BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing
Paper • 2206.15076 • Published • 5
AI & ML interests
We aim to unify the schema across many different biomedical NLP resources.
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karthikrangasai
authored 2
papers about 23 hours ago
Post
4013
🙋🏻♂️ Hey there folks,
since everyone liked my previous announcement post ( https://huggingface.co/posts/Tonic/338509028435394 ) so much , i'm back with more high quality proceedural datasets in the Geospacial domain for SFT training !
Check this one out :
NuTonic/sat-bbox-metadata-sft-v1
the goal is to be able to train vision models on multiple images for remote sensing analysis with one shot .
hope you like it ! 🚀
since everyone liked my previous announcement post ( https://huggingface.co/posts/Tonic/338509028435394 ) so much , i'm back with more high quality proceedural datasets in the Geospacial domain for SFT training !
Check this one out :
NuTonic/sat-bbox-metadata-sft-v1
the goal is to be able to train vision models on multiple images for remote sensing analysis with one shot .
hope you like it ! 🚀
- 2 replies
Post
3505
🙋🏻♂️ Hey there folks ,
I'm sharing huggingface's largest dataset of annotated statelite images today.
check it out here : NuTonic/sat-image-boundingbox-sft-full
I hope you like it , the idea is to be able to use this with small vision models 🚀
I'm sharing huggingface's largest dataset of annotated statelite images today.
check it out here : NuTonic/sat-image-boundingbox-sft-full
I hope you like it , the idea is to be able to use this with small vision models 🚀
minwoosun
authored a
paper 29 days ago
MaziyarPanahi
posted an update about 1 month ago
Post
2210
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
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
Abhijnan
authored a
paper about 1 month ago
MaziyarPanahi
posted an update about 1 month ago
Post
2260
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
Everything is open-sourced: datasets, adapters, and code.
https://huggingface.co/blog/OpenMed/synthvision
- 2 replies
Post
6885
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.
Slight caveat: Trending actually does have some recency bias, but it's not strong/precise enough.
- 3 replies
MaziyarPanahi
posted an update 2 months ago
Post
4859
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! 🤗
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! 🤗
- 2 replies
albertvillanova
posted an update 2 months ago
Post
2563
🚀 TRL v0.29.0 introduces trl-training: an agent-native training skill.
This makes the TRL CLI a structured, agent-readable capability, allowing AI agents to reliably execute training workflows such as:
- Supervised Fine-Tuning (SFT)
- Direct Preference Optimization (DPO)
- Group Relative Policy Optimization (GRPO)
We’re excited to see what the community builds on top of this.
If you’re working on AI agents, alignment research, or scalable RL training infrastructure: give TRL v0.29.0 a try! 🤗
The future of ML tooling is agent-native.
🔗 https://github.com/huggingface/trl/releases/tag/v0.29.0
This makes the TRL CLI a structured, agent-readable capability, allowing AI agents to reliably execute training workflows such as:
- Supervised Fine-Tuning (SFT)
- Direct Preference Optimization (DPO)
- Group Relative Policy Optimization (GRPO)
We’re excited to see what the community builds on top of this.
If you’re working on AI agents, alignment research, or scalable RL training infrastructure: give TRL v0.29.0 a try! 🤗
The future of ML tooling is agent-native.
🔗 https://github.com/huggingface/trl/releases/tag/v0.29.0
Post
3697
🤔 Who would win ?
- a fully subsidized ai lab
- 3 random students named
kurakurai ?
demo : Tonic/fr-on-device
if you like it give the demo a little star and send a shoutout to : @MaxLSB @jddqd and @GAD-cell for absolutely obliterating the pareto frontier of the french language understanding .
- a fully subsidized ai lab
OR - 3 random students named
demo : Tonic/fr-on-device
if you like it give the demo a little star and send a shoutout to : @MaxLSB @jddqd and @GAD-cell for absolutely obliterating the pareto frontier of the french language understanding .
- 4 replies
MaziyarPanahi
authored a
paper 3 months ago
mariagrandury
authored 2
papers 3 months ago
Post
3420
🙋🏻♂️hello my lovelies ,
it is with great pleasure i present to you my working one-click deploy 16GB ram completely free huggingface spaces deployment.
repo : Tonic/hugging-claw (use git clone to inspect)
literally the one-click link : Tonic/hugging-claw
you can also run it locally and see for yourself :
docker run -it -p 7860:7860 --platform=linux/amd64 \
-e HF_TOKEN="YOUR_VALUE_HERE" \
-e OPENCLAW_GATEWAY_TRUSTED_PROXIES="YOUR_VALUE_HERE" \
-e OPENCLAW_GATEWAY_PASSWORD="YOUR_VALUE_HERE" \
-e OPENCLAW_CONTROL_UI_ALLOWED_ORIGINS="YOUR_VALUE_HERE" \
registry.hf.space/tonic-hugging-claw:latest
just a few quite minor details i'll take care of but i wanted to share here first
it is with great pleasure i present to you my working one-click deploy 16GB ram completely free huggingface spaces deployment.
repo : Tonic/hugging-claw (use git clone to inspect)
literally the one-click link : Tonic/hugging-claw
you can also run it locally and see for yourself :
docker run -it -p 7860:7860 --platform=linux/amd64 \
-e HF_TOKEN="YOUR_VALUE_HERE" \
-e OPENCLAW_GATEWAY_TRUSTED_PROXIES="YOUR_VALUE_HERE" \
-e OPENCLAW_GATEWAY_PASSWORD="YOUR_VALUE_HERE" \
-e OPENCLAW_CONTROL_UI_ALLOWED_ORIGINS="YOUR_VALUE_HERE" \
registry.hf.space/tonic-hugging-claw:latest
just a few quite minor details i'll take care of but i wanted to share here first
- 2 replies
albertvillanova
posted an update 3 months ago
Post
1902
5 years already working in democratizing AI 🤗
Grateful to be part of such an awesome team making it happen every day.
Grateful to be part of such an awesome team making it happen every day.
MaziyarPanahi
posted an update 3 months ago
Post
2421
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
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
- 1 reply
MaziyarPanahi
posted an update 3 months ago
Post
1334
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
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 3 months ago
Post
4087
🚨 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:
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
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
- 6 replies