Philippe Chlenski

Philippe Chlenski, Ethan Turok, Antonio Moretti et al.

Hyperbolic geometry is gaining traction in machine learning for its effectiveness at capturing hierarchical structures in real-world data. Hyperbolic spaces, where neighborhoods grow exponentially, offer substantial advantages and consistently deliver state-of-the-art results across diverse applications. However, hyperbolic classifiers often grapple with computational challenges. Methods reliant on Riemannian optimization frequently exhibit sluggishness, stemming from the increased computational demands of operations on Riemannian manifolds. In response to these challenges, we present hyperDT, a novel extension of decision tree algorithms into hyperbolic space. Crucially, hyperDT eliminates the need for computationally intensive Riemannian optimization, numerically unstable exponential and logarithmic maps, or pairwise comparisons between points by leveraging inner products to adapt Euclidean decision tree algorithms to hyperbolic space. Our approach is conceptually straightforward and maintains constant-time decision complexity while mitigating the scalability issues inherent in high-dimensional Euclidean spaces. Building upon hyperDT we introduce hyperRF, a hyperbolic random forest model. Extensive benchmarking across diverse datasets underscores the superior performance of these models, providing a swift, precise, accurate, and user-friendly toolkit for hyperbolic data analysis.

Philippe Chlenski, Kaizhu Du, Dylan Satow et al.

We present Manify, an open-source Python library for non-Euclidean representation learning. Leveraging manifold learning techniques, Manify provides tools for learning embeddings in (products of) non-Euclidean spaces, performing classification and regression with data that lives in such spaces, estimating the curvature of a manifold, and more. Manify aims to advance research and applications in machine learning by offering a comprehensive suite of tools for manifold-based data analysis. Our source code, examples, and documentation are available at https://github.com/pchlenski/manify.

Raiyan R. Khan, Philippe Chlenski, Itsik Pe'er

Current approaches to genomic sequence modeling often struggle to align the inductive biases of machine learning models with the evolutionarily-informed structure of biological systems. To this end, we formulate a novel application of hyperbolic CNNs that exploits this structure, enabling more expressive DNA sequence representations. Our strategy circumvents the need for explicit phylogenetic mapping while discerning key properties of sequences pertaining to core functional and regulatory behavior. Across 37 out of 42 genome interpretation benchmark datasets, our hyperbolic models outperform their Euclidean equivalents. Notably, our approach even surpasses state-of-the-art performance on seven GUE benchmark datasets, consistently outperforming many DNA language models while using orders of magnitude fewer parameters and avoiding pretraining. Our results include a novel set of benchmark datasets--the Transposable Elements Benchmark--which explores a major but understudied component of the genome with deep evolutionary significance. We further motivate our work by exploring how our hyperbolic models recognize genomic signal under various data-generating conditions and by constructing an empirical method for interpreting the hyperbolicity of dataset embeddings. Throughout these assessments, we find persistent evidence highlighting the potential of our hyperbolic framework as a robust paradigm for genome representation learning. Our code and benchmark datasets are available at https://github.com/rrkhan/HGE.

Philippe Chlenski, Itsik Pe'er

Decision trees and models that use them as primitives are workhorses of machine learning in Euclidean spaces. Recent work has further extended these models to the Lorentz model of hyperbolic space by replacing axis-parallel hyperplanes with homogeneous hyperplanes when partitioning the input space. In this paper, we show how the hyperDT algorithm can be elegantly reexpressed in the Beltrami-Klein model of hyperbolic spaces. This preserves the thresholding operation used in Euclidean decision trees, enabling us to further rewrite hyperDT as simple pre- and post-processing steps that form a wrapper around existing tree-based models designed for Euclidean spaces. The wrapper approach unlocks many optimizations already available in Euclidean space models, improving flexibility, speed, and accuracy while offering a simpler, more maintainable, and extensible codebase. Our implementation is available at https://github.com/pchlenski/hyperdt.

Jacob Dunefsky, Philippe Chlenski, Neel Nanda

A key goal in mechanistic interpretability is circuit analysis: finding sparse subgraphs of models corresponding to specific behaviors or capabilities. However, MLP sublayers make fine-grained circuit analysis on transformer-based language models difficult. In particular, interpretable features -- such as those found by sparse autoencoders (SAEs) -- are typically linear combinations of extremely many neurons, each with its own nonlinearity to account for. Circuit analysis in this setting thus either yields intractably large circuits or fails to disentangle local and global behavior. To address this we explore transcoders, which seek to faithfully approximate a densely activating MLP layer with a wider, sparsely-activating MLP layer. We introduce a novel method for using transcoders to perform weights-based circuit analysis through MLP sublayers. The resulting circuits neatly factorize into input-dependent and input-invariant terms. We then successfully train transcoders on language models with 120M, 410M, and 1.4B parameters, and find them to perform at least on par with SAEs in terms of sparsity, faithfulness, and human-interpretability. Finally, we apply transcoders to reverse-engineer unknown circuits in the model, and we obtain novel insights regarding the "greater-than circuit" in GPT2-small. Our results suggest that transcoders can prove effective in decomposing model computations involving MLPs into interpretable circuits. Code is available at https://github.com/jacobdunefsky/transcoder_circuits/.

Philippe Chlenski, Quentin Chu, Itsik Pe'er

We extend decision tree and random forest algorithms to product space manifolds: Cartesian products of Euclidean, hyperspherical, and hyperbolic manifolds. Such spaces have extremely expressive geometries capable of representing many arrangements of distances with low metric distortion. To date, all classifiers for product spaces fit a single linear decision boundary, and no regressor has been described. Our method enables a simple, expressive method for classification and regression in product manifolds. We demonstrate the superior accuracy of our tool compared to Euclidean methods operating in the ambient space or the tangent plane of the manifold across a range of constant-curvature and product manifolds. Code for our implementation and experiments is available at https://github.com/pchlenski/embedders.

Arghamitra Talukder, Philippe Chlenski, Itsik Pe'er

Learned representations are often invariant to rotational transformations, leaving individual dimensions non-identifiable and interchangeable. We study how Matryoshka Representation Learning (MRL) induces a task-aligned privileged basis distinct from variance-based or regularizer-induced orderings. In the linear setting, we prove that full-prefix MRL recovers the ordered principal directions, and can be computed efficiently using shared statistics. Empirically, we demonstrate that MRL yields consistent per-dimension structure aligned with task signal, where coordinate magnitude reflects informativeness.

Hanming Yang, Antonio Khalil Moretti, Sebastian Macaluso et al.

Reconstructing jets, which provide vital insights into the properties and histories of subatomic particles produced in high-energy collisions, is a main problem in data analyses in collider physics. This intricate task deals with estimating the latent structure of a jet (binary tree) and involves parameters such as particle energy, momentum, and types. While Bayesian methods offer a natural approach for handling uncertainty and leveraging prior knowledge, they face significant challenges due to the super-exponential growth of potential jet topologies as the number of observed particles increases. To address this, we introduce a Combinatorial Sequential Monte Carlo approach for inferring jet latent structures. As a second contribution, we leverage the resulting estimator to develop a variational inference algorithm for parameter learning. Building on this, we introduce a variational family using a pseudo-marginal framework for a fully Bayesian treatment of all variables, unifying the generative model with the inference process. We illustrate our method's effectiveness through experiments using data generated with a collider physics generative model, highlighting superior speed and accuracy across a range of tasks.