Ayyuce Demirbas
@ayyuce.bsky.social
Machine Learning Engineer & Published Researcher, BSc in Computer Engineering | Aspiring PhD, GSoC @TensorFlow, Google Dev Expert in ML
I’ve implemented a multi-modal model that integrates histopathological images and gene expression profiles to classify breast cancer subtypes. The model leverages a Graph Mamba encoder for omics data and a Mamba-based image encoder built on a pretrained ConvNeXt model. github.com/ayyucedemirb...
November 12, 2025 at 5:08 PM
I’ve implemented a multi-modal model that integrates histopathological images and gene expression profiles to classify breast cancer subtypes. The model leverages a Graph Mamba encoder for omics data and a Mamba-based image encoder built on a pretrained ConvNeXt model. github.com/ayyucedemirb...
Saved my Linux kernel configuration for future use via
“cp .config kernel-6.6-$(date +%Y%m%d).config”
github.com/ayyucedemirb...
“cp .config kernel-6.6-$(date +%Y%m%d).config”
github.com/ayyucedemirb...
Compiling the Linux kernel, pretraining my image feature extractor using contrastive learning (on a remote GPU via AnyDesk), and working on my paper.
September 20, 2025 at 10:56 PM
Saved my Linux kernel configuration for future use via
“cp .config kernel-6.6-$(date +%Y%m%d).config”
github.com/ayyucedemirb...
“cp .config kernel-6.6-$(date +%Y%m%d).config”
github.com/ayyucedemirb...
Compiling the Linux kernel, pretraining my image feature extractor using contrastive learning (on a remote GPU via AnyDesk), and working on my paper.
September 20, 2025 at 10:01 PM
Compiling the Linux kernel, pretraining my image feature extractor using contrastive learning (on a remote GPU via AnyDesk), and working on my paper.
Happy Star Trek day! Live long and prosper. 🖖🏻 #StarTrek #StarTrekDay
September 8, 2025 at 5:40 PM
Happy Star Trek day! Live long and prosper. 🖖🏻 #StarTrek #StarTrekDay
Training a multimodal model for 200 epochs. This should be done in about a week. Wish me luck. 🤞🏻
September 1, 2025 at 9:13 PM
Training a multimodal model for 200 epochs. This should be done in about a week. Wish me luck. 🤞🏻
Instead of treating molecular features as nodes, I made patients the nodes. Now similar patients share information through graph connections, learning from each other's outcomes. Check out the implementation: github.com/ayyucedemirb...
August 28, 2025 at 6:44 PM
Instead of treating molecular features as nodes, I made patients the nodes. Now similar patients share information through graph connections, learning from each other's outcomes. Check out the implementation: github.com/ayyucedemirb...
I’ve implemented suffix arrays and suffix trees from scratch to find repeats, perform fast pattern matching, and generate the Burrows-Wheeler Transform. It also creates visualizations of the data structures. Check out the code on GitHub: github.com/ayyucedemirb...
August 27, 2025 at 11:03 PM
I’ve implemented suffix arrays and suffix trees from scratch to find repeats, perform fast pattern matching, and generate the Burrows-Wheeler Transform. It also creates visualizations of the data structures. Check out the code on GitHub: github.com/ayyucedemirb...
August 26, 2025 at 1:46 PM
August 26, 2025 at 1:42 PM
This is how you can create a longest common subsequence graph using dynamic programming.
github.com/ayyucedemirb...
github.com/ayyucedemirb...
August 24, 2025 at 10:03 PM
This is how you can create a longest common subsequence graph using dynamic programming.
github.com/ayyucedemirb...
github.com/ayyucedemirb...
A GNN project to classify BRCA patient survival using multi-omics data (RNA-seq, CNV, mutations, proteins).
github.com/ayyucedemirb...
github.com/ayyucedemirb...
August 8, 2025 at 3:17 PM
A GNN project to classify BRCA patient survival using multi-omics data (RNA-seq, CNV, mutations, proteins).
github.com/ayyucedemirb...
github.com/ayyucedemirb...
Now you can link your ORCID account to your GitHub account.
June 7, 2025 at 4:40 PM
Now you can link your ORCID account to your GitHub account.
Predicting cancer subtypes using multi-omics data with Graph Convolutional Networks. I know the results are not good enough but I’m working on it. 🧬
GitHub repo: github.com/ayyucedemirb...
GitHub repo: github.com/ayyucedemirb...
June 1, 2025 at 8:29 PM
Predicting cancer subtypes using multi-omics data with Graph Convolutional Networks. I know the results are not good enough but I’m working on it. 🧬
GitHub repo: github.com/ayyucedemirb...
GitHub repo: github.com/ayyucedemirb...
May 23, 2025 at 12:03 PM
If you are getting a warning that says, "A decoder-only architecture is being used, but right-padding was detected! For correct generation results, please set padding_side='left' when initializing the tokenizer." you should add this to your code: processor.tokenizer.padding_side = 'left'.
May 15, 2025 at 5:47 PM
If you are getting a warning that says, "A decoder-only architecture is being used, but right-padding was detected! For correct generation results, please set padding_side='left' when initializing the tokenizer." you should add this to your code: processor.tokenizer.padding_side = 'left'.
A long time ago in a galaxy far, far away…
May the 4th be with you. ✨⚔️
May the 4th be with you. ✨⚔️
May 3, 2025 at 10:07 PM
A long time ago in a galaxy far, far away…
May the 4th be with you. ✨⚔️
May the 4th be with you. ✨⚔️
Wow, that’s some amazing progress. An epoch takes an hour and the validation loss reduces by only 0.00022.
May 1, 2025 at 3:41 PM
Wow, that’s some amazing progress. An epoch takes an hour and the validation loss reduces by only 0.00022.
There has been a recurring issue with Kaggle notebooks for the past few days, the session freezes while training models. You don't even know which epoch this will happen in, and sometimes hours of training are lost because of this freeze.
April 30, 2025 at 12:51 PM
There has been a recurring issue with Kaggle notebooks for the past few days, the session freezes while training models. You don't even know which epoch this will happen in, and sometimes hours of training are lost because of this freeze.
This weekend, 📝I worked on my IEEE conference paper, 📚 wrote a blog post on Cache-Augmented Generation: ayyucedemirbas.github.io/posts/cag.ht..., and 👩🏻💻solved 9 LeetCode problems: leetcode.com/u/ayyuce.
🎶 Listened to Puccini's Tosca while working: open.spotify.com/album/1muIgA...
Productive weekend.😇
🎶 Listened to Puccini's Tosca while working: open.spotify.com/album/1muIgA...
Productive weekend.😇
Cache-Augmented Generation (CAG) | Ayyuce Demirbas
ayyucedemirbas.github.io
April 27, 2025 at 8:36 PM
This weekend, 📝I worked on my IEEE conference paper, 📚 wrote a blog post on Cache-Augmented Generation: ayyucedemirbas.github.io/posts/cag.ht..., and 👩🏻💻solved 9 LeetCode problems: leetcode.com/u/ayyuce.
🎶 Listened to Puccini's Tosca while working: open.spotify.com/album/1muIgA...
Productive weekend.😇
🎶 Listened to Puccini's Tosca while working: open.spotify.com/album/1muIgA...
Productive weekend.😇
Made a multimodal retrieval-augmented generation example handling images and text.
👩🏻💻 Code: github.com/ayyucedemirb...
🤗 Hugging Face Demo: huggingface.co/spaces/ayyuc...
👩🏻💻 Code: github.com/ayyucedemirb...
🤗 Hugging Face Demo: huggingface.co/spaces/ayyuc...
GitHub - ayyucedemirbas/RAG_techniques
Contribute to ayyucedemirbas/RAG_techniques development by creating an account on GitHub.
github.com
April 20, 2025 at 4:59 PM
Made a multimodal retrieval-augmented generation example handling images and text.
👩🏻💻 Code: github.com/ayyucedemirb...
🤗 Hugging Face Demo: huggingface.co/spaces/ayyuc...
👩🏻💻 Code: github.com/ayyucedemirb...
🤗 Hugging Face Demo: huggingface.co/spaces/ayyuc...
I’m trying to fine-tune the blip-vqa-base model that consists of 385M parameters on my visual instruction tuning dataset named vqa-rad-instructions. Since the dataset contains only 1793 samples for training, I’m using k-fold to prevent overfitting.
April 12, 2025 at 12:59 PM
I’m trying to fine-tune the blip-vqa-base model that consists of 385M parameters on my visual instruction tuning dataset named vqa-rad-instructions. Since the dataset contains only 1793 samples for training, I’m using k-fold to prevent overfitting.
April 11, 2025 at 11:00 PM
You can use these commands to list the sizes of all your conda environments:
for env in $(conda env list | awk '{print $1}' | grep -v "#"); do echo $env; du -sh $(conda env list | grep "$env" | awk '{print $NF}'); done
conda env list | grep -o '/.*' | while read env; do du -sh "$env"; done
for env in $(conda env list | awk '{print $1}' | grep -v "#"); do echo $env; du -sh $(conda env list | grep "$env" | awk '{print $NF}'); done
conda env list | grep -o '/.*' | while read env; do du -sh "$env"; done
April 7, 2025 at 6:38 PM
You can use these commands to list the sizes of all your conda environments:
for env in $(conda env list | awk '{print $1}' | grep -v "#"); do echo $env; du -sh $(conda env list | grep "$env" | awk '{print $NF}'); done
conda env list | grep -o '/.*' | while read env; do du -sh "$env"; done
for env in $(conda env list | awk '{print $1}' | grep -v "#"); do echo $env; du -sh $(conda env list | grep "$env" | awk '{print $NF}'); done
conda env list | grep -o '/.*' | while read env; do du -sh "$env"; done
Now you can visualize folder structures with:
- JSON/TXT exports (--output) for automation
- Custom truncation (--truncate N) to control file listings
Try it:
pip install --upgrade PeekDir
PeekDir your_folder --output structure.json --format json --truncate 8
- JSON/TXT exports (--output) for automation
- Custom truncation (--truncate N) to control file listings
Try it:
pip install --upgrade PeekDir
PeekDir your_folder --output structure.json --format json --truncate 8
April 7, 2025 at 2:29 PM
Now you can visualize folder structures with:
- JSON/TXT exports (--output) for automation
- Custom truncation (--truncate N) to control file listings
Try it:
pip install --upgrade PeekDir
PeekDir your_folder --output structure.json --format json --truncate 8
- JSON/TXT exports (--output) for automation
- Custom truncation (--truncate N) to control file listings
Try it:
pip install --upgrade PeekDir
PeekDir your_folder --output structure.json --format json --truncate 8
To print your computer’s memory size you can use these:
On a Linux distro: grep MemTotal /proc/meminfo | awk '{print $2 / 1024 / 1024 " GB"}'
On macOS: sysctl hw.memsize | awk '{printf "%.2f GB\n", $2 / (1024*1024*1024)}'
On a Linux distro: grep MemTotal /proc/meminfo | awk '{print $2 / 1024 / 1024 " GB"}'
On macOS: sysctl hw.memsize | awk '{printf "%.2f GB\n", $2 / (1024*1024*1024)}'
April 6, 2025 at 12:48 PM
To print your computer’s memory size you can use these:
On a Linux distro: grep MemTotal /proc/meminfo | awk '{print $2 / 1024 / 1024 " GB"}'
On macOS: sysctl hw.memsize | awk '{printf "%.2f GB\n", $2 / (1024*1024*1024)}'
On a Linux distro: grep MemTotal /proc/meminfo | awk '{print $2 / 1024 / 1024 " GB"}'
On macOS: sysctl hw.memsize | awk '{printf "%.2f GB\n", $2 / (1024*1024*1024)}'