Past, ongoing, and future research plans

Some not-up-to-date lists of ongoing work to keep things organized for myself.

Dormant Link to heading

• Minimizers:
  • publish the anti-lex scheme (→ WABI 26?)
  • continue investigation of greedymini to develop ‘understandable’ equivalent schemes.
  • Find exact optimal schemes for all \(k\equiv 1\pmod w\)
  • lower bound for local schemes

Long term plans Link to heading

If anything here interests you, feel free to reach out for collaborations.

• engineer STPD (Becker et al. 2025): write a highly optimized implementation.
  • minimizer space?
  • fuzzy version by only using minimizer start positions?
• Optimal CPU/memory performance given 3D latency and cooling constraints.
• Pairwise alignment review paper based on thesis chapter 2 (this post).
  • Review on approximate string matching, this post (will never happen).
• Minimizers review paper based on thesis part 2 (this post).

Abandoned Link to heading

• Affine A*PA2: too much of an overhaul.
• Spaced $k$-mer similarity: see this post.
• Expected linear time A*PA: see a draft in this post.
• Linear memory WFA: Instead of storing furthest reaching points for all wavefronts, it is sufficient to only store critical points where paths split/merge. This should lower memory usage of WFA to close to linear, without needing BiWFA. See this post. This has similar vibes to TALCO (Walia et al. 2024).
• Local doubling: see this post.

References Link to heading