Ilan Shomorony

Mo Tiwari, Ryan Kang, Je-Yong Lee et al. · harvard

Random forests are some of the most widely used machine learning models today, especially in domains that necessitate interpretability. We present an algorithm that accelerates the training of random forests and other popular tree-based learning methods. At the core of our algorithm is a novel node-splitting subroutine, dubbed MABSplit, used to efficiently find split points when constructing decision trees. Our algorithm borrows techniques from the multi-armed bandit literature to judiciously determine how to allocate samples and computational power across candidate split points. We provide theoretical guarantees that MABSplit improves the sample complexity of each node split from linear to logarithmic in the number of data points. In some settings, MABSplit leads to 100x faster training (an 99% reduction in training time) without any decrease in generalization performance. We demonstrate similar speedups when MABSplit is used across a variety of forest-based variants, such as Extremely Random Forests and Random Patches. We also show our algorithm can be used in both classification and regression tasks. Finally, we show that MABSplit outperforms existing methods in generalization performance and feature importance calculations under a fixed computational budget. All of our experimental results are reproducible via a one-line script at https://github.com/ThrunGroup/FastForest.

Mo Tiwari, Ryan Kang, Je-Yong Lee et al. · harvard

Maximum Inner Product Search (MIPS) is a ubiquitous task in machine learning applications such as recommendation systems. Given a query vector and $n$ atom vectors in $d$-dimensional space, the goal of MIPS is to find the atom that has the highest inner product with the query vector. Existing MIPS algorithms scale at least as $O(\sqrt{d})$, which becomes computationally prohibitive in high-dimensional settings. In this work, we present BanditMIPS, a novel randomized MIPS algorithm whose complexity is independent of $d$. BanditMIPS estimates the inner product for each atom by subsampling coordinates and adaptively evaluates more coordinates for more promising atoms. The specific adaptive sampling strategy is motivated by multi-armed bandits. We provide theoretical guarantees that BanditMIPS returns the correct answer with high probability, while improving the complexity in $d$ from $O(\sqrt{d})$ to $O(1)$. We also perform experiments on four synthetic and real-world datasets and demonstrate that BanditMIPS outperforms prior state-of-the-art algorithms. For example, in the Movie Lens dataset ($n$=4,000, $d$=6,000), BanditMIPS is 20$\times$ faster than the next best algorithm while returning the same answer. BanditMIPS requires no preprocessing of the data and includes a hyperparameter that practitioners may use to trade off accuracy and runtime. We also propose a variant of our algorithm, named BanditMIPS-$α$, which achieves further speedups by employing non-uniform sampling across coordinates. Finally, we demonstrate how known preprocessing techniques can be used to further accelerate BanditMIPS, and discuss applications to Matching Pursuit and Fourier analysis.

Mo Tiwari, Ryan Kang, Donghyun Lee et al.

Clustering is a fundamental task in data science with wide-ranging applications. In $k$-medoids clustering, cluster centers must be actual datapoints and arbitrary distance metrics may be used; these features allow for greater interpretability of the cluster centers and the clustering of exotic objects in $k$-medoids clustering, respectively. $k$-medoids clustering has recently grown in popularity due to the discovery of more efficient $k$-medoids algorithms. In particular, recent research has proposed BanditPAM, a randomized $k$-medoids algorithm with state-of-the-art complexity and clustering accuracy. In this paper, we present BanditPAM++, which accelerates BanditPAM via two algorithmic improvements, and is $O(k)$ faster than BanditPAM in complexity and substantially faster than BanditPAM in wall-clock runtime. First, we demonstrate that BanditPAM has a special structure that allows the reuse of clustering information $\textit{within}$ each iteration. Second, we demonstrate that BanditPAM has additional structure that permits the reuse of information $\textit{across}$ different iterations. These observations inspire our proposed algorithm, BanditPAM++, which returns the same clustering solutions as BanditPAM but often several times faster. For example, on the CIFAR10 dataset, BanditPAM++ returns the same results as BanditPAM but runs over 10$\times$ faster. Finally, we provide a high-performance C++ implementation of BanditPAM++, callable from Python and R, that may be of interest to practitioners at https://github.com/motiwari/BanditPAM. Auxiliary code to reproduce all of our experiments via a one-line script is available at https://github.com/ThrunGroup/BanditPAM_plusplus_experiments.

Yun-Han Li, Ilan Shomorony, Olgica Milenkovic

We study the problem of recovering the relative positions of objects moving along the real line based only on pairwise collision data. While interaction-based sensing systems arise naturally in a variety of practical settings, a systematic theoretical understanding of positional identifiability from collision observations alone remains unexplored. Our contributions are three-fold. First, under the full observability model, in which both the set of collisions and their temporal ordering are known, we show that the relative positions of all objects can be uniquely recovered if and only if the collision history, represented as a graph, is connected. Second, we show that under partial observability, where only colliding pairs are observed without timing information, the problem is related to \emph{function graphs} and introduce a canonical layer decomposition in which each layer corresponds to a maximal clique; the contraction graph induced by this decomposition is an interval graph, and we provide efficient algorithms to recover it. Third, under incomplete observations where even some pairwise collision observations may be missing, we formulate the problem as a graph completion problem and establish its NP-hardness via a $4$-approximation relationship with the graph bandwidth problem.

Aditya Narayan Ravi, Snehal Vadvalkar, Abhishek Pandey et al.

Cell Painting is a microscopy-based, high-content imaging assay that produces rich morphological profiles of cells and can support drug discovery by quantifying cellular responses to chemical perturbations. At scale, however, Cell Painting data is strongly affected by batch effects arising from differences in laboratories, instruments, and protocols, which can obscure biological signal. We present BALANS (Batch Alignment via Local Affinities and Subsampling), a scalable batch-correction method that aligns samples across batches by constructing a smoothed affinity matrix from pairwise distances. Given $n$ data points, BALANS builds a sparse affinity matrix $A \in \mathbb{R}^{n \times n}$ using two ideas. (i) For points $i$ and $j$, it sets a local scale using the distance from $i$ to its $k$-th nearest neighbor within the batch of $j$, then computes $A_{ij}$ via a Gaussian kernel calibrated by these batch-aware local scales. (ii) Rather than forming all $n^2$ entries, BALANS uses an adaptive sampling procedure that prioritizes rows with low cumulative neighbor coverage and retains only the strongest affinities per row, yielding a sparse but informative approximation of $A$. We prove that this sampling strategy is order-optimal in sample complexity and provides an approximation guarantee, and we show that BALANS runs in nearly linear time in $n$. Experiments on diverse real-world Cell Painting datasets and controlled large-scale synthetic benchmarks demonstrate that BALANS scales to large collections while improving runtime over native implementations of widely used batch-correction methods, without sacrificing correction quality.

Aditya Narayan Ravi, Ilan Shomorony

Federated Learning (FL) is a distributed machine learning approach to learn models on decentralized heterogeneous data, without the need for clients to share their data. Many existing FL approaches assume that all clients have equal importance and construct a global objective based on all clients. We consider a version of FL we call Prioritized FL, where the goal is to learn a weighted mean objective of a subset of clients, designated as priority clients. An important question arises: How do we choose and incentivize well aligned non priority clients to participate in the federation, while discarding misaligned clients? We present FedALIGN (Federated Adaptive Learning with Inclusion of Global Needs) to address this challenge. The algorithm employs a matching strategy that chooses non priority clients based on how similar the models loss is on their data compared to the global data, thereby ensuring the use of non priority client gradients only when it is beneficial for priority clients. This approach ensures mutual benefits as non priority clients are motivated to join when the model performs satisfactorily on their data, and priority clients can utilize their updates and computational resources when their goals align. We present a convergence analysis that quantifies the trade off between client selection and speed of convergence. Our algorithm shows faster convergence and higher test accuracy than baselines for various synthetic and benchmark datasets.

Seiyun Shin, Ilan Shomorony, Peter Macgregor

We propose a fast and dynamic algorithm for Density-Based Spatial Clustering of Applications with Noise (DBSCAN) that efficiently supports online updates. Traditional DBSCAN algorithms, designed for batch processing, become computationally expensive when applied to dynamic datasets, particularly in large-scale applications where data continuously evolves. To address this challenge, our algorithm leverages the Euler Tour Trees data structure, enabling dynamic clustering updates without the need to reprocess the entire dataset. This approach preserves a near-optimal accuracy in density estimation, as achieved by the state-of-the-art static DBSCAN method (Esfandiari et al., 2021) Our method achieves an improved time complexity of $O(d \log^3(n) + \log^4(n))$ for every data point insertion and deletion, where $n$ and $d$ denote the total number of updates and the data dimension, respectively. Empirical studies also demonstrate significant speedups over conventional DBSCANs in real-time clustering of dynamic datasets, while maintaining comparable or superior clustering quality.

Kayvon Mazooji, Ilan Shomorony

Clustering is often a challenging problem because of the inherent ambiguity in what the "correct" clustering should be. Even when the number of clusters $K$ is known, this ambiguity often still exists, particularly when there is variation in density among different clusters, and clusters have multiple relatively separated regions of high density. In this paper we propose an information-theoretic characterization of when a $K$-clustering is ambiguous, and design an algorithm that recovers the clustering whenever it is unambiguous. This characterization formalizes the situation when two high density regions within a cluster are separable enough that they look more like two distinct clusters than two truly distinct clusters in the $K$-clustering. The algorithm first identifies $K$ partial clusters (or "seeds") using a density-based approach, and then adds unclustered points to the initial $K$ partial clusters in a greedy manner to form a complete clustering. We implement and test a version of the algorithm that is modified to effectively handle overlapping clusters, and observe that it requires little parameter selection and displays improved performance on many datasets compared to widely used algorithms for non-convex cluster recovery.

Manav Vora, Ilan Shomorony, Melkior Ornik

We study capacity- and budget-constrained multi-agent MDPs (CB-MA-MDPs), a class that captures many maintenance and scheduling tasks in which each agent can irreversibly fail and a planner must decide (i) when to apply a restorative action and (ii) which subset of agents to treat in parallel. The global budget limits the total number of restorations, while the capacity constraint bounds the number of simultaneous actions, turning naïve dynamic programming into a combinatorial search that scales exponentially with the number of agents. We propose a two-stage solution that remains tractable for large systems. First, a Linear Sum Assignment Problem (LSAP)-based grouping partitions the agents into r disjoint sets (r = capacity) that maximise diversity in expected time-to-failure, allocating budget to each set proportionally. Second, a meta-trained PPO policy solves each sub-MDP, leveraging transfer across groups to converge rapidly. To validate our approach, we apply it to the problem of scheduling repairs for a large team of industrial robots, constrained by a limited number of repair technicians and a total repair budget. Our results demonstrate that the proposed method outperforms baseline approaches in terms of maximizing the average uptime of the robot team, particularly for large team sizes. Lastly, we confirm the scalability of our approach through a computational complexity analysis across varying numbers of robots and repair technicians.

Kayvon Mazooji, Roy Dong, Ilan Shomorony

When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We assume that the genetic content of these samples is known to the individual but unknown to the sequencing laboratory. Thus, these DNA samples act as "noise" to the sequencing laboratory, but still allow the individual to recover their own DNA samples afterward. Motivated by this idea, we study the problem of hiding a binary random variable $X$ (a genetic marker) with the additive noise provided by mixing DNA samples, using mutual information as a privacy metric. This is equivalent to the problem of finding a worst-case noise distribution for recovering $X$ from the noisy observation among a set of feasible discrete distributions. We characterize upper and lower bounds to the solution of this problem, which are empirically shown to be very close. The lower bound is obtained through a convex relaxation of the original discrete optimization problem, and yields a closed-form expression. The upper bound is computed via a greedy algorithm for selecting the mixing proportions.

Govinda M. Kamath, Tavor Z. Baharav, Ilan Shomorony

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that are shared by pairs of reads, which can then be used to estimate alignment scores. However, when the number of reads is large, accurately estimating alignment scores for all pairs is still very costly. Moreover, in practice, one is only interested in identifying pairs of reads with large alignment scores. In this work, we propose a new approach to pairwise alignment estimation based on two key new ingredients. The first ingredient is to cast the problem of pairwise alignment estimation under a general framework of rank-one crowdsourcing models, where the workers' responses correspond to k-mer hash collisions. These models can be accurately solved via a spectral decomposition of the response matrix. The second ingredient is to utilise a multi-armed bandit algorithm to adaptively refine this spectral estimator only for read pairs that are likely to have large alignments. The resulting algorithm iteratively performs a spectral decomposition of the response matrix for adaptively chosen subsets of the read pairs.

Mo Tiwari, Martin Jinye Zhang, James Mayclin et al.

Clustering is a ubiquitous task in data science. Compared to the commonly used $k$-means clustering, $k$-medoids clustering requires the cluster centers to be actual data points and support arbitrary distance metrics, which permits greater interpretability and the clustering of structured objects. Current state-of-the-art $k$-medoids clustering algorithms, such as Partitioning Around Medoids (PAM), are iterative and are quadratic in the dataset size $n$ for each iteration, being prohibitively expensive for large datasets. We propose BanditPAM, a randomized algorithm inspired by techniques from multi-armed bandits, that reduces the complexity of each PAM iteration from $O(n^2)$ to $O(n \log n)$ and returns the same results with high probability, under assumptions on the data that often hold in practice. As such, BanditPAM matches state-of-the-art clustering loss while reaching solutions much faster. We empirically validate our results on several large real-world datasets, including a coding exercise submissions dataset, the 10x Genomics 68k PBMC single-cell RNA sequencing dataset, and the MNIST handwritten digits dataset. In these experiments, we observe that BanditPAM returns the same results as state-of-the-art PAM-like algorithms up to 4x faster while performing up to 200x fewer distance computations. The improvements demonstrated by BanditPAM enable $k$-medoids clustering on a wide range of applications, including identifying cell types in large-scale single-cell data and providing scalable feedback for students learning computer science online. We also release highly optimized Python and C++ implementations of our algorithm.