80B: 604,249 samples
3. GPT-OSS-120B: 506,150 samples
4. Nemotron-Nano-30B: 444,544 samples
5. GLM-4.5-Air: 225,179 samples
6. MiniMax-M2.1: 204,773 samples
7. Baichuan-M3-235B: 124,520 samples

TOTAL BEFORE DEDUPLICATION: 2,919,699 samples

TOKEN COUNTS:
- Content tokens: 2.22 Billion
- Reasoning tokens: 1.56 Billion
- Total tokens: 3.78 Billion
- Samples with chain-of-thought: 100%

Quick Start:
from datasets import load_dataset
ds = load_dataset("OpenMed/Medical-Reasoning-SFT-Mega")


All datasets Apache 2.0 licensed. Free for research and commercial use.

Thank you for following OpenMed's release series. I can't wait to see what you build. 🔥

OpenMed/Medical-Reasoning-SFT-Mega
OpenMed/Medical-Reasoning-SFT-GPT-OSS-120B-V2
OpenMed/Medical-Reasoning-SFT-Trinity-Mini
OpenMed/Medical-Reasoning-SFT-GLM_4.5_Air
OpenMed/Medical-Reasoning-SFT-MiniMax-M2.1
OpenMed/Medical-Reasoning-SFT-Qwen3-Next-80B
OpenMed/Medical-Reasoning-SFT-Nemotron-Nano-30B
OpenMed/Medical-Reasoning-SFT-Baichuan-M3-235B



https://huggingface.co/collections/OpenMed/medical-datasets
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Nymbo 
posted an update 3 months ago
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Genuine recommendation: You should really use this AutoHotKey macro. Save the file as macros.ahk and run it. Before sending a prompt to your coding agent, press Ctrl + Alt + 1 and paste your prompt to any regular chatbot. Then send the output to the agent. This is the actual, boring, real way to "10x your prompting". Use the other number keys to avoid repeating yourself over and over again. I use this macro prolly 100-200 times per day. AutoHotKey isn't as new or hype as a lot of other workflows, but there's a reason it's still widely used after 17 years. Don't overcomplicate it.

; Requires AutoHotkey v1.1+

; All macros are `Ctrl + Alt + <variable>`

^!1::
    Send, Please help me more clearly articulate what I mean with this message (write the message in a code block):
return

^!2::
    Send, Please make the following changes:
return

^!3::
    Send, It seems you got cut off by the maximum response limit. Please continue by picking up where you left off.
return


In my experience the past few months, Ctrl + Alt + 1 works best with Instruct models (non-thinking). Reasoning causes some models to ramble and miss the point. I've just been using GPT-5.x for this.
MaziyarPanahi 
posted an update 3 months ago
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🎉 OpenMed 2025 Year in Review: 6 Months of Open Medical AI

I'm thrilled to share what the OpenMed community has accomplished since our July 2025 launch!

📊 The Numbers

29,700,000 downloads Thank you! 🙏

- 481 total models (475 medical NER models + 6 fine-tuned LLMs)
- 475 medical NER models in [OpenMed](
OpenMed ) organization
- 6 fine-tuned LLMs in [openmed-community](
openmed-community )
- 551,800 PyPI downloads of the [openmed package](https://pypi.org/project/openmed/)
- 707 followers on HuggingFace (you!)
- 97 GitHub stars on the [toolkit repo](https://github.com/maziyarpanahi/openmed)

🏆 Top Models by Downloads

1. [OpenMed-NER-PharmaDetect-SuperClinical-434M]( OpenMed/OpenMed-NER-PharmaDetect-SuperClinical-434M) — 147,305 downloads
2. [OpenMed-NER-ChemicalDetect-ElectraMed-33M]( OpenMed/OpenMed-NER-ChemicalDetect-ElectraMed-33M) — 126,785 downloads
3. [OpenMed-NER-BloodCancerDetect-TinyMed-65M]( OpenMed/OpenMed-NER-BloodCancerDetect-TinyMed-65M) — 126,465 downloads

🔬 Model Categories

Our 481 models cover comprehensive medical domains:

- Disease Detection (~50 variants)
- Pharmaceutical Detection (~50 variants)
- Oncology Detection (~50 variants)
- Genomics/DNA Detection (~80 variants)
- Chemical Detection (~50 variants)
- Species/Organism Detection (~60 variants)
- Protein Detection (~50 variants)
- Pathology Detection (~50 variants)
- Blood Cancer Detection (~30 variants)
- Anatomy Detection (~40 variants)
- Zero-Shot NER (GLiNER-based)


OpenMed
OpenMed NER: Open-Source, Domain-Adapted State-of-the-Art Transformers for Biomedical NER Across 12 Public Datasets (2508.01630)
https://huggingface.co/collections/OpenMed/medical-and-clinical-ner
https://huggingface.co/collections/OpenMed/zeroshot-medical-and-clinical-ner
OpenMed/Medical-Reasoning-SFT-GPT-OSS-120B
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Nymbo 
posted an update 4 months ago
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🚨 New tool for the Nymbo/Tools MCP server: The new Agent_Skills tool provides full support for Agent Skills (Claude Skills but open-source).

How it works: The tool exposes the standard discover/info/resources/validate actions. Skills live in /Skills under the same File_System root, and any bundled scripts run through Shell_Command, no new infrastructure required.

Agent_Skills(action="discover")  # List all available skills
Agent_Skills(action="info", skill_name="music-downloader")  # Full SKILL.md
Agent_Skills(action="resources", skill_name="music-downloader")  # Scripts, refs, assets


I've included a music-downloader skill as a working demo, it wraps yt-dlp for YouTube/SoundCloud audio extraction.

Caveat: On HF Spaces, Shell_Command works for most tasks, but some operations (like YouTube downloads) are restricted due to the container environment. For full functionality, run the server locally on your machine.

Try it out ~ https://www.nymbo.net/nymbot
kenobi 
authored 3 papers 4 months ago
Nymbo 
posted an update 5 months ago
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🚀 I've just shipped a major update to the Nymbo/Tools MCP server: the Agent_Terminal, a single "master tool" that cuts token usage by over 90%!

Anthropic found 98.7% context savings using code execution with MCP, Cloudflare published similar findings. This is my open-source implementation of the same idea.

# The Problem

Traditional MCP exposes every tool definition directly to the model. With 12 tools, that's thousands of tokens consumed *before the conversation even starts*. Each tool call also passes intermediate results through the context window — a 10,000-row spreadsheet? That's all going into context just to sum a column.

# The Solution: One Tool to Rule Them All

Agent_Terminal wraps all 12 tools (Web_Search, Web_Fetch, File_System, Generate_Image, Generate_Speech, Generate_Video, Deep_Research, Memory_Manager, Obsidian_Vault, Shell_Command, Code_Interpreter) into a single Python code execution gateway.

Instead of the model making individual tool calls, it writes Python code that orchestrates the tools directly:

# Search for Bitcoin price
result = Web_Search("current price of bitcoin", max_results=3)
print(result)


Don't know what tools are available? The agent can discover them at runtime:

print(search_tools('image'))  # Find tools by keyword
print(usage('Generate_Image'))  # Get full docs for a specific tool


The individual direct tool calls are all still there, but they can be disabled if using the Agent_Terminal. Try it now - https://www.nymbo.net/nymbot
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Nymbo 
posted an update 5 months ago
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I've added an 11th tool to the Nymbo/Tools MCP server, it's for your Obsidian_Vault. I'd argue it's far more context-efficient than any other Obsidian MCP I've seen, and doesn't require any plugins. Also some big improvements to the Web_Search and Web_Fetch tools.

# Obsidian_Vault Tool

It's basically a read-only version of the File_System tool, but it works so well for navigating Obsidian without unnecessary context. It supports recursive (full-text) search across the entire vault, and supports offset so the agent can "scroll" through a document without re-consuming tokens.

Run the server locally and set the OBSIDIAN_VAULT_ROOT environment variable to your vault's root path. If you don't use Obsidian, this is perfectly usable as simply a read-only filesystem.

# Web_Search Improvements

The Web_Search tool previously just used DuckDuckGo as a backend search engine, but now it also supports Bing, Brave, Yahoo, and Wikipedia. Default engine is auto which provides results from all backends in recommended order. Still doesn't require any kind of API or auth for Web_Search.

There's also a new date filter to limit results to those created in the past day, week, month, or year. Oh, and uhh, SafeSearch is now off by default :)

# Web_Fetch Improvements

As context-efficient as the Markdown mode is for web browsing, sometimes it does lose important context in the conversion from HTML to Markdown. So I've added a new HTML mode to the Web_Fetch tool that basically executes a cURL request on the URL, returning the full HTML page if necessary.

# A Note on Claude Skills

I've been having fun with the new File_System and Shell_Command tools. Using Claude Skills doesn't currently work in the public HF space because of environment restrictions, but using Skills works perfectly well running locally.

Happy building ~
Nymbo 
posted an update 6 months ago
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Two new tools added to the Nymbo/Tools MCP server, File_System and Shell_Exec. You can theoretically do basically anything with these two tools, and it should enable support for many Claude Skills.

GPT-5-Codex proves that for many cases, shell commands really are all you need, and Claude Skills seem to lean into this. The thing is, nothing about the design of Claude Skills actually restricts them to proprietary models!

# File_System

There's a new directory inside the repo called Filesystem, that's the agent's "root". It can perform the following actions : list, read, write, append, mkdir, move, copy, delete, info, help. It's able to keep this all within the scope of one tool call by making the Action field required and all other fields optional. Using a filesystem shouldn't require 15 different tools.

Files created in the public HF space live in the space's running container, and gets cleared when the space is restarted. When running the server locally, files are actually stored on disk.

# Shell_Exec

What good is a filesystem if you can't execute commands in that filesystem? This tool automatically detects if the server is running on Windows or Linux, and suggests using the appropriate shell (PowerShell/Bash). Both of these new tools require that the agent uses relative paths, rather than absolute paths. I could be convinced to back pedal on this.

# Closing Thoughts

The File_System and Shell_Exec tools aren't super polished yet, I'll continue to improve the agent's instructions and UX of using the new tools. Most of my testing was done with gpt-oss-20b and if it messes up, it gets the gist after one failed tool call. It should work perfectly fine for the GPU poor.
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vumichien 
authored a paper 6 months ago