pwc-archive/papers-with-abstracts huggingface dataset:
Graph Multi-Similarity Learning for Molecular Property Prediction
Authors: Hao Xu, Zhengyang Zhou, Pengyu Hong
Date: 2024-01-31 00:00:00
Tasks: Attribute, Contrastive Learning, Drug Discovery, Molecular Property Prediction, molecular representation, Prediction, Property Prediction, Representation Learning

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.
IGCN: Integrative Graph Convolution Networks for patient level insights and biomarker discovery in multi-omics integration
Authors: Cagri Ozdemir, Mohammad Al Olaimat, Yashu Vashishath, Serdar Bozdag, Alzheimer's Disease Neuroimaging Initiative
Date: 2024-01-31 00:00:00
Tasks: Node Classification

Developing computational tools for integrative analysis across multiple types of omics data has been of immense importance in cancer molecular biology and precision medicine research. While recent advancements have yielded integrative prediction solutions for multi-omics data, these methods lack a comprehensive and cohesive understanding of the rationale behind their specific predictions. To shed light on personalized medicine and unravel previously unknown characteristics within integrative analysis of multi-omics data, we introduce a novel integrative neural network approach for cancer molecular subtype and biomedical classification applications, named Integrative Graph Convolutional Networks (IGCN). IGCN can identify which types of omics receive more emphasis for each patient to predict a certain class. Additionally, IGCN has the capability to pinpoint significant biomarkers from a range of omics data types. To demonstrate the superiority of IGCN, we compare its performance with other state-of-the-art approaches across different cancer subtype and biomedical classification tasks.
Graph Contrastive Learning with Cohesive Subgraph Awareness
Authors: Yucheng Wu, Leye Wang, Xiao Han, Han-Jia Ye
Date: 2024-01-31 00:00:00
Tasks: Contrastive Learning, Graph Classification, Graph Learning, Graph Representation Learning, Representation Learning

Graph contrastive learning (GCL) has emerged as a state-of-the-art strategy for learning representations of diverse graphs including social and biomedical networks. GCL widely uses stochastic graph topology augmentation, such as uniform node dropping, to generate augmented graphs. However, such stochastic augmentations may severely damage the intrinsic properties of a graph and deteriorate the following representation learning process. We argue that incorporating an awareness of cohesive subgraphs during the graph augmentation and learning processes has the potential to enhance GCL performance. To this end, we propose a novel unified framework called CTAug, to seamlessly integrate cohesion awareness into various existing GCL mechanisms. In particular, CTAug comprises two specialized modules: topology augmentation enhancement and graph learning enhancement. The former module generates augmented graphs that carefully preserve cohesion properties, while the latter module bolsters the graph encoder's ability to discern subgraph patterns. Theoretical analysis shows that CTAug can strictly improve existing GCL mechanisms. Empirical experiments verify that CTAug can achieve state-of-the-art performance for graph representation learning, especially for graphs with high degrees. The code is available at https://doi.org/10.5281/zenodo.10594093, or https://github.com/wuyucheng2002/CTAug.
Scavenging Hyena: Distilling Transformers into Long Convolution Models
Authors: Tokiniaina Raharison Ralambomihanta, Shahrad Mohammadzadeh, Mohammad Sami Nur Islam, Wassim Jabbour, Laurence Liang
Date: 2024-01-31 00:00:00
Tasks: Knowledge Distillation

The rapid evolution of Large Language Models (LLMs), epitomized by architectures like GPT-4, has reshaped the landscape of natural language processing. This paper introduces a pioneering approach to address the efficiency concerns associated with LLM pre-training, proposing the use of knowledge distillation for cross-architecture transfer. Leveraging insights from the efficient Hyena mechanism, our method replaces attention heads in transformer models by Hyena, offering a cost-effective alternative to traditional pre-training while confronting the challenge of processing long contextual information, inherent in quadratic attention mechanisms. Unlike conventional compression-focused methods, our technique not only enhances inference speed but also surpasses pre-training in terms of both accuracy and efficiency. In the era of evolving LLMs, our work contributes to the pursuit of sustainable AI solutions, striking a balance between computational power and environmental impact.
Tensor-based process control and monitoring for semiconductor manufacturing with unstable disturbances
Authors: YanRong Li, Juan Du, Fugee Tsung, Wei Jiang
Date: 2024-01-31 00:00:00
Tasks: parameter estimation

With the development and popularity of sensors installed in manufacturing systems, complex data are collected during manufacturing processes, which brings challenges for traditional process control methods. This paper proposes a novel process control and monitoring method for the complex structure of high-dimensional image-based overlay errors (modeled in tensor form), which are collected in semiconductor manufacturing processes. The proposed method aims to reduce overlay errors using limited control recipes. We first build a high-dimensional process model and propose different tensor-on-vector regression algorithms to estimate parameters in the model to alleviate the curse of dimensionality. Then, based on the estimate of tensor parameters, the exponentially weighted moving average (EWMA) controller for tensor data is designed whose stability is theoretically guaranteed. Considering the fact that low-dimensional control recipes cannot compensate for all high-dimensional disturbances on the image, control residuals are monitored to prevent significant drifts of uncontrollable high-dimensional disturbances. Through extensive simulations and real case studies, the performances of parameter estimation algorithms and the EWMA controller in tensor space are evaluated. Compared with existing image-based feedback controllers, the superiority of our method is verified especially when disturbances are not stable.
Effective Multi-Stage Training Model For Edge Computing Devices In Intrusion Detection
Authors: Thua Huynh Trong, Thanh Nguyen Hoang
Date: 2024-01-31 00:00:00
Tasks: Edge-computing, Intrusion Detection, Model Compression

Intrusion detection poses a significant challenge within expansive and persistently interconnected environments. As malicious code continues to advance and sophisticated attack methodologies proliferate, various advanced deep learning-based detection approaches have been proposed. Nevertheless, the complexity and accuracy of intrusion detection models still need further enhancement to render them more adaptable to diverse system categories, particularly within resource-constrained devices, such as those embedded in edge computing systems. This research introduces a three-stage training paradigm, augmented by an enhanced pruning methodology and model compression techniques. The objective is to elevate the system's effectiveness, concurrently maintaining a high level of accuracy for intrusion detection. Empirical assessments conducted on the UNSW-NB15 dataset evince that this solution notably reduces the model's dimensions, while upholding accuracy levels equivalent to similar proposals.
Towards Understanding Variants of Invariant Risk Minimization through the Lens of Calibration
Authors: Kotaro Yoshida, Hiroki Naganuma
Date: 2024-01-31 00:00:00
Tasks: Out-of-Distribution Generalization

Machine learning models traditionally assume that training and test data are independently and identically distributed. However, in real-world applications, the test distribution often differs from training. This problem, known as out-of-distribution (OOD) generalization, challenges conventional models. Invariant Risk Minimization (IRM) emerges as a solution that aims to identify invariant features across different environments to enhance OOD robustness. However, IRM's complexity, particularly its bi-level optimization, has led to the development of various approximate methods. Our study investigates these approximate IRM techniques, using the consistency and variance of calibration across environments as metrics to measure the invariance aimed for by IRM. Calibration, which measures the reliability of model prediction, serves as an indicator of whether models effectively capture environment-invariant features by showing how uniformly over-confident the model remains across varied environments. Through a comparative analysis of datasets with distributional shifts, we observe that Information Bottleneck-based IRM achieves consistent calibration across different environments. This observation suggests that information compression techniques, such as IB, are potentially effective in achieving model invariance. Furthermore, our empirical evidence indicates that models exhibiting consistent calibration across environments are also well-calibrated. This demonstrates that invariance and cross-environment calibration are empirically equivalent. Additionally, we underscore the necessity for a systematic approach to evaluating OOD generalization. This approach should move beyond traditional metrics, such as accuracy and F1 scores, which fail to account for the model's degree of over-confidence, and instead focus on the nuanced interplay between accuracy, calibration, and model invariance.
Gradient-Free Score-Based Sampling Methods with Ensembles
Authors: Bryan Riel, Tobias Bischoff
Date: 2024-01-31 00:00:00

Recent developments in generative modeling have utilized score-based methods coupled with stochastic differential equations to sample from complex probability distributions. However, these and other performant sampling methods generally require gradients of the target probability distribution, which can be unavailable or computationally prohibitive in many scientific and engineering applications. Here, we introduce ensembles within score-based sampling methods to develop gradient-free approximate sampling techniques that leverage the collective dynamics of particle ensembles to compute approximate reverse diffusion drifts. We introduce the underlying methodology, emphasizing its relationship with generative diffusion models and the previously introduced F\"ollmer sampler. We demonstrate the efficacy of the ensemble strategies through various examples, ranging from low- to medium-dimensionality sampling problems, including multi-modal and highly non-Gaussian probability distributions, and provide comparisons to traditional methods like the No-U-Turn Sampler. Additionally, we showcase these strategies in the context of a high-dimensional Bayesian inversion problem within the geophysical sciences. Our findings highlight the potential of ensemble strategies for modeling complex probability distributions in situations where gradients are unavailable.
Game-Theoretic Unlearnable Example Generator
Authors: Shuang Liu, Yihan Wang, Xiao-Shan Gao
Date: 2024-01-31 00:00:00
Tasks: Data Poisoning

Unlearnable example attacks are data poisoning attacks aiming to degrade the clean test accuracy of deep learning by adding imperceptible perturbations to the training samples, which can be formulated as a bi-level optimization problem. However, directly solving this optimization problem is intractable for deep neural networks. In this paper, we investigate unlearnable example attacks from a game-theoretic perspective, by formulating the attack as a nonzero sum Stackelberg game. First, the existence of game equilibria is proved under the normal setting and the adversarial training setting. It is shown that the game equilibrium gives the most powerful poison attack in that the victim has the lowest test accuracy among all networks within the same hypothesis space, when certain loss functions are used. Second, we propose a novel attack method, called the Game Unlearnable Example (GUE), which has three main gradients. (1) The poisons are obtained by directly solving the equilibrium of the Stackelberg game with a first-order algorithm. (2) We employ an autoencoder-like generative network model as the poison attacker. (3) A novel payoff function is introduced to evaluate the performance of the poison. Comprehensive experiments demonstrate that GUE can effectively poison the model in various scenarios. Furthermore, the GUE still works by using a relatively small percentage of the training data to train the generator, and the poison generator can generalize to unseen data well. Our implementation code can be found at https://github.com/hong-xian/gue.
CaMU: Disentangling Causal Effects in Deep Model Unlearning
Authors: Shaofei Shen, Chenhao Zhang, Alina Bialkowski, Weitong Chen, Miao Xu
Date: 2024-01-30 00:00:00
Tasks: Machine Unlearning, model

Machine unlearning requires removing the information of forgetting data while keeping the necessary information of remaining data. Despite recent advancements in this area, existing methodologies mainly focus on the effect of removing forgetting data without considering the negative impact this can have on the information of the remaining data, resulting in significant performance degradation after data removal. Although some methods try to repair the performance of remaining data after removal, the forgotten information can also return after repair. Such an issue is due to the intricate intertwining of the forgetting and remaining data. Without adequately differentiating the influence of these two kinds of data on the model, existing algorithms take the risk of either inadequate removal of the forgetting data or unnecessary loss of valuable information from the remaining data. To address this shortcoming, the present study undertakes a causal analysis of the unlearning and introduces a novel framework termed Causal Machine Unlearning (CaMU). This framework adds intervention on the information of remaining data to disentangle the causal effects between forgetting data and remaining data. Then CaMU eliminates the causal impact associated with forgetting data while concurrently preserving the causal relevance of the remaining data. Comprehensive empirical results on various datasets and models suggest that CaMU enhances performance on the remaining data and effectively minimizes the influences of forgetting data. Notably, this work is the first to interpret deep model unlearning tasks from a new perspective of causality and provide a solution based on causal analysis, which opens up new possibilities for future research in deep model unlearning.
Rendering Wireless Environments Useful for Gradient Estimators: A Zero-Order Stochastic Federated Learning Method
Authors: Elissa Mhanna, Mohamad Assaad
Date: 2024-01-30 00:00:00
Tasks: Federated Learning

Cross-device federated learning (FL) is a growing machine learning setting whereby multiple edge devices collaborate to train a model without disclosing their raw data. With the great number of mobile devices participating in more FL applications via the wireless environment, the practical implementation of these applications will be hindered due to the limited uplink capacity of devices, causing critical bottlenecks. In this work, we propose a novel doubly communication-efficient zero-order (ZO) method with a one-point gradient estimator that replaces communicating long vectors with scalar values and that harnesses the nature of the wireless communication channel, overcoming the need to know the channel state coefficient. It is the first method that includes the wireless channel in the learning algorithm itself instead of wasting resources to analyze it and remove its impact. We then offer a thorough analysis of the proposed zero-order federated learning (ZOFL) framework and prove that our method converges \textit{almost surely}, which is a novel result in nonconvex ZO optimization. We further prove a convergence rate of $O(\frac{1}{\sqrt[3]{K}})$ in the nonconvex setting. We finally demonstrate the potential of our algorithm with experimental results.
Solving Boltzmann Optimization Problems with Deep Learning
Authors: Fiona Knoll, John T. Daly, Jess J. Meyer
Date: 2024-01-30 00:00:00
Tasks: Deep Learning

Decades of exponential scaling in high performance computing (HPC) efficiency is coming to an end. Transistor based logic in complementary metal-oxide semiconductor (CMOS) technology is approaching physical limits beyond which further miniaturization will be impossible. Future HPC efficiency gains will necessarily rely on new technologies and paradigms of compute. The Ising model shows particular promise as a future framework for highly energy efficient computation. Ising systems are able to operate at energies approaching thermodynamic limits for energy consumption of computation. Ising systems can function as both logic and memory. Thus, they have the potential to significantly reduce energy costs inherent to CMOS computing by eliminating costly data movement. The challenge in creating Ising-based hardware is in optimizing useful circuits that produce correct results on fundamentally nondeterministic hardware. The contribution of this paper is a novel machine learning approach, a combination of deep neural networks and random forests, for efficiently solving optimization problems that minimize sources of error in the Ising model. In addition, we provide a process to express a Boltzmann probability optimization problem as a supervised machine learning problem.
Reproducibility, energy efficiency and performance of pseudorandom number generators in machine learning: a comparative study of python, numpy, tensorflow, and pytorch implementations
Authors: Benjamin Antunes, David R. C Hill
Date: 2024-01-30 00:00:00

Pseudo-Random Number Generators (PRNGs) have become ubiquitous in machine learning technologies because they are interesting for numerous methods. The field of machine learning holds the potential for substantial advancements across various domains, as exemplified by recent breakthroughs in Large Language Models (LLMs). However, despite the growing interest, persistent concerns include issues related to reproducibility and energy consumption. Reproducibility is crucial for robust scientific inquiry and explainability, while energy efficiency underscores the imperative to conserve finite global resources. This study delves into the investigation of whether the leading Pseudo-Random Number Generators (PRNGs) employed in machine learning languages, libraries, and frameworks uphold statistical quality and numerical reproducibility when compared to the original C implementation of the respective PRNG algorithms. Additionally, we aim to evaluate the time efficiency and energy consumption of various implementations. Our experiments encompass Python, NumPy, TensorFlow, and PyTorch, utilizing the Mersenne Twister, PCG, and Philox algorithms. Remarkably, we verified that the temporal performance of machine learning technologies closely aligns with that of C-based implementations, with instances of achieving even superior performances. On the other hand, it is noteworthy that ML technologies consumed only 10% more energy than their C-implementation counterparts. However, while statistical quality was found to be comparable, achieving numerical reproducibility across different platforms for identical seeds and algorithms was not achieved.
Multipath parsing in the brain
Authors: Berta Franzluebbers, Donald Dunagan, Miloš Stanojević, Jan Buys, John T. Hale
Date: 2024-01-31 00:00:00

Humans understand sentences word-by-word, in the order that they hear them. This incrementality entails resolving temporary ambiguities about syntactic relationships. We investigate how humans process these syntactic ambiguities by correlating predictions from incremental generative dependency parsers with timecourse data from people undergoing functional neuroimaging while listening to an audiobook. In particular, we compare competing hypotheses regarding the number of developing syntactic analyses in play during word-by-word comprehension: one vs more than one. This comparison involves evaluating syntactic surprisal from a state-of-the-art dependency parser with LLM-adapted encodings against an existing fMRI dataset. In both English and Chinese data, we find evidence for multipath parsing. Brain regions associated with this multipath effect include bilateral superior temporal gyrus.
Desiderata for the Context Use of Question Answering Systems
Authors: Sagi Shaier, Lawrence E Hunter, Katharina von der Wense
Date: 2024-01-31 00:00:00
Tasks: Question Answering

Prior work has uncovered a set of common problems in state-of-the-art context-based question answering (QA) systems: a lack of attention to the context when the latter conflicts with a model's parametric knowledge, little robustness to noise, and a lack of consistency with their answers. However, most prior work focus on one or two of those problems in isolation, which makes it difficult to see trends across them. We aim to close this gap, by first outlining a set of -- previously discussed as well as novel -- desiderata for QA models. We then survey relevant analysis and methods papers to provide an overview of the state of the field. The second part of our work presents experiments where we evaluate 15 QA systems on 5 datasets according to all desiderata at once. We find many novel trends, including (1) systems that are less susceptible to noise are not necessarily more consistent with their answers when given irrelevant context; (2) most systems that are more susceptible to noise are more likely to correctly answer according to a context that conflicts with their parametric knowledge; and (3) the combination of conflicting knowledge and noise can reduce system performance by up to 96%. As such, our desiderata help increase our understanding of how these models work and reveal potential avenues for improvements.