Dionysis Arvanitakis

Dionysis Arvanitakis, Vaggos Chatziafratis, Yiyuan Luo et al.

Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph theory and biology. Given a random sample containing $m$ noisy quartets, labeled by an unknown ground-truth tree $T$ on $n$ taxa, we want to output a tree $\widehat T$ that is \textit{close} to $T$ in terms of quartet distance and can predict unseen quartets. Unfortunately, the empirical risk minimizer corresponds to the $\mathsf{NP}$-hard problem of finding a tree that maximizes agreements with the sampled quartets, and earlier works in approximation algorithms gave $(1-\eps)$-approximation schemes (PTAS) for dense instances with $m=Θ(n^4)$ quartets, or for $m=Θ(n^2\log n)$ quartets \textit{randomly} sampled from $T$. Prior to our work, it was unknown how many samples are information-theoretically required to learn the tree, and whether there is an efficient reconstruction algorithm. We present optimal results for reconstructing an unknown phylogenetic tree $T$ from a random sample of $m=Θ(n)$ quartets, corrupted under the Random Classification Noise (RCN) model. This matches the $Ω(n)$ lower bound required for any meaningful tree reconstruction. Our contribution is twofold: first, we give a tree reconstruction algorithm that, not only achieves a $(1-\eps)$-approximation, but most importantly \textit{recovers} a tree close to $T$ in quartet distance; second, we show a new $Θ(n)$ bound on the Natarajan dimension of phylogenies (an analog of VC dimension in multiclass classification). Our analysis relies on a new \textit{Quartet-based Embedding and Detection} procedure that identifies and removes well-clustered subtrees from the (unknown) ground-truth $T$ via semidefinite programming.

Dionysis Arvanitakis, Vaggos Chatziafratis, Yiyuan Luo

Embedding-based representations in Euclidean space $\mathbb{R}^d$ are a cornerstone of modern machine learning, where a major goal is to use the \emph{smallest dimension} that faithfully captures data relations. In this work, we prove sharp dimension--accuracy tradeoffs and identify a fundamental information-theoretic limitation: unless the embedding dimension $d$ is chosen close to the ground-truth dimension $D$, accuracy undergoes a sudden collapse. Our main result shows that this phenomenon arises even in standard contrastive learning settings, where supervision is limited to a set of $m$ anchor--positive--negative triplets $(i,j,k)$ encoding distance comparisons $\mathrm{dist}(i,j) < \mathrm{dist}(i,k)$. Specifically, given triplets realizable by an unknown ground-truth embedding in $D$ dimensions, we prove that there exists constant $c < 1$, such that \emph{every embedding of dimension at most $cD$ violates half of the triplets}, yielding accuracy as low as a trivial one-dimensional solution that ignores the input. We complement our information-theoretic bounds with strong computational hardness results: under the Unique Games Conjecture, even if the given triplets are nearly realizable in $D=1$ dimension, no polynomial-time algorithm -- \textit{regardless of its dimension} -- can achieve accuracy above the trivial $50\%$ baseline.