Supervised Learning
AssayMatch: Learning to Select Data for Molecular Activity Models
Fan, Vincent, Barzilay, Regina
The performance of machine learning models in drug discovery is highly dependent on the quality and consistency of the underlying training data. Due to limitations in dataset sizes, many models are trained by aggregating bioactivity data from diverse sources, including public databases such as ChEMBL. However, this approach often introduces significant noise due to variability in experimental protocols. We introduce AssayMatch, a framework for data selection that builds smaller, more homogenous training sets attuned to the test set of interest. AssayMatch leverages data attribution methods to quantify the contribution of each training assay to model performance. These attribution scores are used to finetune language embeddings of text-based assay descriptions to capture not just semantic similarity, but also the compatibility between assays. Unlike existing data attribution methods, our approach enables data selection for a test set with unknown labels, mirroring real-world drug discovery campaigns where the activities of candidate molecules are not known in advance. At test time, embeddings finetuned with AssayMatch are used to rank all available training data. We demonstrate that models trained on data selected by AssayMatch are able to surpass the performance of the model trained on the complete dataset, highlighting its ability to effectively filter out harmful or noisy experiments. We perform experiments on two common machine learning architectures and see increased prediction capability over a strong language-only baseline for 9/12 model-target pairs. AssayMatch provides a data-driven mechanism to curate higher-quality datasets, reducing noise from incompatible experiments and improving the predictive power and data efficiency of models for drug discovery. AssayMatch is available at https://github.com/Ozymandias314/AssayMatch.
Model-Agnostic Private Learning
Raef Bassily, Abhradeep Guha Thakurta, Om Dipakbhai Thakkar
We design differentially private learning algorithms that are agnostic to the learning model assuming access to a limited amount of unlabeled public data. First, we provide a new differentially private algorithm for answering a sequence of m online classification queries (given by a sequence of m unlabeled public feature vectors) based on a private training set. Our algorithm follows the paradigm of subsample-and-aggregate, in which any generic non-private learner is trained on disjoint subsets of the private training set, and then for each classification query, the votes of the resulting classifiers ensemble are aggregated in a differentially private fashion. Our private aggregation is based on a novel combination of the distance-to-instability framework [26], and the sparse-vector technique [15, 18]. We show that our algorithm makes a conservative use of the privacy budget. In particular, if the underlying non-private learner yields a classification error of at most ฮฑ (0, 1), then our construction answers more queries, by at least a factor of 1/ฮฑ in some cases, than what is implied by a straightforward application of the advanced composition theorem for differential privacy. Next, we apply the knowledge transfer technique to construct a private learner that outputs a classifier, which can be used to answer an unlimited number of queries. In the P AC model, we analyze our construction and prove upper bounds on the sample complexity for both the realizable and the non-realizable cases. Similar to non-private sample complexity, our bounds are completely characterized by the VC dimension of the concept class.
LANE: Lexical Adversarial Negative Examples for Word Sense Disambiguation
de Sรก, Jader Martins Camboim, Lee, Jooyoung, Pruski, Cรฉdric, Da Silveira, Marcos
Fine-grained word meaning resolution remains a critical challenge for neural language models (NLMs) as they often overfit to global sentence representations, failing to capture local semantic details. We propose a novel adversarial training strategy, called LANE, to address this limitation by deliberately shifting the model's learning focus to the target word. This method generates challenging negative training examples through the selective marking of alternate words in the training set. The goal is to force the model to create a greater separability between same sentences with different marked words. Experimental results on lexical semantic change detection and word sense disambiguation benchmarks demonstrate that our approach yields more discriminative word representations, improving performance over standard contrastive learning baselines. We further provide qualitative analyses showing that the proposed negatives lead to representations that better capture subtle meaning differences even in challenging environments. Our method is model-agnostic and can be integrated into existing representation learning frameworks.
Reconstruction and Secrecy under Approximate Distance Queries
Moran, Shay, Nesterova, Elizaveta
Consider the task of locating an unknown target point using approximate distance queries: in each round, a reconstructor selects a query point and receives a noisy version of its distance to the target. This problem arises naturally in various contexts ranging from localization in GPS and sensor networks to privacy-aware data access, and spans a wide variety of metric spaces. It is relevant from the perspective of both the reconstructor (seeking accurate recovery) and the responder (aiming to limit information disclosure, e.g., for privacy or security reasons). We study this reconstruction game through a learning-theoretic lens, focusing on the rate and limits of the best possible reconstruction error. Our first result provides a tight geometric characterization of the optimal error in terms of the Chebyshev radius, a classical concept from geometry. This characterization applies to all compact metric spaces (in fact, even to all totally bounded spaces) and yields explicit formulas for natural metric spaces. Our second result addresses the asymptotic behavior of reconstruction, distinguishing between pseudo-finite spaces -- where the optimal error is attained after finitely many queries -- and spaces where the approximation curve exhibits nontrivial decay. We characterize pseudo-finiteness for convex Euclidean spaces.
SQLSpace: A Representation Space for Text-to-SQL to Discover and Mitigate Robustness Gaps
Srikanth, Neha, Bursztyn, Victor, Mathur, Puneet, Nenkova, Ani
We introduce SQLSpace, a human-interpretable, generalizable, compact representation for text-to-SQL examples derived with minimal human intervention. We demonstrate the utility of these representations in evaluation with three use cases: (i) closely comparing and contrasting the composition of popular text-to-SQL benchmarks to identify unique dimensions of examples they evaluate, (ii) understanding model performance at a granular level beyond overall accuracy scores, and (iii) improving model performance through targeted query rewriting based on learned correctness estimation. We show that SQLSpace enables analysis that would be difficult with raw examples alone: it reveals compositional differences between benchmarks, exposes performance patterns obscured by accuracy alone, and supports modeling of query success.
The Temporal Graph of Bitcoin Transactions
Since its 2009 genesis block, the Bitcoin network has processed >1.08 billion (B) transactions representing >8.72B BTC, offering rich potential for machine learning (ML); yet, its pseudonymity and obscured flow of funds inherent in its UTxO-based design, have rendered this data largely inaccessible for ML research. Addressing this gap, we present an ML-compatible graph modeling the Bitcoin's economic topology by reconstructing the flow of funds. This temporal, heterogeneous graph encompasses complete transaction history up to block 863000, consisting of >2.4B nodes and >39.72B edges. Additionally, we provide custom sampling methods yielding node and edge feature vectors of sampled communities, tools to load and analyze the Bitcoin graph data within specialized graph databases, and ready-to-use database snapshots. This comprehensive dataset and toolkit empower the ML community to tackle Bitcoin's intricate ecosystem at scale, driving progress in applications such as anomaly detection, address classification, market analysis, and large-scale graph ML benchmarking. Dataset and code available at https://github.com/B1AAB/EBA
Predict Training Data Quality via Its Geometry in Metric Space
Ba, Yang, Abolhasani, Mohammad Sadeq, Pan, Rong
High-quality training data is the foundation of machine learning and artificial intelligence, shaping how models learn and perform. Although much is known about what types of data are effective for training, the impact of the data's geometric structure on model performance remains largely underexplored. We propose that both the richness of representation and the elimination of redundancy within training data critically influence learning outcomes. To investigate this, we employ persistent homology to extract topological features from data within a metric space, thereby offering a principled way to quantify diversity beyond entropy-based measures. Our findings highlight persistent homology as a powerful tool for analyzing and enhancing the training data that drives AI systems.