Oligonucleotide therapeutics offer great potential to address previously undruggable targets and enable personalized medicine. However, their progress is often hindered by insufficient safety and efficacy profiles. Predictive modeling and machine learning could significantly accelerate oligonucleotide drug discovery by identifying suboptimal compounds early on, but their application in this area lags behind other modalities. A key obstacle to the adoption of machine learning in the field is the scarcity of readily accessible and standardized datasets for model development, as data are often scattered across diverse experiments with inconsistent molecular representations. To overcome this challenge, we introduce OligoGym, a curated collection of standardized, machine learning-ready datasets encompassing various oligonucleotide therapeutic modalities and endpoints. We used OligoGym to benchmark diverse classical and deep learning methods, establishing performance baselines for each dataset across different featurization techniques, model configurations, and splitting strategies. Our work represents a crucial first step in creating a more unified framework for oligonucleotide therapeutic dataset generation and model training.

Quantifying uncertainty in deep regression models is important both for understanding the confidence of the model and for safe decision-making in high-risk domains. Existing approaches that yield prediction intervals overlook distributional information, neglecting the effect of multimodal or asymmetric distributions on decision-making.

Gaussian sketching, which consists of pre-multiplying the data with a random Gaussian matrix, is a widely used technique in data science and machine learning. Beyond computational benefits, this operation also provides differential privacy guarantees due to its inherent randomness. In this work, we revisit this operation through the lens of Rényi Differential Privacy (RDP), providing a refined privacy analysis that yields significantly tighter bounds than prior results. We then demonstrate how this improved analysis leads to performance improvement in different linear regression settings, establishing theoretical utility guarantees. Empirically, our methods improve performance across multiple datasets and, in several cases, reduce runtime.

Local search is a powerful clustering technique that provides high-quality solutions with theoretical guarantees. With distance-based sampling strategies, local search methods can achieve constant approximations for clustering with linear running time in data size. Despite their effectiveness, existing algorithms still face scalability issues as they require scanning the entire dataset for iterative center swaps. This typically leads to an O(ndk) running time, where nis the data size, dis the dimension, k is the number of clusters. To further improve the efficiency of local search algorithms, we propose new methods based on adaptive sampling and bandit strategies.

Counterfactual explanations provide individuals with cost-optimal recommendations to achieve their desired outcomes. However, when a significant number of individuals seek similar state modifications, this individual-centric approach can inadvertently create competition and introduce unforeseen costs. Additionally, disregarding the underlying data distribution may lead to recommendations that individuals perceive as unusual or impractical. To address these challenges, we propose a novel framework that extends standard counterfactual explanations by incorporating a population dynamics model. This framework penalizes deviations from equilibrium after individuals follow the recommendations, effectively mitigating externalities caused by correlated changes across the population. By balancing individual modification costs with their impact on others, our method ensures more equitable and efficient outcomes. We show how this approach reframes the counterfactual explanation problem from an individual-centric task to a collective optimization problem. Augmenting our theoretical insights, we design and implement scalable algorithms for computing collective counterfactuals, showcasing their effectiveness and advantages over existing recourse methods, particularly in aligning with collective objectives.

In this paper, we explore semantic clustering properties of deep reinforcement learning (DRL) to improve its interpretability and deepen our understanding of its internal semantic organization. In this context, semantic clustering refers to the ability of neural networks to cluster inputs based on their semantic similarity in the feature space. We propose a DRL architecture that incorporates a novel semantic clustering module that combines feature dimensionality reduction with online clustering.

We propose a framework for hypothesis testing on conditional probability distributions, which we then use to construct statistical tests of functionals of conditional distributions. These tests identify the inputs where the functionals differ with high probability, and include tests of conditional moments or two-sample tests. Our key idea is to transform confidence bounds of a learning method into a test of conditional expectations.

In this paper, we propose a novel tube-wise local tensor compressed sensing (CS) model under the tensor product framework, where sensing operators are independently applied to each tube of a third-order tensor. To recover the low-rank ground truth tensor, we minimize a non-convex objective via Burer-Monteiro factorization and solve it using gradient descent (GD) with spectral initialization. We prove that this approach achieves exact recovery with a linear convergence rate. Notably, our method attains provably lower sample complexity than existing TCS methods if the low tubal rank ground truth tensor satisfies the defined incoherence condition. Our proof leverages the leave-one-out technique to show that gradient descent generates iterates implicitly biased towards solutions with bounded incoherence, which ensures contraction of optimization error in consecutive iterates. Empirical results validate the effectiveness of GD in solving the proposed local TCS model.

Latent variables (LVs) play a crucial role in encoder-decoder models by enabling effective data compression, prediction, and generation. Although their theoretical properties, such as generalization, have been extensively studied in supervised learning, similar analyses for unsupervised models such as variational autoencoders (VAEs) remain insufficiently explored. In this work, we extend informationtheoretic generalization analysis to vector-quantized (VQ) VAEs with discrete latent spaces, introducing a novel data-dependent prior to rigorously analyze the relationship among LVs, generalization, and data generation. We derive a novel generalization error bound of the reconstruction loss of VQ-VAEs, which depends solely on the complexity of LVs and the encoder, independent of the decoder. Additionally, we provide the upper bound of the 2-Wasserstein distance between the distributions of the true data and the generated data, explaining how the regularization of the LVs contributes to the data generation performance.

Spectral clustering is a fundamental method for graph partitioning, but its reliance on eigenvector computation limits scalability to massive graphs. Classical sparsification methods preserve spectral properties by sampling edges proportionally to their effective resistances, but require expensive preprocessing to estimate these resistances. We study whether uniform edge sampling--a simple, structure-agnostic strategy--can suffice for spectral clustering. Our main result shows that for graphs admitting a well-separated k-clustering, characterized by a large structure ratio Υ(k) = λk+1/ρG(k), uniform sampling preserves the spectral subspace used for clustering. Specifically, we prove that uniformly sampling O(γ2nlogn/ε2) edges, where γ is the Laplacian condition number, yields a sparsifier whose top (n k)dimensional eigenspace is approximately orthogonal to the cluster indicators.