| Date | Title | Categories | Description |
|---|---|---|---|
| Jul 20, 2026 | Closed-form flow matching: posterior concentration and softmax collapse | deep learning, flow matching | The closed-form velocity field of empirical flow matching is a softmax over training examples. Reading that softmax as a Bayesian posterior turns its collapse into a decoding problem, with an information-theoretic threshold that can be evaluated on CIFAR-10. |
| May 12, 2026 | Flow matching as posterior averaging | deep learning, flow matching | A velocity-based introduction to flow matching with Gaussian probability paths: the marginal velocity field is a posterior average of conditional targets, and the gap between the conditional and marginal losses is an irreducible posterior-variance term that can be computed in closed form. |
| Jan 18, 2026 | Analyzing Raman spectra with machine learning | machine learning, chemistry | From inelastic scattering to a calibrated regression model: the physics behind a Raman spectrum, the preprocessing pipeline that makes real spectra usable, and a PLS regression baseline for predicting analyte concentrations. |
| Aug 15, 2025 | Generating slide decks with an LLM: a comparison of formats | LLM | One real presentation, four formats, one model: what Gemini 2.5 Pro actually produces when asked to rebuild an EDF producer booklet in HTML/CSS, Quarto/Reveal.js, the Google Slides API, and python-pptx — and why the failures in the API-driven formats are silent ones. |
| Jun 30, 2025 | LLM observability with Langfuse and a FastHTML chatbot | LLM, python | Instrumenting a chatbot end to end: Langfuse traces a conversation as a span, each model turn as a generation, and each thumbs-up as a score — wired into a FastHTML app that updates over a WebSocket instead of rerunning a script. |
| Mar 20, 2025 | PDF RAG: recovering document structure and querying a corpus | deep learning, LLM, RAG | Page-by-page parsing destroys the structure a reader relies on. This post rebuilds it for PDFs with a vision language model, extracts metadata and a document tree, and then queries a corpus of reports and slide decks with a two-level ReAct agent. |
| Feb 18, 2025 | Parsing PDFs for LLM input | deep learning, LLM | How Docling, Marker, MinerU, pymupdf4llm, LlamaParse, Gemini, and Mistral OCR turn PDFs into Markdown: what the pipelines are made of, and where each one silently gets it wrong on six real documents. |
| Feb 6, 2025 | Predicting MHC-peptide presentation with machine learning | deep learning, biology | Training a neural network to predict which peptides a given MHC class I allele presents, and benchmarking it against MHCflurry. |
| Apr 24, 2024 | Encoding distances in molecules and pockets: GBFPT versus DCEPT | deep learning, biology | Uni-Mol encodes interatomic distances with a Gaussian basis whose parameters receive very large gradients. Replacing it with a discretized categorical embedding, in the spirit of AlphaFold, stabilizes pretraining but degrades the pocket embeddings used for retrieval. |
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