pwc-archive/papers-with-abstracts huggingface dataset:
A Mapper Algorithm with implicit intervals and its optimization
Authors: Yuyang Tao, Shufei Ge
Date: 2024-12-16 00:00:00

The Mapper algorithm is an essential tool for visualizing complex, high dimensional data in topology data analysis (TDA) and has been widely used in biomedical research. It outputs a combinatorial graph whose structure implies the shape of the data. However,the need for manual parameter tuning and fixed intervals, along with fixed overlapping ratios may impede the performance of the standard Mapper algorithm. Variants of the standard Mapper algorithms have been developed to address these limitations, yet most of them still require manual tuning of parameters. Additionally, many of these variants, including the standard version found in the literature, were built within a deterministic framework and overlooked the uncertainty inherent in the data. To relax these limitations, in this work, we introduce a novel framework that implicitly represents intervals through a hidden assignment matrix, enabling automatic parameter optimization via stochastic gradient descent. In this work, we develop a soft Mapper framework based on a Gaussian mixture model(GMM) for flexible and implicit interval construction. We further illustrate the robustness of the soft Mapper algorithm by introducing the Mapper graph mode as a point estimation for the output graph. Moreover, a stochastic gradient descent algorithm with a specific topological loss function is proposed for optimizing parameters in the model. Both simulation and application studies demonstrate its effectiveness in capturing the underlying topological structures. In addition, the application to an RNA expression dataset obtained from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB) successfully identifies a distinct subgroup of Alzheimer's Disease.
QPruner: Probabilistic Decision Quantization for Structured Pruning in Large Language Models
Authors: Changhai Zhou, Yuhua Zhou, Shijie Han, Qian Qiao, Hongguang Li
Date: 2024-12-16 00:00:00
Tasks: Bayesian Optimization, Quantization

The rise of large language models (LLMs) has significantly advanced various natural language processing (NLP) tasks. However, the resource demands of these models pose substantial challenges. Structured pruning is an effective approach to reducing model size, but it often results in significant accuracy degradation, necessitating parameter updates to adapt. Unfortunately, such fine-tuning requires substantial memory, which limits its applicability. To address these challenges, we introduce quantization into the structured pruning framework to reduce memory consumption during both fine-tuning and inference. However, the combined errors from pruning and quantization increase the difficulty of fine-tuning, requiring a more refined quantization scheme. To this end, we propose QPruner, a novel framework that employs structured pruning to reduce model size, followed by a layer-wise mixed-precision quantization scheme. Quantization precisions are assigned to each layer based on their importance to the target task, and Bayesian optimization is employed to refine precision allocation strategies, ensuring a balance between model accuracy and memory efficiency. Extensive experiments on benchmark datasets demonstrate that QPruner significantly outperforms existing methods in memory savings while maintaining or improving model performance.
The dark side of the forces: assessing non-conservative force models for atomistic machine learning
Authors: Filippo Bigi, Marcel Langer, Michele Ceriotti
Date: 2024-12-16 00:00:00
Tasks: Computational chemistry, Computational Efficiency

The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous enforcement of symmetry and conservation laws has traditionally been considered essential. For this reason, interatomic forces are usually computed as the derivatives of the potential energy, ensuring energy conservation. Several recent works have questioned this physically constrained approach, suggesting that directly predicting the forces yields a better trade-off between accuracy and computational efficiency -- and that energy conservation can be learned during training. This work investigates the applicability of such non-conservative models in microscopic simulations. We identify and demonstrate several fundamental issues, from ill-defined convergence of geometry optimization to instability in various types of molecular dynamics. Contrary to the case of rotational symmetry, energy conservation is hard to learn, monitor, and correct for. The best approach to exploit the acceleration afforded by direct force prediction might be to use it in tandem with a conservative model, reducing -- rather than eliminating -- the additional cost of backpropagation, but avoiding the pathological behavior associated with non-conservative forces.
Learning Massive-scale Partial Correlation Networks in Clinical Multi-omics Studies with HP-ACCORD
Authors: Sungdong Lee, Joshua Bang, Youngrae Kim, Hyungwon Choi, Sang-Yun Oh, Joong-Ho Won
Date: 2024-12-16 00:00:00
Tasks: Specificity

Graphical model estimation from modern multi-omics data requires a balance between statistical estimation performance and computational scalability. We introduce a novel pseudolikelihood-based graphical model framework that reparameterizes the target precision matrix while preserving sparsity pattern and estimates it by minimizing an $\ell_1$-penalized empirical risk based on a new loss function. The proposed estimator maintains estimation and selection consistency in various metrics under high-dimensional assumptions. The associated optimization problem allows for a provably fast computation algorithm using a novel operator-splitting approach and communication-avoiding distributed matrix multiplication. A high-performance computing implementation of our framework was tested in simulated data with up to one million variables demonstrating complex dependency structures akin to biological networks. Leveraging this scalability, we estimated partial correlation network from a dual-omic liver cancer data set. The co-expression network estimated from the ultrahigh-dimensional data showed superior specificity in prioritizing key transcription factors and co-activators by excluding the impact of epigenomic regulation, demonstrating the value of computational scalability in multi-omic data analysis. %derived from the gene expression data.
THESAURUS: Contrastive Graph Clustering by Swapping Fused Gromov-Wasserstein Couplings
Authors: Bowen Deng, Tong Wang, Lele Fu, Sheng Huang, Chuan Chen, Tao Zhang
Date: 2024-12-16 00:00:00
Tasks: Clustering, Graph Clustering, Node Clustering

Graph node clustering is a fundamental unsupervised task. Existing methods typically train an encoder through selfsupervised learning and then apply K-means to the encoder output. Some methods use this clustering result directly as the final assignment, while others initialize centroids based on this initial clustering and then finetune both the encoder and these learnable centroids. However, due to their reliance on K-means, these methods inherit its drawbacks when the cluster separability of encoder output is low, facing challenges from the Uniform Effect and Cluster Assimilation. We summarize three reasons for the low cluster separability in existing methods: (1) lack of contextual information prevents discrimination between similar nodes from different clusters; (2) training tasks are not sufficiently aligned with the downstream clustering task; (3) the cluster information in the graph structure is not appropriately exploited. To address these issues, we propose conTrastive grapH clustEring by SwApping fUsed gRomov-wasserstein coUplingS (THESAURUS). Our method introduces semantic prototypes to provide contextual information, and employs a cross-view assignment prediction pretext task that aligns well with the downstream clustering task. Additionally, it utilizes Gromov-Wasserstein Optimal Transport (GW-OT) along with the proposed prototype graph to thoroughly exploit cluster information in the graph structure. To adapt to diverse real-world data, THESAURUS updates the prototype graph and the prototype marginal distribution in OT by using momentum. Extensive experiments demonstrate that THESAURUS achieves higher cluster separability than the prior art, effectively mitigating the Uniform Effect and Cluster Assimilation issues
Probabilities-Informed Machine Learning
Authors: Mohsen Rashki
Date: 2024-12-16 00:00:00
Tasks: Denoising, Experimental Design, Image Denoising, regression

Machine learning (ML) has emerged as a powerful tool for tackling complex regression and classification tasks, yet its success often hinges on the quality of training data. This study introduces an ML paradigm inspired by domain knowledge of the structure of output function, akin to physics-informed ML, but rooted in probabilistic principles rather than physical laws. The proposed approach integrates the probabilistic structure of the target variable (such as its cumulative distribution function) into the training process. This probabilistic information is obtained from historical data or estimated using structural reliability methods during experimental design. By embedding domain-specific probabilistic insights into the learning process, the technique enhances model accuracy and mitigates risks of overfitting and underfitting. Applications in regression, image denoising, and classification demonstrate the approach's effectiveness in addressing real-world problems.
On the Ability of Deep Networks to Learn Symmetries from Data: A Neural Kernel Theory
Authors: Andrea Perin, Stephane Deny
Date: 2024-12-16 00:00:00
Tasks: Rotated MNIST

Symmetries (transformations by group actions) are present in many datasets, and leveraging them holds significant promise for improving predictions in machine learning. In this work, we aim to understand when and how deep networks can learn symmetries from data. We focus on a supervised classification paradigm where data symmetries are only partially observed during training: some classes include all transformations of a cyclic group, while others include only a subset. We ask: can deep networks generalize symmetry invariance to the partially sampled classes? In the infinite-width limit, where kernel analogies apply, we derive a neural kernel theory of symmetry learning to address this question. The group-cyclic nature of the dataset allows us to analyze the spectrum of neural kernels in the Fourier domain; here we find a simple characterization of the generalization error as a function of the interaction between class separation (signal) and class-orbit density (noise). We observe that generalization can only be successful when the local structure of the data prevails over its non-local, symmetric, structure, in the kernel space defined by the architecture. This occurs when (1) classes are sufficiently distinct and (2) class orbits are sufficiently dense. Our framework also applies to equivariant architectures (e.g., CNNs), and recovers their success in the special case where the architecture matches the inherent symmetry of the data. Empirically, our theory reproduces the generalization failure of finite-width networks (MLP, CNN, ViT) trained on partially observed versions of rotated-MNIST. We conclude that conventional networks trained with supervision lack a mechanism to learn symmetries that have not been explicitly embedded in their architecture a priori. Our framework could be extended to guide the design of architectures and training procedures able to learn symmetries from data.
Constructing Confidence Intervals for Average Treatment Effects from Multiple Datasets
Authors: Yuxin Wang, Maresa Schröder, Dennis Frauen, Jonas Schweisthal, Konstantin Hess, Stefan Feuerriegel
Date: 2024-12-16 00:00:00
Tasks: Uncertainty Quantification, valid

Constructing confidence intervals (CIs) for the average treatment effect (ATE) from patient records is crucial to assess the effectiveness and safety of drugs. However, patient records typically come from different hospitals, thus raising the question of how multiple observational datasets can be effectively combined for this purpose. In our paper, we propose a new method that estimates the ATE from multiple observational datasets and provides valid CIs. Our method makes little assumptions about the observational datasets and is thus widely applicable in medical practice. The key idea of our method is that we leverage prediction-powered inferences and thereby essentially `shrink' the CIs so that we offer more precise uncertainty quantification as compared to na\"ive approaches. We further prove the unbiasedness of our method and the validity of our CIs. We confirm our theoretical results through various numerical experiments. Finally, we provide an extension of our method for constructing CIs from combinations of experimental and observational datasets.
Explicit and Implicit Graduated Optimization in Deep Neural Networks
Authors: Naoki Sato, Hideaki Iiduka
Date: 2024-12-16 00:00:00
Tasks: global-optimization, image-classification, Image Classification, Scheduling

Graduated optimization is a global optimization technique that is used to minimize a multimodal nonconvex function by smoothing the objective function with noise and gradually refining the solution. This paper experimentally evaluates the performance of the explicit graduated optimization algorithm with an optimal noise scheduling derived from a previous study and discusses its limitations. It uses traditional benchmark functions and empirical loss functions for modern neural network architectures for evaluating. In addition, this paper extends the implicit graduated optimization algorithm, which is based on the fact that stochastic noise in the optimization process of SGD implicitly smooths the objective function, to SGD with momentum, analyzes its convergence, and demonstrates its effectiveness through experiments on image classification tasks with ResNet architectures.
"They've Stolen My GPL-Licensed Model!": Toward Standardized and Transparent Model Licensing
Authors: Moming Duan, Rui Zhao, Linshan Jiang, Nigel Shadbolt, Bingsheng He
Date: 2024-12-16 00:00:00
Tasks: model

As model parameter sizes reach the billion-level range and their training consumes zettaFLOPs of computation, components reuse and collaborative development are become increasingly prevalent in the Machine Learning (ML) community. These components, including models, software, and datasets, may originate from various sources and be published under different licenses, which govern the use and distribution of licensed works and their derivatives. However, commonly chosen licenses, such as GPL and Apache, are software-specific and are not clearly defined or bounded in the context of model publishing. Meanwhile, the reused components may also have free-content licenses and model licenses, which pose a potential risk of license noncompliance and rights infringement within the model production workflow. In this paper, we propose addressing the above challenges along two lines: 1) For license analysis, we have developed a new vocabulary for ML workflow management and encoded license rules to enable ontological reasoning for analyzing rights granting and compliance issues. 2) For standardized model publishing, we have drafted a set of model licenses that provide flexible options to meet the diverse needs of model publishing. Our analysis tool is built on Turtle language and Notation3 reasoning engine, envisioned as a first step toward Linked Open Model Production Data. We have also encoded our proposed model licenses into rules and demonstrated the effects of GPL and other commonly used licenses in model publishing, along with the flexibility advantages of our licenses, through comparisons and experiments.
NoteContrast: Contrastive Language-Diagnostic Pretraining for Medical Text
Authors: Prajwal Kailas, Max Homilius, Rahul C. Deo, Calum A. MacRae
Date: 2024-12-16 00:00:00
Tasks: Diagnostic, Medical Diagnosis, Specificity

Accurate diagnostic coding of medical notes is crucial for enhancing patient care, medical research, and error-free billing in healthcare organizations. Manual coding is a time-consuming task for providers, and diagnostic codes often exhibit low sensitivity and specificity, whereas the free text in medical notes can be a more precise description of a patients status. Thus, accurate automated diagnostic coding of medical notes has become critical for a learning healthcare system. Recent developments in long-document transformer architectures have enabled attention-based deep-learning models to adjudicate medical notes. In addition, contrastive loss functions have been used to jointly pre-train large language and image models with noisy labels. To further improve the automated adjudication of medical notes, we developed an approach based on i) models for ICD-10 diagnostic code sequences using a large real-world data set, ii) large language models for medical notes, and iii) contrastive pre-training to build an integrated model of both ICD-10 diagnostic codes and corresponding medical text. We demonstrate that a contrastive approach for pre-training improves performance over prior state-of-the-art models for the MIMIC-III-50, MIMIC-III-rare50, and MIMIC-III-full diagnostic coding tasks.
Vertical Federated Unlearning via Backdoor Certification
Authors: Mengde Han, Tianqing Zhu, Lefeng Zhang, Huan Huo, Wanlei Zhou
Date: 2024-12-16 00:00:00
Tasks: Federated Learning, Vertical Federated Learning

Vertical Federated Learning (VFL) offers a novel paradigm in machine learning, enabling distinct entities to train models cooperatively while maintaining data privacy. This method is particularly pertinent when entities possess datasets with identical sample identifiers but diverse attributes. Recent privacy regulations emphasize an individual's \emph{right to be forgotten}, which necessitates the ability for models to unlearn specific training data. The primary challenge is to develop a mechanism to eliminate the influence of a specific client from a model without erasing all relevant data from other clients. Our research investigates the removal of a single client's contribution within the VFL framework. We introduce an innovative modification to traditional VFL by employing a mechanism that inverts the typical learning trajectory with the objective of extracting specific data contributions. This approach seeks to optimize model performance using gradient ascent, guided by a pre-defined constrained model. We also introduce a backdoor mechanism to verify the effectiveness of the unlearning procedure. Our method avoids fully accessing the initial training data and avoids storing parameter updates. Empirical evidence shows that the results align closely with those achieved by retraining from scratch. Utilizing gradient ascent, our unlearning approach addresses key challenges in VFL, laying the groundwork for future advancements in this domain. All the code and implementations related to this paper are publicly available at https://github.com/mengde-han/VFL-unlearn.
Mining In-distribution Attributes in Outliers for Out-of-distribution Detection
Authors: Yutian Lei, Luping Ji, Pei Liu
Date: 2024-12-16 00:00:00
Tasks: Out-of-Distribution Detection, Out of Distribution (OOD) Detection

Out-of-distribution (OOD) detection is indispensable for deploying reliable machine learning systems in real-world scenarios. Recent works, using auxiliary outliers in training, have shown good potential. However, they seldom concern the intrinsic correlations between in-distribution (ID) and OOD data. In this work, we discover an obvious correlation that OOD data usually possesses significant ID attributes. These attributes should be factored into the training process, rather than blindly suppressed as in previous approaches. Based on this insight, we propose a structured multi-view-based out-of-distribution detection learning (MVOL) framework, which facilitates rational handling of the intrinsic in-distribution attributes in outliers. We provide theoretical insights on the effectiveness of MVOL for OOD detection. Extensive experiments demonstrate the superiority of our framework to others. MVOL effectively utilizes both auxiliary OOD datasets and even wild datasets with noisy in-distribution data. Code is available at https://github.com/UESTC-nnLab/MVOL.
Understanding Knowledge Hijack Mechanism in In-context Learning through Associative Memory
Authors: Shuo Wang, Issei Sato
Date: 2024-12-16 00:00:00
Tasks: In-Context Learning

In-context learning (ICL) enables large language models (LLMs) to adapt to new tasks without fine-tuning by leveraging contextual information provided within a prompt. However, ICL relies not only on contextual clues but also on the global knowledge acquired during pretraining for the next token prediction. Analyzing this process has been challenging due to the complex computational circuitry of LLMs. This paper investigates the balance between in-context information and pretrained bigram knowledge in token prediction, focusing on the induction head mechanism, a key component in ICL. Leveraging the fact that a two-layer transformer can implement the induction head mechanism with associative memories, we theoretically analyze the logits when a two-layer transformer is given prompts generated by a bigram model. In the experiments, we design specific prompts to evaluate whether the outputs of a two-layer transformer align with the theoretical results.
Regional Expected Improvement for Efficient Trust Region Selection in High-Dimensional Bayesian Optimization
Authors: Nobuo Namura, Sho Takemori
Date: 2024-12-16 00:00:00
Tasks: Bayesian Optimization, Dimensionality Reduction, Gaussian Processes

Real-world optimization problems often involve complex objective functions with costly evaluations. While Bayesian optimization (BO) with Gaussian processes is effective for these challenges, it suffers in high-dimensional spaces due to performance degradation from limited function evaluations. To overcome this, simplification techniques like dimensionality reduction have been employed, yet they often rely on assumptions about the problem characteristics, potentially underperforming when these assumptions do not hold. Trust-region-based methods, which avoid such assumptions, focus on local search but risk stagnation in local optima. In this study, we propose a novel acquisition function, regional expected improvement (REI), designed to enhance trust-region-based BO in medium to high-dimensional settings. REI identifies regions likely to contain the global optimum, improving performance without relying on specific problem characteristics. We provide a theoretical proof that REI effectively identifies optimal trust regions and empirically demonstrate that incorporating REI into trust-region-based BO outperforms conventional BO and other high-dimensional BO methods in medium to high-dimensional real-world problems.