Yunchao Liu

Yu Wang, Tong Zhao, Yuying Zhao et al.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Zeph Landau, Yunchao Liu

We give a polynomial time algorithm that, given copies of an unknown quantum state $\vertψ\rangle=U\vert 0^n\rangle$ that is prepared by an unknown constant depth circuit $U$ on a finite-dimensional lattice, learns a constant depth quantum circuit that prepares $\vertψ\rangle$. The algorithm extends to the case when the depth of $U$ is $\mathrm{polylog}(n)$, with a quasi-polynomial run-time. The key new idea is a simple and general procedure that efficiently reconstructs the global state $\vertψ\rangle$ from its local reduced density matrices. As an application, we give an efficient algorithm to test whether an unknown quantum state on a lattice has low or high quantum circuit complexity.

Yunchao Liu, Ha Dong, Xin Wang et al.

While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model evaluation framework, the AI community's efforts cannot reach their full potential, thereby slowing the progress and transfer of innovation into real-world drug discovery. Thus, in this paper, we seek to establish a new gold standard for small molecule drug discovery benchmarking, WelQrate. Specifically, our contributions are threefold: WelQrate Dataset Collection - we introduce a meticulously curated collection of 9 datasets spanning 5 therapeutic target classes. Our hierarchical curation pipelines, designed by drug discovery experts, go beyond the primary high-throughput screen by leveraging additional confirmatory and counter screens along with rigorous domain-driven preprocessing, such as Pan-Assay Interference Compounds (PAINS) filtering, to ensure the high-quality data in the datasets; WelQrate Evaluation Framework - we propose a standardized model evaluation framework considering high-quality datasets, featurization, 3D conformation generation, evaluation metrics, and data splits, which provides a reliable benchmarking for drug discovery experts conducting real-world virtual screening; Benchmarking - we evaluate model performance through various research questions using the WelQrate dataset collection, exploring the effects of different models, dataset quality, featurization methods, and data splitting strategies on the results. In summary, we recommend adopting our proposed WelQrate as the gold standard in small molecule drug discovery benchmarking. The WelQrate dataset collection, along with the curation codes, and experimental scripts are all publicly available at WelQrate.org.

Xin Wang, Yu Wang, Yunchao Liu et al.

Ligand-based virtual screening (VS) is an essential step in drug discovery that evaluates large chemical libraries to identify compounds that potentially bind to a therapeutic target. However, VS faces three major challenges: class imbalance due to the low active rate, structural imbalance among active molecules where certain scaffolds dominate, and the need to identify structurally diverse active compounds for novel drug development. We introduce ScaffAug, a scaffold-aware VS framework that addresses these challenges through three modules. The augmentation module first generates synthetic data conditioned on scaffolds of actual hits using generative AI, specifically a graph diffusion model. This helps mitigate the class imbalance and furthermore the structural imbalance, due to our proposed scaffold-aware sampling algorithm, designed to produce more samples for active molecules with underrepresented scaffolds. A model-agnostic self-training module is then used to safely integrate the generated synthetic data from our augmentation module with the original labeled data. Lastly, we introduce a reranking module that improves VS by enhancing scaffold diversity in the top recommended set of molecules, while still maintaining and even enhancing the overall general performance of identifying novel, active compounds. We conduct comprehensive computational experiments across five target classes, comparing ScaffAug against existing baseline methods by reporting the performance of multiple evaluation metrics and performing ablation studies on ScaffAug. Overall, this work introduces novel perspectives on effectively enhancing VS by leveraging generative augmentations, reranking, and general scaffold-awareness.

Xueqi Cheng, Yu Wang, Yunchao Liu et al.

Recent years have witnessed the remarkable success of applying Graph machine learning (GML) to node/graph classification and link prediction. However, edge classification task that enjoys numerous real-world applications such as social network analysis and cybersecurity, has not seen significant advancement. To address this gap, our study pioneers a comprehensive approach to edge classification. We identify a novel `Topological Imbalance Issue', which arises from the skewed distribution of edges across different classes, affecting the local subgraph of each edge and harming the performance of edge classifications. Inspired by the recent studies in node classification that the performance discrepancy exists with varying local structural patterns, we aim to investigate if the performance discrepancy in topological imbalanced edge classification can also be mitigated by characterizing the local class distribution variance. To overcome this challenge, we introduce Topological Entropy (TE), a novel topological-based metric that measures the topological imbalance for each edge. Our empirical studies confirm that TE effectively measures local class distribution variance, and indicate that prioritizing edges with high TE values can help address the issue of topological imbalance. Based on this, we develop two strategies - Topological Reweighting and TE Wedge-based Mixup - to focus training on (synthetic) edges based on their TEs. While topological reweighting directly manipulates training edge weights according to TE, our wedge-based mixup interpolates synthetic edges between high TE wedges. Ultimately, we integrate these strategies into a novel topological imbalance strategy for edge classification: TopoEdge. Through extensive experiments, we demonstrate the efficacy of our proposed strategies on newly curated datasets and thus establish a new benchmark for (imbalanced) edge classification.

Hsin-Yuan Huang, Yunchao Liu, Michael Broughton et al.

Despite fundamental interests in learning quantum circuits, the existence of a computationally efficient algorithm for learning shallow quantum circuits remains an open question. Because shallow quantum circuits can generate distributions that are classically hard to sample from, existing learning algorithms do not apply. In this work, we present a polynomial-time classical algorithm for learning the description of any unknown $n$-qubit shallow quantum circuit $U$ (with arbitrary unknown architecture) within a small diamond distance using single-qubit measurement data on the output states of $U$. We also provide a polynomial-time classical algorithm for learning the description of any unknown $n$-qubit state $\lvert ψ\rangle = U \lvert 0^n \rangle$ prepared by a shallow quantum circuit $U$ (on a 2D lattice) within a small trace distance using single-qubit measurements on copies of $\lvert ψ\rangle$. Our approach uses a quantum circuit representation based on local inversions and a technique to combine these inversions. This circuit representation yields an optimization landscape that can be efficiently navigated and enables efficient learning of quantum circuits that are classically hard to simulate.

Yunchao Liu, Srinivasan Arunachalam, Kristan Temme

Over the past few years several quantum machine learning algorithms were proposed that promise quantum speed-ups over their classical counterparts. Most of these learning algorithms either assume quantum access to data -- making it unclear if quantum speed-ups still exist without making these strong assumptions, or are heuristic in nature with no provable advantage over classical algorithms. In this paper, we establish a rigorous quantum speed-up for supervised classification using a general-purpose quantum learning algorithm that only requires classical access to data. Our quantum classifier is a conventional support vector machine that uses a fault-tolerant quantum computer to estimate a kernel function. Data samples are mapped to a quantum feature space and the kernel entries can be estimated as the transition amplitude of a quantum circuit. We construct a family of datasets and show that no classical learner can classify the data inverse-polynomially better than random guessing, assuming the widely-believed hardness of the discrete logarithm problem. Meanwhile, the quantum classifier achieves high accuracy and is robust against additive errors in the kernel entries that arise from finite sampling statistics.