pwc-archive/papers-with-abstracts huggingface dataset:
Multi-Type Point Cloud Autoencoder: A Complete Equivariant Embedding for Molecule Conformation and Pose
Authors: Michael Kilgour, Mark Tuckerman, Jutta Rogal
Date: 2024-05-22 00:00:00
Tasks: Property Prediction

The point cloud is a flexible representation for a wide variety of data types, and is a particularly natural fit for the 3D conformations of molecules. Extant molecule embedding/representation schemes typically focus on internal degrees of freedom, ignoring the global 3D orientation. For tasks that depend on knowledge of both molecular conformation and 3D orientation, such as the generation of molecular dimers, clusters, or condensed phases, we require a representation which is provably complete in the types and positions of atomic nuclei and roto-inversion equivariant with respect to the input point cloud. We develop, train, and evaluate a new type of autoencoder, molecular O(3) encoding net (Mo3ENet), for multi-type point clouds, for which we propose a new reconstruction loss, capitalizing on a Gaussian mixture representation of the input and output point clouds. Mo3ENet is end-to-end equivariant, meaning the learned representation can be manipulated on O(3), a practical bonus for downstream learning tasks. An appropriately trained Mo3ENet latent space comprises a universal embedding for scalar and vector molecule property prediction tasks, as well as other downstream tasks incorporating the 3D molecular pose.
Disentangle Sample Size and Initialization Effect on Perfect Generalization for Single-Neuron Target
Authors: Jiajie Zhao, Zhiwei Bai, Yaoyu Zhang
Date: 2024-05-22 00:00:00

Overparameterized models like deep neural networks have the intriguing ability to recover target functions with fewer sampled data points than parameters (see arXiv:2307.08921). To gain insights into this phenomenon, we concentrate on a single-neuron target recovery scenario, offering a systematic examination of how initialization and sample size influence the performance of two-layer neural networks. Our experiments reveal that a smaller initialization scale is associated with improved generalization, and we identify a critical quantity called the "initial imbalance ratio" that governs training dynamics and generalization under small initialization, supported by theoretical proofs. Additionally, we empirically delineate two critical thresholds in sample size--termed the "optimistic sample size" and the "separation sample size"--that align with the theoretical frameworks established by (see arXiv:2307.08921 and arXiv:2309.00508). Our results indicate a transition in the model's ability to recover the target function: below the optimistic sample size, recovery is unattainable; at the optimistic sample size, recovery becomes attainable albeit with a set of initialization of zero measure. Upon reaching the separation sample size, the set of initialization that can successfully recover the target function shifts from zero to positive measure. These insights, derived from a simplified context, provide a perspective on the intricate yet decipherable complexities of perfect generalization in overparameterized neural networks.
Multi-Dataset Multi-Task Learning for COVID-19 Prognosis
Authors: Filippo Ruffini, Lorenzo Tronchin, Zhuoru Wu, WenTing Chen, Paolo Soda, Linlin Shen, Valerio Guarrasi
Date: 2024-05-22 00:00:00
Tasks: Multi-Task Learning, Prognosis, Transfer Learning

In the fight against the COVID-19 pandemic, leveraging artificial intelligence to predict disease outcomes from chest radiographic images represents a significant scientific aim. The challenge, however, lies in the scarcity of large, labeled datasets with compatible tasks for training deep learning models without leading to overfitting. Addressing this issue, we introduce a novel multi-dataset multi-task training framework that predicts COVID-19 prognostic outcomes from chest X-rays (CXR) by integrating correlated datasets from disparate sources, distant from conventional multi-task learning approaches, which rely on datasets with multiple and correlated labeling schemes. Our framework hypothesizes that assessing severity scores enhances the model's ability to classify prognostic severity groups, thereby improving its robustness and predictive power. The proposed architecture comprises a deep convolutional network that receives inputs from two publicly available CXR datasets, AIforCOVID for severity prognostic prediction and BRIXIA for severity score assessment, and branches into task-specific fully connected output networks. Moreover, we propose a multi-task loss function, incorporating an indicator function, to exploit multi-dataset integration. The effectiveness and robustness of the proposed approach are demonstrated through significant performance improvements in prognosis classification tasks across 18 different convolutional neural network backbones in different evaluation strategies. This improvement is evident over single-task baselines and standard transfer learning strategies, supported by extensive statistical analysis, showing great application potential.
On the stability of gradient descent with second order dynamics for time-varying cost functions
Authors: Travis E. Gibson, Sawal Acharya, Anjali Parashar, Joseph E. Gaudio, Anurdha M. Annaswamy
Date: 2024-05-22 00:00:00
Tasks: Stochastic Optimization

Gradient based optimization algorithms deployed in Machine Learning (ML) applications are often analyzed and compared by their convergence rates or regret bounds. While these rates and bounds convey valuable information they don't always directly translate to stability guarantees. Stability and similar concepts, like robustness, will become ever more important as we move towards deploying models in real-time and safety critical systems. In this work we build upon the results in Gaudio et al. 2021 and Moreu & Annaswamy 2022 for gradient descent with second order dynamics when applied to explicitly time varying cost functions and provide more general stability guarantees. These more general results can aid in the design and certification of these optimization schemes so as to help ensure safe and reliable deployment for real-time learning applications. We also hope that the techniques provided here will stimulate and cross-fertilize the analysis that occurs on the same algorithms from the online learning and stochastic optimization communities.
Banded Square Root Matrix Factorization for Differentially Private Model Training
Authors: Nikita P. Kalinin, Christoph Lampert
Date: 2024-05-22 00:00:00
Tasks: Federated Learning

Current state-of-the-art methods for differentially private model training are based on matrix factorization techniques. However, these methods suffer from high computational overhead because they require numerically solving a demanding optimization problem to determine an approximately optimal factorization prior to the actual model training. In this work, we present a new matrix factorization approach, BSR, which overcomes this computational bottleneck. By exploiting properties of the standard matrix square root, BSR allows to efficiently handle also large-scale problems. For the key scenario of stochastic gradient descent with momentum and weight decay, we even derive analytical expressions for BSR that render the computational overhead negligible. We prove bounds on the approximation quality that hold both in the centralized and in the federated learning setting. Our numerical experiments demonstrate that models trained using BSR perform on par with the best existing methods, while completely avoiding their computational overhead.
A Versatile Diffusion Transformer with Mixture of Noise Levels for Audiovisual Generation
Authors: Gwanghyun Kim, Alonso Martinez, Yu-Chuan Su, Brendan Jou, José Lezama, Agrim Gupta, Lijun Yu, Lu Jiang, Aren Jansen, Jacob Walker, Krishna Somandepalli
Date: 2024-05-22 00:00:00

Training diffusion models for audiovisual sequences allows for a range of generation tasks by learning conditional distributions of various input-output combinations of the two modalities. Nevertheless, this strategy often requires training a separate model for each task which is expensive. Here, we propose a novel training approach to effectively learn arbitrary conditional distributions in the audiovisual space.Our key contribution lies in how we parameterize the diffusion timestep in the forward diffusion process. Instead of the standard fixed diffusion timestep, we propose applying variable diffusion timesteps across the temporal dimension and across modalities of the inputs. This formulation offers flexibility to introduce variable noise levels for various portions of the input, hence the term mixture of noise levels. We propose a transformer-based audiovisual latent diffusion model and show that it can be trained in a task-agnostic fashion using our approach to enable a variety of audiovisual generation tasks at inference time. Experiments demonstrate the versatility of our method in tackling cross-modal and multimodal interpolation tasks in the audiovisual space. Notably, our proposed approach surpasses baselines in generating temporally and perceptually consistent samples conditioned on the input. Project page: avdit2024.github.io
Enhancing Multiscale Simulations with Constitutive Relations-Aware Deep Operator Networks
Authors: Hamidreza Eivazi, Mahyar Alikhani, Jendrik-Alexander Tröger, Stefan Wittek, Stefan Hartmann, Andreas Rausch
Date: 2024-05-22 00:00:00

Multiscale problems are widely observed across diverse domains in physics and engineering. Translating these problems into numerical simulations and solving them using numerical schemes, e.g. the finite element method, is costly due to the demand of solving initial boundary-value problems at multiple scales. On the other hand, multiscale finite element computations are commended for their ability to integrate micro-structural properties into macroscopic computational analyses using homogenization techniques. Recently, neural operator-based surrogate models have shown trustworthy performance for solving a wide range of partial differential equations. In this work, we propose a hybrid method in which we utilize deep operator networks for surrogate modeling of the microscale physics. This allows us to embed the constitutive relations of the microscale into the model architecture and to predict microscale strains and stresses based on the prescribed macroscale strain inputs. Furthermore, numerical homogenization is carried out to obtain the macroscale quantities of interest. We apply the proposed approach to quasi-static problems of solid mechanics. The results demonstrate that our constitutive relations-aware DeepONet can yield accurate solutions even when being confronted with a restricted dataset during model development.
A label-free and data-free training strategy for vasculature segmentation in serial sectioning OCT data
Authors: Etienne Chollet, Yael Balbastre, Caroline Magnain, Bruce Fischl, Hui Wang
Date: 2024-05-22 00:00:00
Tasks: Segmentation

Serial sectioning Optical Coherence Tomography (sOCT) is a high-throughput, label free microscopic imaging technique that is becoming increasingly popular to study post-mortem neurovasculature. Quantitative analysis of the vasculature requires highly accurate segmentation; however, sOCT has low signal-to-noise-ratio and displays a wide range of contrasts and artifacts that depend on acquisition parameters. Furthermore, labeled data is scarce and extremely time consuming to generate. Here, we leverage synthetic datasets of vessels to train a deep learning segmentation model. We construct the vessels with semi-realistic splines that simulate the vascular geometry and compare our model with realistic vascular labels generated by constrained constructive optimization. Both approaches yield similar Dice scores, although with very different false positive and false negative rates. This method addresses the complexity inherent in OCT images and paves the way for more accurate and efficient analysis of neurovascular structures.
Offline RL via Feature-Occupancy Gradient Ascent
Authors: Gergely Neu, Nneka Okolo
Date: 2024-05-22 00:00:00
Tasks: Offline RL

We study offline Reinforcement Learning in large infinite-horizon discounted Markov Decision Processes (MDPs) when the reward and transition models are linearly realizable under a known feature map. Starting from the classic linear-program formulation of the optimal control problem in MDPs, we develop a new algorithm that performs a form of gradient ascent in the space of feature occupancies, defined as the expected feature vectors that can potentially be generated by executing policies in the environment. We show that the resulting simple algorithm satisfies strong computational and sample complexity guarantees, achieved under the least restrictive data coverage assumptions known in the literature. In particular, we show that the sample complexity of our method scales optimally with the desired accuracy level and depends on a weak notion of coverage that only requires the empirical feature covariance matrix to cover a single direction in the feature space (as opposed to covering a full subspace). Additionally, our method is easy to implement and requires no prior knowledge of the coverage ratio (or even an upper bound on it), which altogether make it the strongest known algorithm for this setting to date.
Mining Action Rules for Defect Reduction Planning
Authors: Khouloud Oueslati, Gabriel Laberge, Maxime Lamothe, Foutse khomh
Date: 2024-05-22 00:00:00
Tasks: counterfactual, Counterfactual Explanation

Defect reduction planning plays a vital role in enhancing software quality and minimizing software maintenance costs. By training a black box machine learning model and "explaining" its predictions, explainable AI for software engineering aims to identify the code characteristics that impact maintenance risks. However, post-hoc explanations do not always faithfully reflect what the original model computes. In this paper, we introduce CounterACT, a Counterfactual ACTion rule mining approach that can generate defect reduction plans without black-box models. By leveraging action rules, CounterACT provides a course of action that can be considered as a counterfactual explanation for the class (e.g., buggy or not buggy) assigned to a piece of code. We compare the effectiveness of CounterACT with the original action rule mining algorithm and six established defect reduction approaches on 9 software projects. Our evaluation is based on (a) overlap scores between proposed code changes and actual developer modifications; (b) improvement scores in future releases; and (c) the precision, recall, and F1-score of the plans. Our results show that, compared to competing approaches, CounterACT's explainable plans achieve higher overlap scores at the release level (median 95%) and commit level (median 85.97%), and they offer better trade-off between precision and recall (median F1-score 88.12%). Finally, we venture beyond planning and explore leveraging Large Language models (LLM) for generating code edits from our generated plans. Our results show that suggested LLM code edits supported by our plans are actionable and are more likely to pass relevant test cases than vanilla LLM code recommendations.
Interpolation with deep neural networks with non-polynomial activations: necessary and sufficient numbers of neurons
Authors: Liam Madden
Date: 2024-05-22 00:00:00

The minimal number of neurons required for a feedforward neural network to interpolate $n$ generic input-output pairs from $\mathbb{R}^d\times \mathbb{R}^{d'}$ is $\Theta(\sqrt{nd'})$. While previous results have shown that $\Theta(\sqrt{nd'})$ neurons are sufficient, they have been limited to sigmoid, Heaviside, and rectified linear unit (ReLU) as the activation function. Using a different approach, we prove that $\Theta(\sqrt{nd'})$ neurons are sufficient as long as the activation function is real analytic at a point and not a polynomial there. Thus, the only practical activation functions that our result does not apply to are piecewise polynomials. Importantly, this means that activation functions can be freely chosen in a problem-dependent manner without loss of interpolation power.
Control, Transport and Sampling: Towards Better Loss Design
Authors: Qijia Jiang, David Nabergoj
Date: 2024-05-22 00:00:00
Tasks: Inductive Bias, valid

Leveraging connections between diffusion-based sampling, optimal transport, and stochastic optimal control through their shared links to the Schr\"odinger bridge problem, we propose novel objective functions that can be used to transport $\nu$ to $\mu$, consequently sample from the target $\mu$, via optimally controlled dynamics. We highlight the importance of the pathwise perspective and the role various optimality conditions on the path measure can play for the design of valid training losses, the careful choice of which offer numerical advantages in implementation. Basing the formalism on Schr\"odinger bridge comes with the additional practical capability of baking in inductive bias when it comes to Neural Network training.
Score-based Generative Models with Adaptive Momentum
Authors: Ziqing Wen, Xiaoge Deng, Ping Luo, Tao Sun, Dongsheng Li
Date: 2024-05-22 00:00:00
Tasks: Denoising, Graph Generation

Score-based generative models have demonstrated significant practical success in data-generating tasks. The models establish a diffusion process that perturbs the ground truth data to Gaussian noise and then learn the reverse process to transform noise into data. However, existing denoising methods such as Langevin dynamic and numerical stochastic differential equation solvers enjoy randomness but generate data slowly with a large number of score function evaluations, and the ordinary differential equation solvers enjoy faster sampling speed but no randomness may influence the sample quality. To this end, motivated by the Stochastic Gradient Descent (SGD) optimization methods and the high connection between the model sampling process with the SGD, we propose adaptive momentum sampling to accelerate the transforming process without introducing additional hyperparameters. Theoretically, we proved our method promises convergence under given conditions. In addition, we empirically show that our sampler can produce more faithful images/graphs in small sampling steps with 2 to 5 times speed up and obtain competitive scores compared to the baselines on image and graph generation tasks.
Connectivity Shapes Implicit Regularization in Matrix Factorization Models for Matrix Completion
Authors: Zhiwei Bai, Jiajie Zhao, Yaoyu Zhang
Date: 2024-05-22 00:00:00
Tasks: Matrix Completion

Matrix factorization models have been extensively studied as a valuable test-bed for understanding the implicit biases of overparameterized models. Although both low nuclear norm and low rank regularization have been studied for these models, a unified understanding of when, how, and why they achieve different implicit regularization effects remains elusive. In this work, we systematically investigate the implicit regularization of matrix factorization for solving matrix completion problems. We empirically discover that the connectivity of observed data plays a crucial role in the implicit bias, with a transition from low nuclear norm to low rank as data shifts from disconnected to connected with increased observations. We identify a hierarchy of intrinsic invariant manifolds in the loss landscape that guide the training trajectory to evolve from low-rank to higher-rank solutions. Based on this finding, we theoretically characterize the training trajectory as following the hierarchical invariant manifold traversal process, generalizing the characterization of Li et al. (2020) to include the disconnected case. Furthermore, we establish conditions that guarantee minimum nuclear norm, closely aligning with our experimental findings, and we provide a dynamics characterization condition for ensuring minimum rank. Our work reveals the intricate interplay between data connectivity, training dynamics, and implicit regularization in matrix factorization models.
Next-token prediction capacity: general upper bounds and a lower bound for transformers
Authors: Liam Madden, Curtis Fox, Christos Thrampoulidis
Date: 2024-05-22 00:00:00
Tasks: Decoder, Memorization

Given a sequence of tokens, such as words, the task of next-token prediction is to predict the next-token conditional probability distribution. Decoder-only transformers have become effective models for this task, but their properties are still not fully understood. In particular, the largest number of distinct context sequences that a decoder-only transformer can interpolate next-token distributions for has not been established. To fill this gap, we prove upper and lower bounds on this number, which are equal up to a multiplicative constant. We prove these bounds in the general setting where next-token distributions can be arbitrary as well as the empirical setting where they are calculated from a finite number of document sequences. Our lower bounds are for one-layer multi-head decoder-only transformers and our proofs highlight an important injectivity property satisfied by self-attention. Furthermore, we provide numerical evidence that the minimal number of parameters for memorization is sufficient for being able to train the model to the entropy lower bound.
Learning Diffusion Priors from Observations by Expectation Maximization
Authors: François Rozet, Gérôme Andry, François Lanusse, Gilles Louppe
Date: 2024-05-22 00:00:00

Diffusion models recently proved to be remarkable priors for Bayesian inverse problems. However, training these models typically requires access to large amounts of clean data, which could prove difficult in some settings. In this work, we present a novel method based on the expectation-maximization algorithm for training diffusion models from incomplete and noisy observations only. Unlike previous works, our method leads to proper diffusion models, which is crucial for downstream tasks. As part of our method, we propose and motivate an improved posterior sampling scheme for unconditional diffusion models. We present empirical evidence supporting the effectiveness of our method.
Optimizing Lymphocyte Detection in Breast Cancer Whole Slide Imaging through Data-Centric Strategies
Authors: Amine Marzouki, Zhuxian Guo, Qinghe Zeng, Camille Kurtz, Nicolas Loménie
Date: 2024-05-22 00:00:00

Efficient and precise quantification of lymphocytes in histopathology slides is imperative for the characterization of the tumor microenvironment and immunotherapy response insights. We developed a data-centric optimization pipeline that attain great lymphocyte detection performance using an off-the-shelf YOLOv5 model, without any architectural modifications. Our contribution that rely on strategic dataset augmentation strategies, includes novel biological upsampling and custom visual cohesion transformations tailored to the unique properties of tissue imagery, and enables to dramatically improve model performances. Our optimization reveals a pivotal realization: given intensive customization, standard computational pathology models can achieve high-capability biomarker development, without increasing the architectural complexity. We showcase the interest of this approach in the context of breast cancer where our strategies lead to good lymphocyte detection performances, echoing a broadly impactful paradigm shift. Furthermore, our data curation techniques enable crucial histological analysis benchmarks, highlighting improved generalizable potential.