pwc-archive/papers-with-abstracts huggingface dataset:
Metricizing the Euclidean Space towards Desired Distance Relations in Point Clouds
Authors: Stefan Rass, Sandra König, Shahzad Ahmad, Maksim Goman
Date: 2022-11-07 00:00:00
Tasks: Clustering

Given a set of points in the Euclidean space $\mathbb{R}^\ell$ with $\ell>1$, the pairwise distances between the points are determined by their spatial location and the metric $d$ that we endow $\mathbb{R}^\ell$ with. Hence, the distance $d(\mathbf x,\mathbf y)=\delta$ between two points is fixed by the choice of $\mathbf x$ and $\mathbf y$ and $d$. We study the related problem of fixing the value $\delta$, and the points $\mathbf x,\mathbf y$, and ask if there is a topological metric $d$ that computes the desired distance $\delta$. We demonstrate this problem to be solvable by constructing a metric to simultaneously give desired pairwise distances between up to $O(\sqrt\ell)$ many points in $\mathbb{R}^\ell$. We then introduce the notion of an $\varepsilon$-semimetric $\tilde{d}$ to formulate our main result: for all $\varepsilon>0$, for all $m\geq 1$, for any choice of $m$ points $\mathbf y_1,\ldots,\mathbf y_m\in\mathbb{R}^\ell$, and all chosen sets of values $\{\delta_{ij}\geq 0: 1\leq i<j\leq m\}$, there exists an $\varepsilon$-semimetric $\tilde{\delta}:\mathbb{R}^\ell\times \mathbb{R}^\ell\to\mathbb{R}$ such that $\tilde{d}(\mathbf y_i,\mathbf y_j)=\delta_{ij}$, i.e., the desired distances are accomplished, irrespectively of the topology that the Euclidean or other norms would induce. We showcase our results by using them to attack unsupervised learning algorithms, specifically $k$-Means and density-based (DBSCAN) clustering algorithms. These have manifold applications in artificial intelligence, and letting them run with externally provided distance measures constructed in the way as shown here, can make clustering algorithms produce results that are pre-determined and hence malleable. This demonstrates that the results of clustering algorithms may not generally be trustworthy, unless there is a standardized and fixed prescription to use a specific distance function.
Application of Graph Neural Networks and graph descriptors for graph classification
Authors: Jakub Adamczyk
Date: 2022-11-07 00:00:00
Tasks: Classification, Drug Discovery, Experimental Design, Graph Classification, Graph Neural Network, Graph Representation Learning, Representation Learning

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with the pace of new research, proper experimental design, fair evaluation, and independent benchmarks are essential. Design of strong baselines is an indispensable element of such works. In this thesis, we explore multiple approaches to graph classification. We focus on Graph Neural Networks (GNNs), which emerged as a de facto standard deep learning technique for graph representation learning. Classical approaches, such as graph descriptors and molecular fingerprints, are also addressed. We design fair evaluation experimental protocol and choose proper datasets collection. This allows us to perform numerous experiments and rigorously analyze modern approaches. We arrive to many conclusions, which shed new light on performance and quality of novel algorithms. We investigate application of Jumping Knowledge GNN architecture to graph classification, which proves to be an efficient tool for improving base graph neural network architectures. Multiple improvements to baseline models are also proposed and experimentally verified, which constitutes an important contribution to the field of fair model comparison.
Towards learning to explain with concept bottleneck models: mitigating information leakage
Authors: Joshua Lockhart, Nicolas Marchesotti, Daniele Magazzeni, Manuela Veloso
Date: 2022-11-07 00:00:00

Concept bottleneck models perform classification by first predicting which of a list of human provided concepts are true about a datapoint. Then a downstream model uses these predicted concept labels to predict the target label. The predicted concepts act as a rationale for the target prediction. Model trust issues emerge in this paradigm when soft concept labels are used: it has previously been observed that extra information about the data distribution leaks into the concept predictions. In this work we show how Monte-Carlo Dropout can be used to attain soft concept predictions that do not contain leaked information.
Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling
Authors: Romain Lopez, Nataša Tagasovska, Stephen Ra, Kyunghyn Cho, Jonathan K. Pritchard, Aviv Regev
Date: 2022-11-07 00:00:00
Tasks: Disentanglement, Domain Generalization, Transfer Learning

Latent variable models such as the Variational Auto-Encoder (VAE) have become a go-to tool for analyzing biological data, especially in the field of single-cell genomics. One remaining challenge is the interpretability of latent variables as biological processes that define a cell's identity. Outside of biological applications, this problem is commonly referred to as learning disentangled representations. Although several disentanglement-promoting variants of the VAE were introduced, and applied to single-cell genomics data, this task has been shown to be infeasible from independent and identically distributed measurements, without additional structure. Instead, recent methods propose to leverage non-stationary data, as well as the sparse mechanism shift assumption in order to learn disentangled representations with a causal semantic. Here, we extend the application of these methodological advances to the analysis of single-cell genomics data with genetic or chemical perturbations. More precisely, we propose a deep generative model of single-cell gene expression data for which each perturbation is treated as a stochastic intervention targeting an unknown, but sparse, subset of latent variables. We benchmark these methods on simulated single-cell data to evaluate their performance at latent units recovery, causal target identification and out-of-domain generalization. Finally, we apply those approaches to two real-world large-scale gene perturbation data sets and find that models that exploit the sparse mechanism shift hypothesis surpass contemporary methods on a transfer learning task. We implement our new model and benchmarks using the scvi-tools library, and release it as open-source software at https://github.com/Genentech/sVAE.
Decentralized Complete Dictionary Learning via $\ell^{4}$-Norm Maximization
Authors: Qiheng Lu, Lixiang Lian
Date: 2022-11-07 00:00:00
Tasks: Dictionary Learning, Representation Learning

With the rapid development of information technologies, centralized data processing is subject to many limitations, such as computational overheads, communication delays, and data privacy leakage. Decentralized data processing over networked terminal nodes becomes an important technology in the era of big data. Dictionary learning is a powerful representation learning method to exploit the low-dimensional structure from the high-dimensional data. By exploiting the low-dimensional structure, the storage and the processing overhead of data can be effectively reduced. In this paper, we propose a novel decentralized complete dictionary learning algorithm, which is based on $\ell^{4}$-norm maximization. Compared with existing decentralized dictionary learning algorithms, comprehensive numerical experiments show that the novel algorithm has significant advantages in terms of per-iteration computational complexity, communication cost, and convergence rate in many scenarios. Moreover, a rigorous theoretical analysis shows that the dictionaries learned by the proposed algorithm can converge to the one learned by a centralized dictionary learning algorithm at a linear rate with high probability under certain conditions.
A Deep Double Ritz Method (D$^2$RM) for solving Partial Differential Equations using Neural Networks
Authors: Carlos Uriarte, David Pardo, Ignacio Muga, Judit Muñoz-Matute
Date: 2022-11-07 00:00:00

Residual minimization is a widely used technique for solving Partial Differential Equations in variational form. It minimizes the dual norm of the residual, which naturally yields a saddle-point (min-max) problem over the so-called trial and test spaces. In the context of neural networks, we can address this min-max approach by employing one network to seek the trial minimum, while another network seeks the test maximizers. However, the resulting method is numerically unstable as we approach the trial solution. To overcome this, we reformulate the residual minimization as an equivalent minimization of a Ritz functional fed by optimal test functions computed from another Ritz functional minimization. We call the resulting scheme the Deep Double Ritz Method (D$^2$RM), which combines two neural networks for approximating trial functions and optimal test functions along a nested double Ritz minimization strategy. Numerical results on different diffusion and convection problems support the robustness of our method, up to the approximation properties of the networks and the training capacity of the optimizers.
Retention Time Prediction for Chromatographic Enantioseparation by Quantile Geometry-enhanced Graph Neural Network
Authors: Hao Xu, Jinglong Lin, Dongxiao Zhang, Fanyang Mo
Date: 2022-11-07 00:00:00
Tasks: Graph Neural Network, Prediction, scientific discovery

A new research framework is proposed to incorporate machine learning techniques into the field of experimental chemistry to facilitate chromatographic enantioseparation. A documentary dataset of chiral molecular retention times (CMRT dataset) in high-performance liquid chromatography is established to handle the challenge of data acquisition. Based on the CMRT dataset, a quantile geometry-enhanced graph neural network is proposed to learn the molecular structure-retention time relationship, which shows a satisfactory predictive ability for enantiomers. The domain knowledge of chromatography is incorporated into the machine learning model to achieve multi-column prediction, which paves the way for chromatographic enantioseparation prediction by calculating the separation probability. Experiments confirm that the proposed research framework works well in retention time prediction and chromatographic enantioseparation facilitation, which sheds light on the application of machine learning techniques to the experimental scene and improves the efficiency of experimenters to speed up scientific discovery.
From Denoising Diffusions to Denoising Markov Models
Authors: Joe Benton, Yuyang Shi, Valentin De Bortoli, George Deligiannidis, Arnaud Doucet
Date: 2022-11-07 00:00:00
Tasks: Denoising

Denoising diffusions are state-of-the-art generative models exhibiting remarkable empirical performance. They work by diffusing the data distribution into a Gaussian distribution and then learning to reverse this noising process to obtain synthetic datapoints. The denoising diffusion relies on approximations of the logarithmic derivatives of the noised data densities using score matching. Such models can also be used to perform approximate posterior simulation when one can only sample from the prior and likelihood. We propose a unifying framework generalising this approach to a wide class of spaces and leading to an original extension of score matching. We illustrate the resulting models on various applications.
pyGSL: A Graph Structure Learning Toolkit
Authors: Max Wasserman, Gonzalo Mateos
Date: 2022-11-07 00:00:00
Tasks: GPU, Graph Learning, Graph structure learning, Rolling Shutter Correction

We introduce pyGSL, a Python library that provides efficient implementations of state-of-the-art graph structure learning models along with diverse datasets to evaluate them on. The implementations are written in GPU-friendly ways, allowing one to scale to much larger network tasks. A common interface is introduced for algorithm unrolling methods, unifying implementations of recent state-of-the-art techniques and allowing new methods to be quickly developed by avoiding the need to rebuild the underlying unrolling infrastructure. Implementations of differentiable graph structure learning models are written in PyTorch, allowing us to leverage the rich software ecosystem that exists e.g., around logging, hyperparameter search, and GPU-communication. This also makes it easy to incorporate these models as components in larger gradient based learning systems where differentiable estimates of graph structure may be useful, e.g. in latent graph learning. Diverse datasets and performance metrics allow consistent comparisons across models in this fast growing field. The full code repository can be found on https://github.com/maxwass/pyGSL.
TLP: A Deep Learning-based Cost Model for Tensor Program Tuning
Authors: Yi Zhai, Yu Zhang, Shuo Liu, Xiaomeng Chu, Jie Peng, Jianmin Ji, Yanyong Zhang
Date: 2022-11-07 00:00:00
Tasks: CPU, GPU, Multi-Task Learning

Tensor program tuning is a non-convex objective optimization problem, to which search-based approaches have proven to be effective. At the core of the search-based approaches lies the design of the cost model. Though deep learning-based cost models perform significantly better than other methods, they still fall short and suffer from the following problems. First, their feature extraction heavily relies on expert-level domain knowledge in hardware architectures. Even so, the extracted features are often unsatisfactory and require separate considerations for CPUs and GPUs. Second, a cost model trained on one hardware platform usually performs poorly on another, a problem we call cross-hardware unavailability. In order to address these problems, we propose TLP and MTLTLP. TLP is a deep learning-based cost model that facilitates tensor program tuning. Instead of extracting features from the tensor program itself, TLP extracts features from the schedule primitives. We treat schedule primitives as tensor languages. TLP is thus a Tensor Language Processing task. In this way, the task of predicting the tensor program latency through the cost model is transformed into a natural language processing (NLP) regression task. MTL-TLP combines Multi-Task Learning and TLP to cope with the cross-hardware unavailability problem. We incorporate these techniques into the Ansor framework and conduct detailed experiments. Results show that TLP can speed up the average search time by 9.1X and 3.0X on CPU and GPU workloads, respectively, compared to the state-of-the-art implementation. MTL-TLP can achieve a speed-up of 4.7X and 2.9X on CPU and GPU workloads, respectively, using only 7% of the target hardware data.
Do highly over-parameterized neural networks generalize since bad solutions are rare?
Authors: Julius Martinetz, Thomas Martinetz
Date: 2022-11-07 00:00:00

We study over-parameterized classifiers where Empirical Risk Minimization (ERM) for learning leads to zero training error. In these over-parameterized settings there are many global minima with zero training error, some of which generalize better than others. We show that under certain conditions the fraction of "bad" global minima with a true error larger than {\epsilon} decays to zero exponentially fast with the number of training data n. The bound depends on the distribution of the true error over the set of classifier functions used for the given classification problem, and does not necessarily depend on the size or complexity (e.g. the number of parameters) of the classifier function set. This insight may provide a novel perspective on the unexpectedly good generalization even of highly over-parameterized neural networks. We substantiate our theoretical findings through experiments on synthetic data and a subset of MNIST. Additionally, we assess our hypothesis using VGG19 and ResNet18 on a subset of Caltech101.
How Much Does Attention Actually Attend? Questioning the Importance of Attention in Pretrained Transformers
Authors: Michael Hassid, Hao Peng, Daniel Rotem, Jungo Kasai, Ivan Montero, Noah A. Smith, Roy Schwartz
Date: 2022-11-07 00:00:00

The attention mechanism is considered the backbone of the widely-used Transformer architecture. It contextualizes the input by computing input-specific attention matrices. We find that this mechanism, while powerful and elegant, is not as important as typically thought for pretrained language models. We introduce PAPA, a new probing method that replaces the input-dependent attention matrices with constant ones -- the average attention weights over multiple inputs. We use PAPA to analyze several established pretrained Transformers on six downstream tasks. We find that without any input-dependent attention, all models achieve competitive performance -- an average relative drop of only 8% from the probing baseline. Further, little or no performance drop is observed when replacing half of the input-dependent attention matrices with constant (input-independent) ones. Interestingly, we show that better-performing models lose more from applying our method than weaker models, suggesting that the utilization of the input-dependent attention mechanism might be a factor in their success. Our results motivate research on simpler alternatives to input-dependent attention, as well as on methods for better utilization of this mechanism in the Transformer architecture.
A Targeted Sampling Strategy for Compressive Cryo Focused Ion Beam Scanning Electron Microscopy
Authors: Daniel Nicholls, Jack Wells, Alex W. Robinson, Amirafshar Moshtaghpour, Maryna Kobylynska, Roland A. Fleck, Angus I. Kirkland, Nigel D. Browning
Date: 2022-11-07 00:00:00
Tasks: Compressive Sensing, Dictionary Learning, GPU

Cryo Focused Ion-Beam Scanning Electron Microscopy (cryo FIB-SEM) enables three-dimensional and nanoscale imaging of biological specimens via a slice and view mechanism. The FIB-SEM experiments are, however, limited by a slow (typically, several hours) acquisition process and the high electron doses imposed on the beam sensitive specimen can cause damage. In this work, we present a compressive sensing variant of cryo FIB-SEM capable of reducing the operational electron dose and increasing speed. We propose two Targeted Sampling (TS) strategies that leverage the reconstructed image of the previous sample layer as a prior for designing the next subsampling mask. Our image recovery is based on a blind Bayesian dictionary learning approach, i.e., Beta Process Factor Analysis (BPFA). This method is experimentally viable due to our ultra-fast GPU-based implementation of BPFA. Simulations on artificial compressive FIB-SEM measurements validate the success of proposed methods: the operational electron dose can be reduced by up to 20 times. These methods have large implications for the cryo FIB-SEM community, in which the imaging of beam sensitive biological materials without beam damage is crucial.
Resilience of Wireless Ad Hoc Federated Learning against Model Poisoning Attacks
Authors: Naoya Tezuka, Hideya Ochiai, Yuwei Sun, Hiroshi Esaki
Date: 2022-11-07 00:00:00
Tasks: Federated Learning, Model Poisoning

Wireless ad hoc federated learning (WAFL) is a fully decentralized collaborative machine learning framework organized by opportunistically encountered mobile nodes. Compared to conventional federated learning, WAFL performs model training by weakly synchronizing the model parameters with others, and this shows great resilience to a poisoned model injected by an attacker. In this paper, we provide our theoretical analysis of the WAFL's resilience against model poisoning attacks, by formulating the force balance between the poisoned model and the legitimate model. According to our experiments, we confirmed that the nodes directly encountered the attacker has been somehow compromised to the poisoned model but other nodes have shown great resilience. More importantly, after the attacker has left the network, all the nodes have finally found stronger model parameters combined with the poisoned model. Most of the attack-experienced cases achieved higher accuracy than the no-attack-experienced cases.
Predictive Coding beyond Gaussian Distributions
Authors: Luca Pinchetti, Tommaso Salvatori, Yordan Yordanov, Beren Millidge, Yuhang Song, Thomas Lukasiewicz
Date: 2022-11-07 00:00:00

A large amount of recent research has the far-reaching goal of finding training methods for deep neural networks that can serve as alternatives to backpropagation (BP). A prominent example is predictive coding (PC), which is a neuroscience-inspired method that performs inference on hierarchical Gaussian generative models. These methods, however, fail to keep up with modern neural networks, as they are unable to replicate the dynamics of complex layers and activation functions. In this work, we solve this problem by generalizing PC to arbitrary probability distributions, enabling the training of architectures, such as transformers, that are hard to approximate with only Gaussian assumptions. We perform three experimental analyses. First, we study the gap between our method and the standard formulation of PC on multiple toy examples. Second, we test the reconstruction quality on variational autoencoders, where our method reaches the same reconstruction quality as BP. Third, we show that our method allows us to train transformer networks and achieve a performance comparable with BP on conditional language models. More broadly, this method allows neuroscience-inspired learning to be applied to multiple domains, since the internal distributions can be flexibly adapted to the data, tasks, and architectures used.
Closing the Gap between Client and Global Model Performance in Heterogeneous Federated Learning
Authors: Hongrui Shi, Valentin Radu, Po Yang
Date: 2022-11-07 00:00:00
Tasks: Federated Learning, Knowledge Distillation

The heterogeneity of hardware and data is a well-known and studied problem in the community of Federated Learning (FL) as running under heterogeneous settings. Recently, custom-size client models trained with Knowledge Distillation (KD) has emerged as a viable strategy for tackling the heterogeneity challenge. However, previous efforts in this direction are aimed at client model tuning rather than their impact onto the knowledge aggregation of the global model. Despite performance of global models being the primary objective of FL systems, under heterogeneous settings client models have received more attention. Here, we provide more insights into how the chosen approach for training custom client models has an impact on the global model, which is essential for any FL application. We show the global model can fully leverage the strength of KD with heterogeneous data. Driven by empirical observations, we further propose a new approach that combines KD and Learning without Forgetting (LwoF) to produce improved personalised models. We bring heterogeneous FL on pair with the mighty FedAvg of homogeneous FL, in realistic deployment scenarios with dropping clients.