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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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About Me
About Me
Posts
How to limit the number of Twitter posts in your timeline using JavaScript BLOG
Published:
I have a bit of a problem scrolling too much of the awesome content on Twitter. There are just too many other people creating cool ideas and software! At first I justified it by the fact that I find academic papers (my feed is curated to mostly academic CS/ML/SE), but now I admit it’s too much! In a bid to waste more time in order to waste less time, I created a simple script that puts an extra UI onto each post in my Twitter feed:
- For the first five posts, it numbers them to remind me how many I’ve browsed.
- After that, it blocks them out with a reminder of the limit I set (currently I keep it at five posts).
How to set up a shared cache for HuggingFace libraries BLOG
Published:
TL;DR
I set up a shared cache for HuggingFace libraries like transformers and datasets. See the repository: https://github.com/bstee615/shared-hf-cache. To use it, create a shared directory which can be edited by all interested users and set the environment variable export HF_HOME="/huggingface".
How to fix docker-compose: command not found error with newer versions of Docker BLOG
Published:
The docker-compose command is missing from recent versions of Docker, replaced by a plugin built into Docker: docker compose. To restore compatibility with scripts which use docker-compose, we can create a wrapper script which forwards its arguments to docker compose. Here’s the script:
# Switch to root
sudo su -
# Write script to file
cat << EOF > /usr/local/bin/docker-compose
#!/bin/bash
docker compose $@
EOF
# Make the script executable so that we can invoke it directly from the shell
chmod +x /usr/local/bin/docker-compose
How to use task-spooler as a shared queueing system BLOG
Published:
TL;DR
I set up a wrapper around task-spooler. See the repository: https://github.com/bstee615/shared-task-spooler. To use it, create a file containing the below script and invoke it using the same arguments as task-spooler.
#!/bin/bash
# Dependency: sudo apt install -y task-spooler
TS_SOCKET=$(dirname -- "$0")/TS_SOCKET exec tsp -L "$USER" $@
Siamese network and triplet loss
Published:
Siamese network is an architecture which runs two networks with shared weights (effectively runs the same network twice) on two different inputs simultaneously. It is commonly trained with a contrastive loss such as triplet loss in order to draw together the representations of similar inputs and push apart the representations of contrasting inputs.
Get filepath of Bash activation script
Published:
Use ${BASH_SOURCE[0]} to reference the filepath of a Bash script. Unlike $0, this works if the script is called via bash script.sh or source script.sh.
webcam-mods for Linux background blur & swap
Published:
webcam-mods is the best method I have found for webcam background blur/swap on Linux. I use this for my meetings on Google Meet and Webex.
Beware any vs len
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I fell into the habit of using any() to check if a list is empty. It’s nice because it works for any enumerable, including generators, even if len() is not defined. However, it has a pitfall where if the list is nonempty but contains only falsy values, any() returns False. For this reason, I advise to use len() to check if a list is empty.
Use head -n -0 to get all items in list
Published:
You may know that you can use head -n $n to get the first N lines of a list. But you may not know that you can supply n=-0 to get all items in the list.
Use hard links to replicate log files in a generated directory
Published:
Recently I wanted to write program logs to a file, then copy it to the directory where I store my checkpoints. Because I want to log things before I create the checkpoint directory, I attached my logger to a file in my root directory.
Beware metric auto-reduce with PyTorch Lightning + TorchMetrics
Published:
PyTorch Lightning + TorchMetrics can log metrics per step and per epoch. It also has MetricCollection, which can be used to compute several metrics at once, getting rid of redundant code. Here is how I have it set up:
Print pandas Series as percent
Published:
Use this snippet to print a pd.Series of floats as percentages.
.apply(lambda x: x * 100).apply("{:,.2f}%".format)
Encoder-decoder models
Published:
Encoder decoder is a deep neural network architecture that consists of 2 components:
- Encoder: input -> encoder memory (real-valued vector),
- Decoder: encoder memory -> output. Input is variable length, encoder memory is fixed length.
Print item keys with jq
Published:
I can use jq to print the keys in an array of JSON objects quickly.
jq '.[0] | keys[]' $filename
Neural Network Embeddings
Published:
Embeddings are used to map high-dimensional data to low-dimensional floating-point representation. This may improve the performance because it improves the representation of the input given to the model.
Meditations on Meditations: I-IV BLOG
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I’m reading Marcus Aurelius’s Meditations in Marcus Aurelius and His Times (Transition from Paganism to Christianity) [0].
Programming problem: Gematria BLOG
Published:
I’ve recently been studying history in the Bible by following along with the phenomenal podcast of the same name, History in the Bible by Garry Stevens. As part of his series, I learned about gematria, which is the ancient practice of assigning a number to a name based on the letters in the name.
No pain no gain? Comparing 3 program analysis frameworks for C BLOG
Published:
Program analysis methods often represent programs as graphs. These graphs should be automatically generated from the source code. There are many tools that have been implemented to do this, but they are often painful to set up. In this post, I will compare 3 program analysis frameworks which I have used to generate graph representations of C programs.
publications
Validating static warnings via testing code fragments PAPER
Published in ISSTA, 2021
In this paper, we present a novel solution that automatically generates test cases based on static warnings to validate true and false positives.
Recommended citation: Ashwin Kallingal Joshy, Xueyuan Chen, Benjamin Steenhoek, and Wei Le. 2021. Validating static warnings via testing code fragments. In Proceedings of the 30th ACM SIGSOFT International Symposium on Software Testing and Analysis (ISSTA 2021). Association for Computing Machinery, New York, NY, USA, 540–552. https://doi.org/10.1145/3460319.3464832
Refactoring programs to improve the performance of deep learning for vulnerability detection THESIS
Published in Iowa State University, ProQuest Dissertations & Theses Global, 2021
This paper is about refactoring programs as a method of data augmentation.
Recommended citation: Steenhoek, Benjamin. (2021). Refactoring programs to improve the performance of deep learning for vulnerability detection (Order No. 28648161). Available from Dissertations & Theses @ Iowa State University; ProQuest Dissertations & Theses Global. (2625295478). https://www.proquest.com/dissertations-theses/refactoring-programs-improve-performance-deep/docview/2625295478/se-2?accountid=10906
Refactoring programs to improve the performance of deep learning for vulnerability detection POSTER
Published in Iowa State University 6th Annual Research Day, 2022
This poster is about refactoring programs as a method of data augmentation.
Recommended citation: Steenhoek, Benjamin. (2022). Refactoring programs to improve the performance of deep learning for vulnerability detection (Poster). Presented at: Iowa State University 6th Annual Research Day. https://benjijang.com/files/2022-04-01-poster.pdf
An Empirical Study of Open-Source Development Practices for Safety Certified Software COURSE PROJECT
Published in Iowa State University, COM S 515 Final Project, 2022
This paper extends a dataset of open-source safety-critical software with details about the project’s development practices and safety goals.
Recommended citation: Steenhoek, Benjamin. (2022). An Empirical Study of Open-Source Development Practices for Safety Certified Software (Final Project). Iowa State University COM S 515. https://benjijang.com/files/2022-04-26-coms515-opensource.pdf
A Study of Static Warning Cascading Tools (Experience Paper) PREPRINT
Published in ArXiv, 2023
In this paper, we report the challenges of cascading warnings generated from two versions of programs. We investigated program differencing tools and extend them to perform warning cascading automatically.
Recommended citation: Guo, X., Joshy, A. K., Steenhoek, B., Le, W., & Flynn, L. (2023). A Study of Static Warning Cascading Tools (Experience Paper). ArXiv. https://doi.org/10.48550/arXiv.2305.02515
An Empirical Study of Deep Learning Models for Vulnerability Detection PAPER
Published in ICSE, 2023
In this paper, we surveyed and reproduced 9 state-of-the-art (SOTA) deep learning models on 2 widely used vulnerability detection datasets: Devign and MSR.
Recommended citation: Benjamin Steenhoek, Md Mahbubur Rahman, Richard Jiles, and Wei Le. 2023. An Empirical Study of Deep Learning Models for Vulnerability Detection. In Proceedings of the 45th International Conference on Software Engineering (ICSE 2023). Association for Computing Machinery, New York, NY, USA. https://doi.org/10.48550/arXiv.2212.08109
Reinforcement Learning from Automatic Feedback for High-Quality Unit Test Generation PAPER
Published in ArXiv, 2023
We propose a novel technique called Reinforcement Learning from Static Quality Metrics (RLSQM).
Recommended citation: Benjamin Steenhoek, Michele Tufano, Neel Sundaresan, and Alexey Svyatkovskiy. (2023). Reinforcement Learning from Automatic Feedback for High-Quality Unit Test Generation. ArXiv. https://arxiv.org/abs/2310.02368
Do Language Models Learn Semantics of Code? A Case Study in Vulnerability Detection PAPER
Published in ArXiv, 2023
In this paper, we analyze language models to investigate whether the models have learned the semantics of code relevant to vulnerability detection, namely bug semantics, and if so, how the alignment to bug semantics relates to model performance.
Recommended citation: Benjamin Steenhoek, Md Mahbubur Rahman, Shaila Sharmin, & Wei Le. (2023). Do Language Models Learn Semantics of Code? A Case Study in Vulnerability Detection. ArXiv. https://arxiv.org/abs/2311.04109
A Comprehensive Study of the Capabilities of Large Language Models for Vulnerability Detection PAPER
Published in ArXiv, 2024
We evaluated the vulnerability detection capabilities of SOTA LLMs. We systematically searched for the best-performing prompts and analyzed their reasoning.
Recommended citation: Benjamin Steenhoek, Md Mahbubur Rahman, Monoshi Kumar Roy, Mirza Sanjida Alam, Earl T Barr, and Wei Le. 2024. A Comprehensive Study of the Capabilities of Large Language Models for Vulnerability Detection. ArXiv. https://arxiv.org/pdf/2403.17218
TRACED: Execution-aware Pre-training for Source Code PAPER
Published in ICSE, 2024
We introduce TRACED, an execution-aware pre-training strategy for source code wherein we pre-train code language models with a combination of source code, executable inputs, and corresponding execution traces.
Recommended citation: Yangruibo Ding, Benjamin Steenhoek, Kexin Pei, Gail Kaiser, Wei Le, and Baishakhi Ray. 2024. TRACED: Execution-aware Pre-training for Source Code. In 2024 IEEE/ACM 46th International Conference on Software Engineering (ICSE ’24), April 14–20, 2024, Lisbon, Portugal. ACM, New York, NY, USA, 12 pages. https://doi.org/10.48550/arXiv.2306.07487
Dataflow Analysis-Inspired Deep Learning for Efficient Vulnerability Detection PAPER
Published in ICSE, 2024
We present DeepDFA, a dataflow analysis-inspired graph learning framework and an embedding technique that enables graph learning to simulate dataflow computation.
Recommended citation: Benjamin Steenhoek, Hongyang Gao, and Wei Le. 2024. Dataflow Analysis-Inspired Deep Learning for Efficient Vulnerability Detection. In 2024 IEEE/ACM 46th International Conference on Software Engineering (ICSE ’24), April 14–20, 2024, Lisbon, Portugal. ACM, New York, NY, USA, 13 pages. https://doi.org/10.48550/arXiv.2212.08108