pwc-archive/papers-with-abstracts huggingface dataset:
Automatic Functional Differentiation in JAX
Authors: Min Lin
Date: 2023-11-30 00:00:00

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .
AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunities
Authors: Yuhan Li, Hongtao Zhang, Keaven Anderson, Songzi Li, Ruoqing Zhu
Date: 2023-11-30 00:00:00
Tasks: Decision Making, Drug Discovery, Marketing, Protein Structure Prediction, Sequential Decision Making

In the pharmaceutical industry, the use of artificial intelligence (AI) has seen consistent growth over the past decade. This rise is attributed to major advancements in statistical machine learning methodologies, computational capabilities and the increased availability of large datasets. AI techniques are applied throughout different stages of drug development, ranging from drug discovery to post-marketing benefit-risk assessment. Kolluri et al. provided a review of several case studies that span these stages, featuring key applications such as protein structure prediction, success probability estimation, subgroup identification, and AI-assisted clinical trial monitoring. From a regulatory standpoint, there was a notable uptick in submissions incorporating AI components in 2021. The most prevalent therapeutic areas leveraging AI were oncology (27%), psychiatry (15%), gastroenterology (12%), and neurology (11%). The paradigm of personalized or precision medicine has gained significant traction in recent research, partly due to advancements in AI techniques \cite{hamburg2010path}. This shift has had a transformative impact on the pharmaceutical industry. Departing from the traditional "one-size-fits-all" model, personalized medicine incorporates various individual factors, such as environmental conditions, lifestyle choices, and health histories, to formulate customized treatment plans. By utilizing sophisticated machine learning algorithms, clinicians and researchers are better equipped to make informed decisions in areas such as disease prevention, diagnosis, and treatment selection, thereby optimizing health outcomes for each individual.
The Feature Speed Formula: a flexible approach to scale hyper-parameters of deep neural networks
Authors: Lénaïc Chizat, Praneeth Netrapalli
Date: 2023-11-30 00:00:00

Deep learning succeeds by doing hierarchical feature learning, yet tuning hyper-parameters (HP) such as initialization scales, learning rates etc., only give indirect control over this behavior. In this paper, we introduce a key notion to predict and control feature learning: the angle $\theta_\ell$ between the feature updates and the backward pass (at layer index $\ell$). We show that the magnitude of feature updates after one GD step, at any training time, can be expressed via a simple and general \emph{feature speed formula} in terms of this angle $\theta_\ell$, the loss decay, and the magnitude of the backward pass. This angle $\theta_\ell$ is controlled by the conditioning of the layer-to-layer Jacobians and at random initialization, it is determined by the spectrum of a certain kernel, which coincides with the Neural Tangent Kernel when $\ell=\text{depth}$. Given $\theta_\ell$, the feature speed formula provides us with rules to adjust HPs (scales and learning rates) so as to satisfy certain dynamical properties, such as feature learning and loss decay. We investigate the implications of our approach for ReLU MLPs and ResNets in the large width-then-depth limit. Relying on prior work, we show that in ReLU MLPs with iid initialization, the angle degenerates with depth as $\cos(\theta_\ell)=\Theta(1/\sqrt{\ell})$. In contrast, ResNets with branch scale $O(1/\sqrt{\text{depth}})$ maintain a non-degenerate angle $\cos(\theta_\ell)=\Theta(1)$. We use these insights to recover key properties of known HP scalings and also to introduce a new HP scaling for large depth ReLU MLPs with favorable theoretical properties.
Balancing Summarization and Change Detection in Graph Streams
Authors: Shintaro Fukushima, Kenji Yamanishi
Date: 2023-11-30 00:00:00
Tasks: Change Detection

This study addresses the issue of balancing graph summarization and graph change detection. Graph summarization compresses large-scale graphs into a smaller scale. However, the question remains: To what extent should the original graph be compressed? This problem is solved from the perspective of graph change detection, aiming to detect statistically significant changes using a stream of summary graphs. If the compression rate is extremely high, important changes can be ignored, whereas if the compression rate is extremely low, false alarms may increase with more memory. This implies that there is a trade-off between compression rate in graph summarization and accuracy in change detection. We propose a novel quantitative methodology to balance this trade-off to simultaneously realize reliable graph summarization and change detection. We introduce a probabilistic structure of hierarchical latent variable model into a graph, thereby designing a parameterized summary graph on the basis of the minimum description length principle. The parameter specifying the summary graph is then optimized so that the accuracy of change detection is guaranteed to suppress Type I error probability (probability of raising false alarms) to be less than a given confidence level. First, we provide a theoretical framework for connecting graph summarization with change detection. Then, we empirically demonstrate its effectiveness on synthetic and real datasets.
Handling Cost and Constraints with Off-Policy Deep Reinforcement Learning
Authors: Jared Markowitz, Jesse Silverberg, Gary Collins
Date: 2023-11-30 00:00:00
Tasks: Deep Reinforcement Learning, reinforcement-learning, Reinforcement Learning

By reusing data throughout training, off-policy deep reinforcement learning algorithms offer improved sample efficiency relative to on-policy approaches. For continuous action spaces, the most popular methods for off-policy learning include policy improvement steps where a learned state-action ($Q$) value function is maximized over selected batches of data. These updates are often paired with regularization to combat associated overestimation of $Q$ values. With an eye toward safety, we revisit this strategy in environments with "mixed-sign" reward functions; that is, with reward functions that include independent positive (incentive) and negative (cost) terms. This setting is common in real-world applications, and may be addressed with or without constraints on the cost terms. We find the combination of function approximation and a term that maximizes $Q$ in the policy update to be problematic in such environments, because systematic errors in value estimation impact the contributions from the competing terms asymmetrically. This results in overemphasis of either incentives or costs and may severely limit learning. We explore two remedies to this issue. First, consistent with prior work, we find that periodic resetting of $Q$ and policy networks can be used to reduce value estimation error and improve learning in this setting. Second, we formulate novel off-policy actor-critic methods for both unconstrained and constrained learning that do not explicitly maximize $Q$ in the policy update. We find that this second approach, when applied to continuous action spaces with mixed-sign rewards, consistently and significantly outperforms state-of-the-art methods augmented by resetting. We further find that our approach produces agents that are both competitive with popular methods overall and more reliably competent on frequently-studied control problems that do not have mixed-sign rewards.
A Comparison Between Invariant and Equivariant Classical and Quantum Graph Neural Networks
Authors: Roy T. Forestano, Marçal Comajoan Cara, Gopal Ramesh Dahale, Zhongtian Dong, Sergei Gleyzer, Daniel Justice, Kyoungchul Kong, Tom Magorsch, Konstantin T. Matchev, Katia Matcheva, Eyup B. Unlu
Date: 2023-11-30 00:00:00
Tasks: Binary Classification, Jet Tagging

Machine learning algorithms are heavily relied on to understand the vast amounts of data from high-energy particle collisions at the CERN Large Hadron Collider (LHC). The data from such collision events can naturally be represented with graph structures. Therefore, deep geometric methods, such as graph neural networks (GNNs), have been leveraged for various data analysis tasks in high-energy physics. One typical task is jet tagging, where jets are viewed as point clouds with distinct features and edge connections between their constituent particles. The increasing size and complexity of the LHC particle datasets, as well as the computational models used for their analysis, greatly motivate the development of alternative fast and efficient computational paradigms such as quantum computation. In addition, to enhance the validity and robustness of deep networks, one can leverage the fundamental symmetries present in the data through the use of invariant inputs and equivariant layers. In this paper, we perform a fair and comprehensive comparison between classical graph neural networks (GNNs) and equivariant graph neural networks (EGNNs) and their quantum counterparts: quantum graph neural networks (QGNNs) and equivariant quantum graph neural networks (EQGNN). The four architectures were benchmarked on a binary classification task to classify the parton-level particle initiating the jet. Based on their AUC scores, the quantum networks were shown to outperform the classical networks. However, seeing the computational advantage of the quantum networks in practice may have to wait for the further development of quantum technology and its associated APIs.
Targeted Reduction of Causal Models
Authors: Armin Kekić, Bernhard Schölkopf, Michel Besserve
Date: 2023-11-30 00:00:00
Tasks: Representation Learning

Why does a phenomenon occur? Addressing this question is central to most scientific inquiries and often relies on simulations of scientific models. As models become more intricate, deciphering the causes behind phenomena in high-dimensional spaces of interconnected variables becomes increasingly challenging. Causal Representation Learning (CRL) offers a promising avenue to uncover interpretable causal patterns within these simulations through an interventional lens. However, developing general CRL frameworks suitable for practical applications remains an open challenge. We introduce Targeted Causal Reduction (TCR), a method for condensing complex intervenable models into a concise set of causal factors that explain a specific target phenomenon. We propose an information theoretic objective to learn TCR from interventional data of simulations, establish identifiability for continuous variables under shift interventions and present a practical algorithm for learning TCRs. Its ability to generate interpretable high-level explanations from complex models is demonstrated on toy and mechanical systems, illustrating its potential to assist scientists in the study of complex phenomena in a broad range of disciplines.
Optimizing ZX-Diagrams with Deep Reinforcement Learning
Authors: Maximilian Nägele, Florian Marquardt
Date: 2023-11-30 00:00:00
Tasks: Decision Making, Deep Reinforcement Learning, reinforcement-learning, Reinforcement Learning

ZX-diagrams are a powerful graphical language for the description of quantum processes with applications in fundamental quantum mechanics, quantum circuit optimization, tensor network simulation, and many more. The utility of ZX-diagrams relies on a set of local transformation rules that can be applied to them without changing the underlying quantum process they describe. These rules can be exploited to optimize the structure of ZX-diagrams for a range of applications. However, finding an optimal sequence of transformation rules is generally an open problem. In this work, we bring together ZX-diagrams with reinforcement learning, a machine learning technique designed to discover an optimal sequence of actions in a decision-making problem and show that a trained reinforcement learning agent can significantly outperform other optimization techniques like a greedy strategy, simulated annealing, and state-of-the-art hand-crafted algorithms. The use of graph neural networks to encode the policy of the agent enables generalization to diagrams much bigger than seen during the training phase.
Class Distribution Shifts in Zero-Shot Learning: Learning Robust Representations
Authors: Yuli Slavutsky, Yuval Benjamini
Date: 2023-11-30 00:00:00
Tasks: Attribute, Out-of-Distribution Generalization, Person Identification, Zero-Shot Learning

Zero-shot learning methods typically assume that the new, unseen classes encountered during deployment come from the same distribution as the the classes in the training set. However, real-world scenarios often involve class distribution shifts (e.g., in age or gender for person identification), posing challenges for zero-shot classifiers that rely on learned representations from training classes. In this work, we propose and analyze a model that assumes that the attribute responsible for the shift is unknown in advance. We show that in this setting, standard training may lead to non-robust representations. To mitigate this, we develop an algorithm for learning robust representations in which (a) synthetic data environments are constructed via hierarchical sampling, and (b) environment balancing penalization, inspired by out-of-distribution problems, is applied. We show that our algorithm improves generalization to diverse class distributions in both simulations and experiments on real-world datasets.
Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking
Authors: Jiaxian Yan, Zaixi Zhang, Kai Zhang, Qi Liu
Date: 2023-11-30 00:00:00
Tasks: Blind Docking, GPU, Molecular Docking

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.
Learning Radio Environments by Differentiable Ray Tracing
Authors: Jakob Hoydis, Fayçal Aït Aoudia, Sebastian Cammerer, Florian Euchner, Merlin Nimier-David, Stephan ten Brink, Alexander Keller
Date: 2023-11-30 00:00:00

Ray tracing (RT) is instrumental in 6G research in order to generate spatially-consistent and environment-specific channel impulse responses (CIRs). While acquiring accurate scene geometries is now relatively straightforward, determining material characteristics requires precise calibration using channel measurements. We therefore introduce a novel gradient-based calibration method, complemented by differentiable parametrizations of material properties, scattering and antenna patterns. Our method seamlessly integrates with differentiable ray tracers that enable the computation of derivatives of CIRs with respect to these parameters. Essentially, we approach field computation as a large computational graph wherein parameters are trainable akin to weights of a neural network (NN). We have validated our method using both synthetic data and real-world indoor channel measurements, employing a distributed multiple-input multiple-output (MIMO) channel sounder.
Can semi-supervised learning use all the data effectively? A lower bound perspective
Authors: Alexandru Ţifrea, Gizem Yüce, Amartya Sanyal, Fanny Yang
Date: 2023-11-30 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: All

Prior works have shown that semi-supervised learning algorithms can leverage unlabeled data to improve over the labeled sample complexity of supervised learning (SL) algorithms. However, existing theoretical analyses focus on regimes where the unlabeled data is sufficient to learn a good decision boundary using unsupervised learning (UL) alone. This begs the question: Can SSL algorithms simultaneously improve upon both UL and SL? To this end, we derive a tight lower bound for 2-Gaussian mixture models that explicitly depends on the labeled and the unlabeled dataset size as well as the signal-to-noise ratio of the mixture distribution. Surprisingly, our result implies that no SSL algorithm can improve upon the minimax-optimal statistical error rates of SL or UL algorithms for these distributions. Nevertheless, we show empirically on real-world data that SSL algorithms can still outperform UL and SL methods. Therefore, our work suggests that, while proving performance gains for SSL algorithms is possible, it requires careful tracking of constants.
HOT: Higher-Order Dynamic Graph Representation Learning with Efficient Transformers
Authors: Maciej Besta, Afonso Claudino Catarino, Lukas Gianinazzi, Nils Blach, Piotr Nyczyk, Hubert Niewiadomski, Torsten Hoefler
Date: 2023-11-30 00:00:00
Tasks: Dynamic Link Prediction, Graph Representation Learning, Link Prediction, Prediction, Representation Learning

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.
Detecting Anomalous Network Communication Patterns Using Graph Convolutional Networks
Authors: Yizhak Vaisman, Gilad Katz, Yuval Elovici, Asaf Shabtai
Date: 2023-11-30 00:00:00

To protect an organizations' endpoints from sophisticated cyberattacks, advanced detection methods are required. In this research, we present GCNetOmaly: a graph convolutional network (GCN)-based variational autoencoder (VAE) anomaly detector trained on data that include connection events among internal and external machines. As input, the proposed GCN-based VAE model receives two matrices: (i) the normalized adjacency matrix, which represents the connections among the machines, and (ii) the feature matrix, which includes various features (demographic, statistical, process-related, and Node2vec structural features) that are used to profile the individual nodes/machines. After training the model on data collected for a predefined time window, the model is applied on the same data; the reconstruction score obtained by the model for a given machine then serves as the machine's anomaly score. GCNetOmaly was evaluated on real, large-scale data logged by Carbon Black EDR from a large financial organization's automated teller machines (ATMs) as well as communication with Active Directory (AD) servers in two setups: unsupervised and supervised. The results of our evaluation demonstrate GCNetOmaly's effectiveness in detecting anomalous behavior of machines on unsupervised data.
Combining deep generative models with extreme value theory for synthetic hazard simulation: a multivariate and spatially coherent approach
Authors: Alison Peard, Jim Hall
Date: 2023-11-30 00:00:00

Climate hazards can cause major disasters when they occur simultaneously as compound hazards. To understand the distribution of climate risk and inform adaptation policies, scientists need to simulate a large number of physically realistic and spatially coherent events. Current methods are limited by computational constraints and the probabilistic spatial distribution of compound events is not given sufficient attention. The bottleneck in current approaches lies in modelling the dependence structure between variables, as inference on parametric models suffers from the curse of dimensionality. Generative adversarial networks (GANs) are well-suited to such a problem due to their ability to implicitly learn the distribution of data in high-dimensional settings. We employ a GAN to model the dependence structure for daily maximum wind speed, significant wave height, and total precipitation over the Bay of Bengal, combining this with traditional extreme value theory for controlled extrapolation of the tails. Once trained, the model can be used to efficiently generate thousands of realistic compound hazard events, which can inform climate risk assessments for climate adaptation and disaster preparedness. The method developed is flexible and transferable to other multivariate and spatial climate datasets.