Skip to the page
A. Flores Sepúlveda
Research notebook · Page 1Bern · 2026

Alejandro Flores Sepúlveda1,2,3

  • 1Reymond group, University of Bern. PhD candidate, 2024–2028; currently on generative methods.
  • 2SPAR. Research fellow in AI safety, Fall 2026; escalation detection in AI agents.
  • 3Mafer.ai. Software Engineer from October 2026; building the chemical AI tech stack.

AbstractI work on machine learning for drug discovery and on AI safety, and I build things at hackathons when I get the chance. My PhD started with maps of very large chemical libraries and has since moved on to generative methods. Below are my projects, papers and some longer notes.

Keywords:

1Now

  • from Oct 2026Software Engineer at Mafer.aiBuilding the chemical AI tech stack.
  • Fall 2026SPAR research fellow, AI safetyEscalation detection in AI agents.
  • 2024–2028PhD candidate, Reymond group, University of BernCurrently working on generative methods.

2WorkProjects and research, newest threads first.

  • Escalation detection

    Can turn-averaged sparse autoencoders tell when an AI agent starts taking more extreme measures to get past an obstacle, and when it should pause and hand the problem to a human?

    AI safetySPAR · Fall 2026
    in progress
  • Generative methods

    Current PhD work in the Reymond group.

    Drug discoveryPhD · 2024–2028
    in progress
  • Chelombus

    A searchable map of 9.6 billion drug-like molecules from Enamine REAL. Runs end to end in about 4.5 hours on one desktop GPU; it used to take about 14 days.

    Drug discoveryJ. Chem. Inf. Model. 2026
    chelombus.gdb.tools
    180k+ maps served
  • TMAP 2.0

    A rewrite of the TMAP layout library in Numba, about 3× faster. Maps for datasets too large to read as tables.

    Drug discoveryChemRxiv preprint 2026
  • SmilesDrawer

    Turns SMILES strings into molecule drawings in the browser. Ring perception is now rebuilt on Vismara’s algorithm.

    Drug discovery~26k npm downloads a week
  • Rosario AI

    An AI voice receptionist for medical clinics. It answers every call, checks the clinic’s real calendar and books, moves or cancels appointments, in a dozen languages. Built in 48 hours at HackSpain; we were one of 5 teams, out of ~60, selected for the final.

    Buildingrosario.fyi
    HackSpain · Sep 2026
    grand finalist
  • REFUGIO

    A hackathon project, with a postmortem built from interactive widgets.

    Buildingpostmortem · Jul 2026

3WritingInteractive notes, newest first.

  • REFUGIO postmortem

    What worked, what broke, and what I took away from a hackathon project.

4Papers

  1. Alejandro Flores Sepúlveda, Maarten Boneschansker, Jean-Louis Reymond, Daniel Probst. From Proteins and Molecules to Cats and Dogs: Visualization as Scalable Minimum Spanning Trees. ChemRxiv 2026.doi:10.26434/chemrxiv.15008307/v2 ↗
  2. Alejandro Flores Sepúlveda, Jean-Louis Reymond. Nested TMAPs to Visualize Billions of Molecules. J. Chem. Inf. Model. 2026, 66, 5595–5601.doi:10.1021/acs.jcim.6c00420 ↗
  3. Aline Carrel, Alejandro Flores, Maedeh Darsaraee, Jean-Louis Reymond. Spirocyclic Diamine Scaffolds for Medicinal Chemistry. Helv. Chim. Acta 2025.doi:10.1002/hlca.202500207 ↗
  4. Luis Apaza Ticona, Javier Sánchez Sánchez-Corral, Alejandro Flores Sepúlveda, Carmen Soriano Vázquez, Carmen Hernán Vieco, Ángel Rumbero Sánchez. Novel 1,2,4-oxadiazole compounds as PPAR-α ligand agonists: a new strategy for the design of antitumour compounds. RSC Med. Chem. 2023, 14, 1377–1388.doi:10.1039/D3MD00063J ↗

5Mini-gamesFor staying a while. The other one is behind the Room 6 door, sound on.

Score 0Best 0Rings 0
Chain CCC
Game 1. SMILES Snake. Eat atoms to grow a chain, and bite your own body to close a ring. On a square grid every loop has an even number of atoms, so rings come in fours, sixes and eights; six is the most stable. Click the figure, then steer with the arrow keys or WASD. P pauses.
Ring catalogue 0 of 26 found

Every named ring you close stays here, on this device. Unfound rings show only their size and heteroatoms.

    6Contact

    Write to afloresep01@gmail.com
    GitHubX @afloresepLinkedInAbout / CV