pwc-archive/papers-with-abstracts huggingface dataset:
Cell Morphology-Guided Small Molecule Generation with GFlowNets
Authors: Stephen Zhewen Lu, Ziqing Lu, Ehsan Hajiramezanali, Tommaso Biancalani, Yoshua Bengio, Gabriele Scalia, Michał Koziarski
Date: 2024-08-09 00:00:00
Tasks: Drug Discovery

High-content phenotypic screening, including high-content imaging (HCI), has gained popularity in the last few years for its ability to characterize novel therapeutics without prior knowledge of the protein target. When combined with deep learning techniques to predict and represent molecular-phenotype interactions, these advancements hold the potential to significantly accelerate and enhance drug discovery applications. This work focuses on the novel task of HCI-guided molecular design. Generative models for molecule design could be guided by HCI data, for example with a supervised model that links molecules to phenotypes of interest as a reward function. However, limited labeled data, combined with the high-dimensional readouts, can make training these methods challenging and impractical. We consider an alternative approach in which we leverage an unsupervised multimodal joint embedding to define a latent similarity as a reward for GFlowNets. The proposed model learns to generate new molecules that could produce phenotypic effects similar to those of the given image target, without relying on pre-annotated phenotypic labels. We demonstrate that the proposed method generates molecules with high morphological and structural similarity to the target, increasing the likelihood of similar biological activity, as confirmed by an independent oracle model.
ECG-FM: An Open Electrocardiogram Foundation Model
Authors: Kaden McKeen, Laura Oliva, Sameer Masood, Augustin Toma, Barry Rubin, Bo wang
Date: 2024-08-09 00:00:00
Tasks: Contrastive Learning, Diagnostic, model, Transfer Learning

The electrocardiogram (ECG) is a ubiquitous diagnostic test. Conventional task-specific ECG analysis models require large numbers of expensive ECG annotations or associated labels to train. Transfer learning techniques have been shown to improve generalization and reduce reliance on labeled data. We present ECG-FM, an open foundation model for ECG analysis, and conduct a comprehensive study performed on a dataset of 1.66 million ECGs sourced from both publicly available and private institutional sources. ECG-FM adopts a transformer-based architecture and is pretrained on 2.5 million samples using ECG-specific augmentations and contrastive learning, as well as a continuous signal masking objective. Our transparent evaluation includes a diverse range of downstream tasks, where we predict ECG interpretation labels, reduced left ventricular ejection fraction, and abnormal cardiac troponin. Affirming ECG-FM's effectiveness as a foundation model, we demonstrate how its command of contextual information results in strong performance, rich pretrained embeddings, and reliable interpretability. Due to a lack of open-weight practices, we highlight how ECG analysis is lagging behind other medical machine learning subfields in terms of foundation model adoption. Our code is available at https://github.com/bowang-lab/ECG-FM/.
Beyond Closure Models: Learning Chaotic-Systems via Physics-Informed Neural Operators
Authors: Chuwei Wang, Julius Berner, Zongyi Li, Di Zhou, Jiayun Wang, Jane Bae, Anima Anandkumar
Date: 2024-08-09 00:00:00

Accurately predicting the long-term behavior of chaotic systems is crucial for various applications such as climate modeling. However, achieving such predictions typically requires iterative computations over a dense spatiotemporal grid to account for the unstable nature of chaotic systems, which is expensive and impractical in many real-world situations. An alternative approach to such a full-resolved simulation is using a coarse grid and then correcting its errors through a \textit{closure model}, which approximates the overall information from fine scales not captured in the coarse-grid simulation. Recently, ML approaches have been used for closure modeling, but they typically require a large number of training samples from expensive fully-resolved simulations (FRS). In this work, we prove an even more fundamental limitation, i.e., the standard approach to learning closure models suffers from a large approximation error for generic problems, no matter how large the model is, and it stems from the non-uniqueness of the mapping. We propose an alternative end-to-end learning approach using a physics-informed neural operator (PINO) that overcomes this limitation by not using a closure model or a coarse-grid solver. We first train the PINO model on data from a coarse-grid solver and then fine-tune it with (a small amount of) FRS and physics-based losses on a fine grid. The discretization-free nature of neural operators means that they do not suffer from the restriction of a coarse grid that closure models face, and they can provably approximate the long-term statistics of chaotic systems. In our experiments, our PINO model achieves a 330x speedup compared to FRS with a relative error $\sim 10\%$. In contrast, the closure model coupled with a coarse-grid solver is $60$x slower than PINO while having a much higher error $\sim186\%$ when the closure model is trained on the same FRS dataset.
Decoding Quantum LDPC Codes Using Graph Neural Networks
Authors: Vukan Ninkovic, Ognjen Kundacina, Dejan Vukobratovic, Christian Häger, Alexandre Graell i Amat
Date: 2024-08-09 00:00:00
Tasks: Decoder

In this paper, we propose a novel decoding method for Quantum Low-Density Parity-Check (QLDPC) codes based on Graph Neural Networks (GNNs). Similar to the Belief Propagation (BP)-based QLDPC decoders, the proposed GNN-based QLDPC decoder exploits the sparse graph structure of QLDPC codes and can be implemented as a message-passing decoding algorithm. We compare the proposed GNN-based decoding algorithm against selected classes of both conventional and neural-enhanced QLDPC decoding algorithms across several QLDPC code designs. The simulation results demonstrate excellent performance of GNN-based decoders along with their low complexity compared to competing methods.
Federated Hypergraph Learning: Hyperedge Completion with Local Differential Privacy
Authors: linfeng Luo, Fengxiao Tang, Xiyu Liu, Zhiqi Guo, Zihao Qiu, Ming Zhao
Date: 2024-08-09 00:00:00
Tasks: Federated Learning, Graph Learning

As the volume and complexity increase, graph-structured data commonly need to be split and stored across distributed systems. To enable data mining on subgraphs within these distributed systems, federated graph learning has been proposed, allowing collaborative training of Graph Neural Networks (GNNs) across clients without sharing raw node features. However, when dealing with graph structures that involve high-order relationships between nodes, known as hypergraphs, existing federated graph learning methods are less effective. In this study, we introduce FedHGL, an innovative federated hypergraph learning algorithm. FedHGL is designed to collaboratively train a comprehensive hypergraph neural network across multiple clients, facilitating mining tasks on subgraphs of a hypergraph where relationships are not merely pairwise. To address the high-order information loss between subgraphs caused by distributed storage, we introduce a pre-propagation hyperedge completion operation before the federated training process. In this pre-propagation step, cross-client feature aggregation is performed and distributed at the central server to ensure that this information can be utilized by the clients. Furthermore, by incorporating local differential privacy (LDP) mechanisms, we ensure that the original node features are not disclosed during this aggregation process. Experimental results on seven real-world datasets confirm the effectiveness of our approach and demonstrate its performance advantages over traditional federated graph learning methods.
Impacts of floating-point non-associativity on reproducibility for HPC and deep learning applications
Authors: Sanjif Shanmugavelu, Mathieu Taillefumier, Christopher Culver, Oscar Hernandez, Mark Coletti, Ada Sedova
Date: 2024-08-09 00:00:00
Tasks: Deep Learning, GPU, Sensitivity

Run to run variability in parallel programs caused by floating-point non-associativity has been known to significantly affect reproducibility in iterative algorithms, due to accumulating errors. Non-reproducibility can critically affect the efficiency and effectiveness of correctness testing for stochastic programs. Recently, the sensitivity of deep learning training and inference pipelines to floating-point non-associativity has been found to sometimes be extreme. It can prevent certification for commercial applications, accurate assessment of robustness and sensitivity, and bug detection. New approaches in scientific computing applications have coupled deep learning models with high-performance computing, leading to an aggravation of debugging and testing challenges. Here we perform an investigation of the statistical properties of floating-point non-associativity within modern parallel programming models, and analyze performance and productivity impacts of replacing atomic operations with deterministic alternatives on GPUs. We examine the recently-added deterministic options in PyTorch within the context of GPU deployment for deep learning, uncovering and quantifying the impacts of input parameters triggering run to run variability and reporting on the reliability and completeness of the documentation. Finally, we evaluate the strategy of exploiting automatic determinism that could be provided by deterministic hardware, using the Groq accelerator for inference portions of the deep learning pipeline. We demonstrate the benefits that a hardware-based strategy can provide within reproducibility and correctness efforts.
Performative Prediction on Games and Mechanism Design
Authors: António Góis, Mehrnaz Mofakhami, Fernando P. Santos, Gauthier Gidel, Simon Lacoste-Julien
Date: 2024-08-09 00:00:00
Tasks: Prediction

Agents often have individual goals which depend on a group's actions. If agents trust a forecast of collective action and adapt strategically, such prediction can influence outcomes non-trivially, resulting in a form of performative prediction. This effect is ubiquitous in scenarios ranging from pandemic predictions to election polls, but existing work has ignored interdependencies among predicted agents. As a first step in this direction, we study a collective risk dilemma where agents dynamically decide whether to trust predictions based on past accuracy. As predictions shape collective outcomes, social welfare arises naturally as a metric of concern. We explore the resulting interplay between accuracy and welfare, and demonstrate that searching for stable accurate predictions can minimize social welfare with high probability in our setting. By assuming knowledge of a Bayesian agent behavior model, we then show how to achieve better trade-offs and use them for mechanism design.
Cycle-Configuration: A Novel Graph-theoretic Descriptor Set for Molecular Inference
Authors: Bowen Song, Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Tatsuya Akutsu
Date: 2024-08-09 00:00:00

In this paper, we propose a novel family of descriptors of chemical graphs, named cycle-configuration (CC), that can be used in the standard "two-layered (2L) model" of mol-infer, a molecular inference framework based on mixed integer linear programming (MILP) and machine learning (ML). Proposed descriptors capture the notion of ortho/meta/para patterns that appear in aromatic rings, which has been impossible in the framework so far. Computational experiments show that, when the new descriptors are supplied, we can construct prediction functions of similar or better performance for all of the 27 tested chemical properties. We also provide an MILP formulation that asks for a chemical graph with desired properties under the 2L model with CC descriptors (2L+CC model). We show that a chemical graph with up to 50 non-hydrogen vertices can be inferred in a practical time.
Range Membership Inference Attacks
Authors: Jiashu Tao, Reza Shokri
Date: 2024-08-09 00:00:00

Machine learning models can leak private information about their training data, but the standard methods to measure this risk, based on membership inference attacks (MIAs), have a major limitation. They only check if a given data point \textit{exactly} matches a training point, neglecting the potential of similar or partially overlapping data revealing the same private information. To address this issue, we introduce the class of range membership inference attacks (RaMIAs), testing if the model was trained on any data in a specified range (defined based on the semantics of privacy). We formulate the RaMIAs game and design a principled statistical test for its complex hypotheses. We show that RaMIAs can capture privacy loss more accurately and comprehensively than MIAs on various types of data, such as tabular, image, and language. RaMIA paves the way for a more comprehensive and meaningful privacy auditing of machine learning algorithms.
Concept learning of parameterized quantum models from limited measurements
Authors: Beng Yee Gan, Po-Wei Huang, Elies Gil-Fuster, Patrick Rebentrost
Date: 2024-08-09 00:00:00

Classical learning of the expectation values of observables for quantum states is a natural variant of learning quantum states or channels. While learning-theoretic frameworks establish the sample complexity and the number of measurement shots per sample required for learning such statistical quantities, the interplay between these two variables has not been adequately quantified before. In this work, we take the probabilistic nature of quantum measurements into account in classical modelling and discuss these quantities under a single unified learning framework. We provide provable guarantees for learning parameterized quantum models that also quantify the asymmetrical effects and interplay of the two variables on the performance of learning algorithms. These results show that while increasing the sample size enhances the learning performance of classical machines, even with single-shot estimates, the improvements from increasing measurements become asymptotically trivial beyond a constant factor. We further apply our framework and theoretical guarantees to study the impact of measurement noise on the classical surrogation of parameterized quantum circuit models. Our work provides new tools to analyse the operational influence of finite measurement noise in the classical learning of quantum systems.
Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning
Authors: Yunhui Liu, Huaisong Zhang, Tieke He, Tao Zheng, Jianhua Zhao
Date: 2024-08-09 00:00:00
Tasks: Contrastive Learning, Node Classification, Node Clustering, Representation Learning, Self-Supervised Learning

Contrastive learning is a significant paradigm in graph self-supervised learning. However, it requires negative samples to prevent model collapse and learn discriminative representations. These negative samples inevitably lead to heavy computation, memory overhead and class collision, compromising the representation learning. Recent studies present that methods obviating negative samples can attain competitive performance and scalability enhancements, exemplified by bootstrapped graph latents (BGRL). However, BGRL neglects the inherent graph homophily, which provides valuable insights into underlying positive pairs. Our motivation arises from the observation that subtly introducing a few ground-truth positive pairs significantly improves BGRL. Although we can't obtain ground-truth positive pairs without labels under the self-supervised setting, edges in the graph can reflect noisy positive pairs, i.e., neighboring nodes often share the same label. Therefore, we propose to expand the positive pair set with node-neighbor pairs. Subsequently, we introduce a cross-attention module to predict the supportiveness score of a neighbor with respect to the anchor node. This score quantifies the positive support from each neighboring node, and is encoded into the training objective. Consequently, our method mitigates class collision from negative and noisy positive samples, concurrently enhancing intra-class compactness. Extensive experiments are conducted on five benchmark datasets and three downstream task node classification, node clustering, and node similarity search. The results demonstrate that our method generates node representations with enhanced intra-class compactness and achieves state-of-the-art performance.
Masked adversarial neural network for cell type deconvolution in spatial transcriptomics
Authors: Lin Huang, Xiaofei Liu, Shunfang Wang, Wenwen Min
Date: 2024-08-09 00:00:00

Accurately determining cell type composition in disease-relevant tissues is crucial for identifying disease targets. Most existing spatial transcriptomics (ST) technologies cannot achieve single-cell resolution, making it challenging to accurately determine cell types. To address this issue, various deconvolution methods have been developed. Most of these methods use single-cell RNA sequencing (scRNA-seq) data from the same tissue as a reference to infer cell types in ST data spots. However, they often overlook the differences between scRNA-seq and ST data. To overcome this limitation, we propose a Masked Adversarial Neural Network (MACD). MACD employs adversarial learning to align real ST data with simulated ST data generated from scRNA-seq data. By mapping them into a unified latent space, it can minimize the differences between the two types of data. Additionally, MACD uses masking techniques to effectively learn the features of real ST data and mitigate noise. We evaluated MACD on 32 simulated datasets and 2 real datasets, demonstrating its accuracy in performing cell type deconvolution. All code and public datasets used in this paper are available at https://github.com/wenwenmin/MACD and https://zenodo.org/records/12804822.
Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions
Authors: Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang
Date: 2024-08-09 00:00:00
Tasks: Stochastic Optimization

Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the complicated space of phylogenetic trees, especially when the number of sequences is large. An alternative approach is variational Bayesian phylogenetic inference (VBPI) which transforms the inference problem into an optimization problem. While effective, the default diagonal lognormal approximation for the branch lengths of the tree used in VBPI is often insufficient to capture the complexity of the exact posterior. In this work, we propose a more flexible family of branch length variational posteriors based on semi-implicit hierarchical distributions using graph neural networks. We show that this semi-implicit construction emits straightforward permutation equivariant distributions, and therefore can handle the non-Euclidean branch length space across different tree topologies with ease. To deal with the intractable marginal probability of semi-implicit variational distributions, we develop several alternative lower bounds for stochastic optimization. We demonstrate the effectiveness of our proposed method over baseline methods on benchmark data examples, in terms of both marginal likelihood estimation and branch length posterior approximation.
Graph Neural Networks as Ordering Heuristics for Parallel Graph Coloring
Authors: Kenneth Langedal, Fredrik Manne
Date: 2024-08-09 00:00:00
Tasks: Graph Neural Network

The graph coloring problem asks for an assignment of the minimum number of distinct colors to vertices in an undirected graph with the constraint that no pair of adjacent vertices share the same color. The problem is a thoroughly studied NP-hard combinatorial problem with several real-world applications. As such, a number of greedy heuristics have been suggested that strike a good balance between coloring quality, execution time, and also parallel scalability. In this work, we introduce a graph neural network (GNN) based ordering heuristic and demonstrate that it outperforms existing greedy ordering heuristics both on quality and performance. Previous results have demonstrated that GNNs can produce high-quality colorings but at the expense of excessive running time. The current paper is the first that brings the execution time down to compete with existing greedy heuristics. Our GNN model is trained using both supervised and unsupervised techniques. The experimental results show that a 2-layer GNN model can achieve execution times between the largest degree first (LF) and smallest degree last (SL) ordering heuristics while outperforming both on coloring quality. Increasing the number of layers improves the coloring quality further, and it is only at four layers that SL becomes faster than the GNN. Finally, our GNN-based coloring heuristic achieves superior scaling in the parallel setting compared to both SL and LF.
BoFire: Bayesian Optimization Framework Intended for Real Experiments
Authors: Johannes P. Dürholt, Thomas S. Asche, Johanna Kleinekorte, Gabriel Mancino-Ball, Benjamin Schiller, Simon Sung, Julian Keupp, Aaron Osburg, Toby Boyne, Ruth Misener, Rosona Eldred, Wagner Steuer Costa, Chrysoula Kappatou, Robert M. Lee, Dominik Linzner, David Walz, Niklas Wulkow, Behrang Shafei
Date: 2024-08-09 00:00:00
Tasks: Bayesian Optimization

Our open-source Python package BoFire combines Bayesian Optimization (BO) with other design of experiments (DoE) strategies focusing on developing and optimizing new chemistry. Previous BO implementations, for example as they exist in the literature or software, require substantial adaptation for effective real-world deployment in chemical industry. BoFire provides a rich feature-set with extensive configurability and realizes our vision of fast-tracking research contributions into industrial use via maintainable open-source software. Owing to quality-of-life features like JSON-serializability of problem formulations, BoFire enables seamless integration of BO into RESTful APIs, a common architecture component for both self-driving laboratories and human-in-the-loop setups. This paper discusses the differences between BoFire and other BO implementations and outlines ways that BO research needs to be adapted for real-world use in a chemistry setting.
A conformalized learning of a prediction set with applications to medical imaging classification
Authors: Roy Hirsch, Jacob Goldberger
Date: 2024-08-09 00:00:00
Tasks: Conformal Prediction, Prediction

Medical imaging classifiers can achieve high predictive accuracy, but quantifying their uncertainty remains an unresolved challenge, which prevents their deployment in medical clinics. We present an algorithm that can modify any classifier to produce a prediction set containing the true label with a user-specified probability, such as 90%. We train a network to predict an instance-based version of the Conformal Prediction threshold. The threshold is then conformalized to ensure the required coverage. We applied the proposed algorithm to several standard medical imaging classification datasets. The experimental results demonstrate that our method outperforms current approaches in terms of smaller average size of the prediction set while maintaining the desired coverage.