nils-herrmann/clean_scirepeval huggingface dataset:
Granger causal inference on DAGs identifies genomic loci regulating transcription
Authors: Alexander P Wu, Rohit Singh, Bonnie Berger

When a dynamical system can be modeled as a sequence of observations, Granger causality is a powerful approach for detecting predictive interactions between its variables. However, traditional Granger causal inference has limited utility in domains where the dynamics need to be represented as directed acyclic graphs (DAGs) rather than as a linear sequence, such as with cell differentiation trajectories. Here, we present GrID-Net, a framework based on graph neural networks with lagged message passing for Granger causal inference on DAG-structured systems. Our motivating application is the analysis of single-cell multimodal data to identify genomic loci that mediate the regulation of specific genes. To our knowledge, GrID-Net is the first single-cell analysis tool that accounts for the temporal lag between a genomic locus becoming accessible and its downstream effect on a target gene's expression. We applied GrID-Net on multimodal single-cell assays that profile chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) in the same cell and show that it dramatically outperforms existing methods for inferring regulatory locus-gene links, achieving up to 71% greater agreement with independent population genetics-based estimates. By extending Granger causality to DAG-structured dynamical systems, our work unlocks new domains for causal analyses and, more specifically, opens a path towards elucidating gene regulatory interactions relevant to cellular differentiation and complex human diseases at unprecedented scale and resolution.
Starfire: Regularization-Free Adversarially-Robust Structured Sparse Training
Authors: Noah Gamboa, Kais Kudrolli, Anand Dhoot, Ardavan Pedram

This paper studies structured sparse training of CNNs with a gradual pruning technique that leads to fixed, sparse weight matrices after a set number of epochs. We simplify the structure of the enforced sparsity so that it reduces overhead caused by regularization. The proposed training methodology explores several options for structured sparsity.

We study various tradeoffs with respect to pruning duration, learning-rate configuration, and the total length of training.
We show that our method creates a sparse version of ResNet50 and ResNet50v1.5 on full ImageNet while remaining within a negligible <1% margin of accuracy loss. To make sure that this type of sparse training does not harm the robustness of the network, we also demonstrate how the network behaves in the presence of adversarial attacks.  Our results show that with 70% target sparsity, over 75% top-1 accuracy is achievable.
Is Heterophily A Real Nightmare For Graph Neural Networks on Performing Node Classification?
Authors: Sitao Luan, Chenqing Hua, Qincheng Lu, Jiaqi Zhu, Mingde Zhao, Shuyuan Zhang, Xiao-Wen Chang, Doina Precup

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by using the graph structures based on the relational inductive bias (homophily assumption). Though GNNs are believed to outperform NNs in real-world tasks, performance advantages of GNNs over graph-agnostic NNs seem not generally satisfactory. Heterophily has been considered as a main cause and numerous works have been put forward to address it. In this paper, we first show that not all cases of heterophily are harmful for GNNs with aggregation operation. Then, we propose new metrics based on a similarity matrix which considers the influence of both graph structure and input features on GNNs. The metrics demonstrate advantages over the commonly used homophily metrics in tests on synthetic graphs. From the metrics and the observations, we find that some cases of harmful heterophily can be addressed by diversification operation. By using this fact and knowledge of filterbanks, we propose the Adaptive Channel Mixing (ACM) framework to adaptively exploit aggregation, diversification and identity channels in each GNN layer, in order to address harmful heterophily. We validate the ACM-augmented baselines with 10 real-world node classification tasks. They consistently achieve significant performance gain and exceed the state-of-the-art GNNs on most of the tasks without incurring significant computational burden.
DIVA: Dataset Derivative of a Learning Task
Authors: Yonatan Dukler, Alessandro Achille, Giovanni Paolini, Avinash Ravichandran, Marzia Polito, Stefano Soatto

We present a method to compute the derivative of a learning task with respect to a dataset. A learning task is a function from a training set to the validation error, which can be represented by a trained deep neural network (DNN). The ``dataset derivative'' is a linear operator, computed around the trained model, that informs how perturbations of the weight of each training sample affect the validation error, usually computed on a separate validation dataset.  Our method, DIVA (Differentiable Validation) hinges on a closed-form differentiable expression of the leave-one-out cross-validation error around a pre-trained DNN. Such expression constitutes the dataset derivative. DIVA could be used for dataset auto-curation, for example removing samples with faulty annotations, augmenting a dataset with additional relevant samples, or rebalancing. More generally, DIVA can be used to optimize the dataset, along with the parameters of the model, as part of the training process without the need for a separate validation dataset, unlike bi-level optimization methods customary in AutoML. To illustrate the flexibility of DIVA, we report experiments on sample auto-curation tasks such as outlier rejection, dataset extension, and automatic aggregation of multi-modal data.
Neural Spatio-Temporal Point Processes
Authors: Ricky T. Q. Chen, Brandon Amos, Maximilian Nickel

We propose a new class of parameterizations for spatio-temporal point processes which leverage Neural ODEs as a computational method and enable flexible, high-fidelity models of discrete events that are localized in continuous time and space. Central to our approach is a combination of continuous-time neural networks with two novel neural architectures, \ie, Jump and Attentive Continuous-time Normalizing Flows. This approach allows us to learn complex distributions for both the spatial and temporal domain and to condition non-trivially on the observed event history. We validate our models on data sets from a wide variety of contexts such as seismology, epidemiology, urban mobility, and neuroscience.
Reinforcement Learning Algorithm Selection
Authors: Romain Laroche, Raphael Feraud

This paper formalises the problem of online algorithm selection in the context of Reinforcement Learning (RL). The setup is as follows: given an episodic task and a finite number of off-policy RL algorithms, a meta-algorithm has to decide which RL algorithm is in control during the next episode so as to maximize the expected return. The article presents a novel meta-algorithm, called Epochal Stochastic Bandit Algorithm Selection (ESBAS). Its principle is to freeze the policy updates at each epoch, and to leave a rebooted stochastic bandit in charge of the algorithm selection. Under some assumptions, a thorough theoretical analysis demonstrates its near-optimality considering the structural sampling budget limitations. ESBAS is first empirically evaluated on a dialogue task where it is shown to outperform each individual algorithm in most configurations. ESBAS is then adapted to a true online setting where algorithms update their policies after each transition, which we call SSBAS. SSBAS is evaluated on a fruit collection task where it is shown to adapt the stepsize parameter more efficiently than the classical hyperbolic decay, and on an Atari game, where it improves the performance by a wide margin.
An Energy-Based Framework for Arbitrary Label Noise Correction
Authors: Jaspreet Sahota, Divya Shanmugam, Janahan Ramanan, Sepehr Eghbali, Marcus Brubaker

We propose an energy-based framework for correcting mislabelled training examples in the context of binary classification. While existing work addresses random and class-dependent label noise, we focus on feature dependent label noise, which is ubiquitous in real-world data and difficult to model. Two elements distinguish our approach from others: 1) instead of relying on the original feature space, we employ an autoencoder to learn a discriminative representation and 2) we introduce an energy-based formalism for the label correction problem. We prove that a discriminative representation can be learned by training a generative model using a loss function comprised of the difference of energies corresponding to each class. The learned energy value for each training instance is compared to the original training labels and contradictions between energy assignment and training label are used to correct labels. We validate our method across eight datasets, spanning synthetic and realistic settings, and demonstrate the technique's state-of-the-art label correction performance. Furthermore, we derive analytical expressions to show the effect of label noise on the gradients of empirical risk.
Radial Basis Feature Transformation to Arm CNNs Against Adversarial Attacks
Authors: Saeid Asgari Taghanaki, Shekoofeh Azizi, Ghassan Hamarneh

The linear and non-flexible nature of deep convolutional models makes them vulnerable to carefully crafted adversarial perturbations. To tackle this problem, in this paper, we propose a nonlinear radial basis convolutional feature transformation by learning the Mahalanobis distance function that maps the input convolutional features from the same class into tight clusters. In such a space, the clusters become compact and well-separated, which prevent small adversarial perturbations from forcing a sample to cross the decision boundary. We test the proposed method on three publicly available image classification and segmentation data-sets namely, MNIST, ISBI ISIC skin lesion, and NIH ChestX-ray14. We evaluate the robustness of our method to different gradient (targeted and untargeted) and non-gradient based attacks and compare it to several non-gradient masking defense strategies. Our results demonstrate that the proposed method can boost the performance of deep convolutional neural networks against adversarial perturbations without accuracy drop on clean data.
Neural Program Synthesis By Self-Learning
Authors: Yifan Xu, Lu Dai, Udaikaran Singh, Kening Zhang, Zhuowen Tu

Neural inductive program synthesis is a task generating instructions that can produce desired outputs from given inputs. In this paper, we focus on the generation of a chunk of assembly code that can be executed to match a state change inside the CPU. We develop a neural program synthesis algorithm, AutoAssemblet, learned via self-learning reinforcement learning that explores the large code space efficiently. Policy networks and value networks are learned to reduce the breadth and depth of the Monte Carlo Tree Search, resulting in better synthesis performance.  We also propose an effective multi-entropy policy sampling technique to alleviate online update correlations.  We apply AutoAssemblet to basic programming tasks and show significant higher success rates compared to several competing baselines.
Interpreting and Boosting Dropout from a Game-Theoretic View
Authors: Hao Zhang, Sen Li, YinChao Ma, Mingjie Li, Yichen Xie, Quanshi Zhang

This paper aims to understand and improve the utility of the dropout operation from the perspective of game-theoretical interactions. We prove that dropout can suppress the strength of interactions between input variables of deep neural networks (DNNs). The theoretical proof is also verified by various experiments. Furthermore, we find that such interactions were strongly related to the over-fitting problem in deep learning. So, the utility of dropout can be regarded as decreasing interactions to alleviating the significance of over-fitting. Based on this understanding, we propose the interaction loss to further improve the utility of dropout. Experimental results on various DNNs and datasets have shown that the interaction loss can effectively improve the utility of dropout and boost the performance of DNNs.
On the Geometry of Deep Bayesian Active Learning
Authors: Xiaofeng Cao, Ivor Tsang

We present  geometric Bayesian active learning by disagreements (GBALD), a framework that performs BALD on its geometric interpretation interacting with a deep learning model. There are two main components in GBALD: initial acquisitions based on core-set construction and model uncertainty estimation with those initial acquisitions. Our key innovation is to construct the core-set on an ellipsoid, not typical sphere, preventing its updates towards the boundary regions of the distributions. Main improvements over BALD are twofold: relieving sensitivity to uninformative prior and reducing redundant information of model uncertainty. To guarantee the improvements, our generalization analysis proves that, compared to typical Bayesian  spherical interpretation, geodesic search with ellipsoid can derive a tighter lower error bound and achieve higher probability to obtain  a nearly zero error. Experiments on acquisitions with several scenarios demonstrate that, yielding slight perturbations to noisy and repeated samples,  GBALD further achieves significant accuracy improvements  than BALD, BatchBALD and other baselines.
Initialized Equilibrium Propagation for Backprop-Free Training
Authors: Peter O'Connor, Efstratios Gavves, Max Welling

Deep neural networks are almost universally trained with reverse-mode automatic differentiation (a.k.a. backpropagation). Biological networks, on the other hand, appear to lack any mechanism for sending gradients back to their input neurons, and thus cannot be learning in this way. In response to this, Scellier & Bengio (2017) proposed Equilibrium Propagation - a method for gradient-based train- ing of neural networks which uses only local learning rules and, crucially, does not rely on neurons having a mechanism for back-propagating an error gradient. Equilibrium propagation, however, has a major practical limitation: inference involves doing an iterative optimization of neural activations to find a fixed-point, and the number of steps required to closely approximate this fixed point scales poorly with the depth of the network. In response to this problem, we propose Initialized Equilibrium Propagation, which trains a feedforward network to initialize the iterative inference procedure for Equilibrium propagation. This feed-forward network learns to approximate the state of the fixed-point using a local learning rule. After training, we can simply use this initializing network for inference, resulting in a learned feedforward network. Our experiments show that this network appears to work as well or better than the original version of Equilibrium propagation. This shows how we might go about training deep networks without using backpropagation.
Understanding Isomorphism Bias in Graph Data Sets 
Authors: Ivanov Sergey, Sviridov Sergey, Evgeny Burnaev

In recent years there has been a rapid increase in classification methods on graph structured data. Both in graph kernels and graph neural networks, one of the implicit assumptions of successful state-of-the-art models was that incorporating graph isomorphism features into the architecture leads to better empirical performance. However, as we discover in this work, commonly used data sets for graph classification have repeating instances which cause the problem of isomorphism bias, i.e. artificially increasing the accuracy of the models by memorizing target information from the training set. This prevents fair competition of the algorithms and raises a question of the validity of the obtained results. We analyze 54 data sets, previously extensively used for graph-related tasks, on the existence of isomorphism bias, give a set of recommendations to machine learning practitioners to properly set up their models, and open source new data sets for the future experiments.
Information Dropout: learning optimal representations through noise
Authors: Alessandro Achille, Stefano Soatto

We introduce Information Dropout, a generalization of dropout that is motivated by the Information Bottleneck principle and highlights the way in which injecting noise in the activations can help in learning optimal representations of the data. Information Dropout is rooted in information theoretic principles, it includes as special cases several existing dropout methods, like Gaussian Dropout and Variational Dropout, and, unlike classical dropout, it can learn and build representations that are invariant to nuisances of the data, like occlusions and clutter. When the task is the reconstruction of the input, we show that the information dropout method yields a variational autoencoder as a special case, thus providing a link between representation learning, information theory and variational inference. Our experiments validate the theoretical intuitions behind our method, and we find that information dropout achieves a comparable or better generalization performance than binary dropout, especially on smaller models, since it can automatically adapt the noise to the structure of the network, as well as to the test sample.
GNN-LM: Language Modeling based on Global Contexts via GNN
Authors: Yuxian Meng, Shi Zong, Xiaoya Li, Xiaofei Sun, Tianwei Zhang, Fei Wu, Jiwei Li

Inspired by the notion that "it to copy is easier than to memorize", in this work, we introduce GNN-LM, which extends vanilla neural language model (LM) by allowing to reference similar contexts in the entire training corpus. We build a directed heterogeneous graph between an input context and its semantically related neighbors selected from the training corpus, where nodes are tokens in the input context and retrieved neighbor contexts, and edges represent connections between nodes. Graph neural networks (GNNs) are constructed upon the graph to aggregate information from similar contexts to decode the token. This learning paradigm provides direct access to the reference contexts and helps improve a model's generalization ability. We conduct comprehensive experiments to validate the effectiveness of the GNN-LM: GNN-LM achieves a new state-of-the-art perplexity of 14.8 on WikiText-103 (a 3.9 point improvement over its counterpart of the vanilla  LM model), and shows substantial improvement on One Billion Word and Enwiki8 datasets against strong baselines. In-depth ablation studies are performed to understand the mechanics of GNN-LM. The code can be found at https://github.com/ShannonAI/GNN-LM.
MARGINALIZED AVERAGE ATTENTIONAL NETWORK FOR WEAKLY-SUPERVISED LEARNING
Authors: Yuan Yuan, Yueming Lyu, Xi Shen, Ivor W. Tsang, Dit-Yan Yeung

In weakly-supervised temporal action localization, previous works have failed to locate dense and integral regions for each entire action due to the overestimation of the most salient regions. To alleviate this issue, we propose a marginalized average attentional network (MAAN) to suppress the dominant response of the most salient regions in a principled manner. The MAAN employs a novel marginalized average aggregation (MAA) module and learns a set of latent discriminative probabilities in an end-to-end fashion.  MAA samples multiple subsets from the video snippet features according to a set of latent discriminative probabilities and takes the expectation over all the averaged subset features. Theoretically, we prove that the MAA module with learned latent discriminative probabilities successfully reduces the difference in responses between the most salient regions and the others. Therefore, MAAN is able to generate better class activation sequences and identify dense and integral action regions in the videos. Moreover, we propose a fast algorithm to reduce the complexity of constructing MAA from $O(2^T)$ to $O(T^2)$. Extensive experiments on two large-scale video datasets show that our MAAN achieves a superior performance on weakly-supervised temporal action localization.
Fast Adaptive Anomaly Detection
Authors: Ze Wang, Yipin Zhou, Rui Wang, Tsung-Yu Lin, Ashish Shah, Ser-Nam Lim

The ability to detect anomaly has long been recognized as an inherent human ability, yet to date, practical AI solutions to mimic such capability have been lacking.This lack of progress can be attributed to several factors.  To begin with, the distribution of “abnormalities” is intractable.   Anything outside of a given normal population is by definition an anomaly. This explains why a large volume of workin this area has been dedicated to modeling the normal distribution of a given task followed by detecting deviations from it. This direction is however unsatisfying as it would require modeling the normal distribution of every task that comes along, which includes tedious data collection.  In this paper, we report our work aiming to handle these issues. To deal with the intractability of abnormal distribution, we leverage Energy Based Model (EBM). EBMs learn to associates low energies to correct values and higher energies to incorrect values.  As its core, the EBM em-ploys Langevin Dynamics (LD) in generating these incorrect samples based on an iterative optimization procedure, alleviating the intractable problem of modeling the world of anomalies.  Then, in order to avoid training an anomaly detector for every task, we utilize an adaptive sparse coding layer. Our intention is to design a plug and play feature that can be used to quickly update what is normal during inference time. Lastly, to avoid tedious data collection, this mentioned update of the sparse coding layer needs to be achievable with just a few shots. Here, we employ a meta learning scheme that simulates such a few shot setting during training. We support our findings with strong empirical evidence.
On Optimal Early Stopping: Overparametrization versus Underparametrization
Authors: Ruoqi Shen, Liyao Gao, Yian Ma

Early stopping is a simple and widely used method to prevent over-training neural networks. We develop theoretical results to reveal the relationship between optimal early stopping time and model dimension as well as sample size of the dataset for certain linear regression models. Our results demonstrate two very different behaviors when the model dimension exceeds the number of features versus the opposite scenario. While most previous works on linear models focus on the latter setting, we observe that in common deep learning tasks, the dimension of the model often exceeds the number of features arising from data. We demonstrate experimentally that our theoretical results on optimal early stopping time corresponds to the training process of deep neural network. Moreover, we study the effect of early stopping on generalization and demonstrate that optimal early stopping can help mitigate ''descent'' in various settings.