OpenRaiser/Intern-Atlas huggingface dataset:
A Field Guide to Scientific XAI: Transparent and Interpretable Deep Learning for Bioinformatics Research
Venue: arXiv cs.LG 2021
Year: 2021

Deep learning has become popular because of its potential to achieve high accuracy in prediction tasks. However, accuracy is not always the only goal of statistical modelling, especially for models developed as part of scientific research. Rather, many scientific models are developed to facilitate scientific discovery, by which we mean to abstract a human-understandable representation of the natural world. Unfortunately, the opacity of deep neural networks limit their role in scientific discovery, creating a new demand for models that are transparently interpretable. This article is a field guide to transparent model design. It provides a taxonomy of transparent model design concepts, a practical workflow for putting design concepts into practice, and a general template for reporting design choices. We hope this field guide will help researchers more effectively design transparently interpretable models, and thus enable them to use deep learning for scientific discovery.
Memory-augmented Adversarial Autoencoders for Multivariate Time-series Anomaly Detection with Deep Reconstruction and Prediction
Venue: arXiv cs.LG 2021
Year: 2021

Detecting anomalies for multivariate time-series without manual supervision continues a challenging problem due to the increased scale of dimensions and complexity of today's IT monitoring systems. Recent progress of unsupervised time-series anomaly detection mainly use deep autoencoders to solve this problem, i.e. training on normal samples and producing significant reconstruction error on abnormal inputs. However, in practice, autoencoders can reconstruct anomalies so well, due to powerful capabilites of neural networks. Besides, these approaches can be ineffective for identifying non-point anomalies, e.g. contextual anomalies and collective anomalies, since they solely utilze a point-wise reconstruction objective. To tackle the above issues, we propose MemAAE (\textit{Memory-augmented Adversarial Autoencoders with Deep Reconstruction and Prediction}), a novel unsupervised anomaly detection method for time-series. By jointly training two complementary proxy tasks, reconstruction and prediction, with a shared network architecture, we show that detecting anomalies via multiple tasks obtains superior performance rather than single-task training. Additionally, a compressive memory module is introduced to preserve normal patterns, avoiding unexpected generalization on abnormal inputs. Through extensive experiments, MemAAE achieves an overall F1 score of 0.90 on four public datasets, significantly outperforming the best baseline by 0.02.
Coverage Probability of Double-IRS Assisted Communication Systems
Venue: arXiv cs.IT 2021
Year: 2021

In this paper, we focus on the coverage probability of a double-intelligent reflecting surface (IRS) assisted wireless network and study the impact of multiplicative beamforming gain and correlated Rayleigh fading. In particular, we obtain a novel closed-form expression of the coverage probability of a single-input single-output (SISO) system assisted by two large IRSs while being dependent on the corresponding arbitrary reflecting beamforming matrices (RBMs) and large-scale statistics in terms of correlation matrices. Taking advantage of the large-scale statistics, i.e., statistical channel state information (CSI), we perform optimization of the RBMs of both IRSs once per several coherence intervals rather than at each interval. Hence, we achieve a reduction of the computational complexity, otherwise increased in multi-IRS-assisted networks during their RBM optimization. Numerical results validate the analytical expressions even for small IRSs, confirm enhanced performance over the conventional single-IRS counterpart, and reveal insightful properties.
Dynamic probabilistic logic models for effective abstractions in RL
Venue: arXiv cs.AI 2021
Year: 2021

State abstraction enables sample-efficient learning and better task transfer in complex reinforcement learning environments. Recently, we proposed RePReL (Kokel et al. 2021), a hierarchical framework that leverages a relational planner to provide useful state abstractions for learning. We present a brief overview of this framework and the use of a dynamic probabilistic logic model to design these state abstractions. Our experiments show that RePReL not only achieves better performance and efficient learning on the task at hand but also demonstrates better generalization to unseen tasks.
Robustness of different loss functions and their impact on networks learning capability
Venue: arXiv cs.LG 2021
Year: 2021

Recent developments in AI have made it ubiquitous, every industry is trying to adopt some form of intelligent processing of their data. Despite so many advances in the field, AIs full capability is yet to be exploited by the industry. Industries that involve some risk factors still remain cautious about the usage of AI due to the lack of trust in such autonomous systems. Present-day AI might be very good in a lot of things but it is very bad in reasoning and this behavior of AI can lead to catastrophic results. Autonomous cars crashing into a person or a drone getting stuck in a tree are a few examples where AI decisions lead to catastrophic results. To develop insight and generate an explanation about the learning capability of AI, we will try to analyze the working of loss functions. For our case, we will use two sets of loss functions, generalized loss functions like Binary cross-entropy or BCE and specialized loss functions like Dice loss or focal loss. Through a series of experiments, we will establish whether combining different loss functions is better than using a single loss function and if yes, then what is the reason behind it. In order to establish the difference between generalized loss and specialized losses, we will train several models using the above-mentioned losses and then compare their robustness on adversarial examples. In particular, we will look at how fast the accuracy of different models decreases when we change the pixels corresponding to the most salient gradients.
Mitigating Membership Inference Attacks by Self-Distillation Through a Novel Ensemble Architecture
Venue: arXiv cs.CR 2021
Year: 2021

Membership inference attacks are a key measure to evaluate privacy leakage in machine learning (ML) models. These attacks aim to distinguish training members from non-members by exploiting differential behavior of the models on member and non-member inputs. The goal of this work is to train ML models that have high membership privacy while largely preserving their utility; we therefore aim for an empirical membership privacy guarantee as opposed to the provable privacy guarantees provided by techniques like differential privacy, as such techniques are shown to deteriorate model utility. Specifically, we propose a new framework to train privacy-preserving models that induces similar behavior on member and non-member inputs to mitigate membership inference attacks. Our framework, called SELENA, has two major components. The first component and the core of our defense is a novel ensemble architecture for training. This architecture, which we call Split-AI, splits the training data into random subsets, and trains a model on each subset of the data. We use an adaptive inference strategy at test time: our ensemble architecture aggregates the outputs of only those models that did not contain the input sample in their training data. We prove that our Split-AI architecture defends against a large family of membership inference attacks, however, it is susceptible to new adaptive attacks. Therefore, we use a second component in our framework called Self-Distillation to protect against such stronger attacks. The Self-Distillation component (self-)distills the training dataset through our Split-AI ensemble, without using any external public datasets. Through extensive experiments on major benchmark datasets we show that SELENA presents a superior trade-off between membership privacy and utility compared to the state of the art.
A New Approach for Interpretability and Reliability in Clinical Risk Prediction: Acute Coronary Syndrome Scenario
Venue: arXiv cs.LG 2021
Year: 2021

We intend to create a new risk assessment methodology that combines the best characteristics of both risk score and machine learning models. More specifically, we aim to develop a method that, besides having a good performance, offers a personalized model and outcome for each patient, presents high interpretability, and incorporates an estimation of the prediction reliability which is not usually available. By combining these features in the same approach we expect that it can boost the confidence of physicians to use such a tool in their daily activity. In order to achieve the mentioned goals, a three-step methodology was developed: several rules were created by dichotomizing risk factors; such rules were trained with a machine learning classifier to predict the acceptance degree of each rule (the probability that the rule is correct) for each patient; that information was combined and used to compute the risk of mortality and the reliability of such prediction. The methodology was applied to a dataset of patients admitted with any type of acute coronary syndromes (ACS), to assess the 30-days all-cause mortality risk. The performance was compared with state-of-the-art approaches: logistic regression (LR), artificial neural network (ANN), and clinical risk score model (Global Registry of Acute Coronary Events - GRACE). The proposed approach achieved testing results identical to the standard LR, but offers superior interpretability and personalization; it also significantly outperforms the GRACE risk model and the standard ANN model. The calibration curve also suggests a very good generalization ability of the obtained model as it approaches the ideal curve. Finally, the reliability estimation of individual predictions presented a great correlation with the misclassifications rate. Those properties may have a beneficial application in other clinical scenarios as well. [abridged]
A Neural Network Ensemble Approach to System Identification
Venue: arXiv cs.LG 2021
Year: 2021

We present a new algorithm for learning unknown governing equations from trajectory data, using and ensemble of neural networks. Given samples of solutions $x(t)$ to an unknown dynamical system $\dot{x}(t)=f(t,x(t))$, we approximate the function $f$ using an ensemble of neural networks. We express the equation in integral form and use Euler method to predict the solution at every successive time step using at each iteration a different neural network as a prior for $f$. This procedure yields M-1 time-independent networks, where M is the number of time steps at which $x(t)$ is observed. Finally, we obtain a single function $f(t,x(t))$ by neural network interpolation. Unlike our earlier work, where we numerically computed the derivatives of data, and used them as target in a Lipschitz regularized neural network to approximate $f$, our new method avoids numerical differentiations, which are unstable in presence of noise. We test the new algorithm on multiple examples both with and without noise in the data. We empirically show that generalization and recovery of the governing equation improve by adding a Lipschitz regularization term in our loss function and that this method improves our previous one especially in presence of noise, when numerical differentiation provides low quality target data. Finally, we compare our results with the method proposed by Raissi, et al. arXiv:1801.01236 (2018) and with SINDy.
Comparing Human and Machine Bias in Face Recognition
Venue: arXiv cs.CV 2021
Year: 2021

Much recent research has uncovered and discussed serious concerns of bias in facial analysis technologies, finding performance disparities between groups of people based on perceived gender, skin type, lighting condition, etc. These audits are immensely important and successful at measuring algorithmic bias but have two major challenges: the audits (1) use facial recognition datasets which lack quality metadata, like LFW and CelebA, and (2) do not compare their observed algorithmic bias to the biases of their human alternatives. In this paper, we release improvements to the LFW and CelebA datasets which will enable future researchers to obtain measurements of algorithmic bias that are not tainted by major flaws in the dataset (e.g. identical images appearing in both the gallery and test set). We also use these new data to develop a series of challenging facial identification and verification questions that we administered to various algorithms and a large, balanced sample of human reviewers. We find that both computer models and human survey participants perform significantly better at the verification task, generally obtain lower accuracy rates on dark-skinned or female subjects for both tasks, and obtain higher accuracy rates when their demographics match that of the question. Computer models are observed to achieve a higher level of accuracy than the survey participants on both tasks and exhibit bias to similar degrees as the human survey participants.
sbp-env: Sampling-based Motion Planners' Testing Environment
Venue: arXiv cs.RO 2021
Year: 2021

Sampling-based motion planners' testing environment (sbp-env) is a full feature framework to quickly test different sampling-based algorithms for motion planning. sbp-env focuses on the flexibility of tinkering with different aspects of the framework, and had divided the main planning components into two categories (i) samplers and (ii) planners. The focus of motion planning research had been mainly on (i) improving the sampling efficiency (with methods such as heuristic or learned distribution) and (ii) the algorithmic aspect of the planner using different routines to build a connected graph. Therefore, by separating the two components one can quickly swap out different components to test novel ideas.
Toward Uncensorable, Anonymous and Private Access Over Satoshi Blockchains
Venue: arXiv cs.CR 2021
Year: 2021

Providing unrestricted access to sensitive content such as news and software is difficult in the presence of adaptive and resourceful surveillance and censoring adversaries. In this paper we leverage the distributed and resilient nature of commercial Satoshi blockchains to develop the first provably secure, censorship resistant, cost-efficient storage system with anonymous and private access, built on top of commercial cryptocurrency transactions. We introduce max-rate transactions, a practical construct to persist data of arbitrary size entirely in a Satoshi blockchain. We leverage max-rate transactions to develop UWeb, a blockchain-based storage system that charges publishers to self-sustain its decentralized infrastructure. UWeb organizes blockchainstored content for easy retrieval, and enables clients to store and access content with provable anonymity, privacy and censorship resistance properties. We present results from UWeb experiments with writing 268.21 MB of data into the live Litecoin blockchain, including 4.5 months of live-feed BBC articles, and 41 censorship resistant tools. The max-rate writing throughput (183 KB/s) and blockchain utilization (88%) exceed those of state-of-the-art solutions by 2-3 orders of magnitude and broke Litecoin's record of the daily average block size. Our simulations with up to 3,000 concurrent UWeb writers confirm that UWeb does not impact the confirmation delays of financial transactions.
FedMM: Saddle Point Optimization for Federated Adversarial Domain Adaptation
Venue: arXiv cs.LG 2021
Year: 2021

Federated adversary domain adaptation is a unique distributed minimax training task due to the prevalence of label imbalance among clients, with each client only seeing a subset of the classes of labels required to train a global model. To tackle this problem, we propose a distributed minimax optimizer referred to as FedMM, designed specifically for the federated adversary domain adaptation problem. It works well even in the extreme case where each client has different label classes and some clients only have unsupervised tasks. We prove that FedMM ensures convergence to a stationary point with domain-shifted unsupervised data. On a variety of benchmark datasets, extensive experiments show that FedMM consistently achieves either significant communication savings or significant accuracy improvements over federated optimizers based on the gradient descent ascent (GDA) algorithm. When training from scratch, for example, it outperforms other GDA based federated average methods by around $20\%$ in accuracy over the same communication rounds; and it consistently outperforms when training from pre-trained models with an accuracy improvement from $5.4\%$ to $9\%$ for different networks.
Substructure Distribution Projection for Zero-Shot Cross-Lingual Dependency Parsing
Venue: arXiv cs.CL 2021
Year: 2021

We present substructure distribution projection (SubDP), a technique that projects a distribution over structures in one domain to another, by projecting substructure distributions separately. Models for the target domains can be then trained, using the projected distributions as soft silver labels. We evaluate SubDP on zero-shot cross-lingual dependency parsing, taking dependency arcs as substructures: we project the predicted dependency arc distributions in the source language(s) to target language(s), and train a target language parser to fit the resulting distributions. When an English treebank is the only annotation that involves human effort, SubDP achieves better unlabeled attachment score than all prior work on the Universal Dependencies v2.2 (Nivre et al., 2020) test set across eight diverse target languages, as well as the best labeled attachment score on six out of eight languages. In addition, SubDP improves zero-shot cross-lingual dependency parsing with very few (e.g., 50) supervised bitext pairs, across a broader range of target languages.
Neural Network Pruning Through Constrained Reinforcement Learning
Venue: arXiv cs.CV 2021
Year: 2021

Network pruning reduces the size of neural networks by removing (pruning) neurons such that the performance drop is minimal. Traditional pruning approaches focus on designing metrics to quantify the usefulness of a neuron which is often quite tedious and sub-optimal. More recent approaches have instead focused on training auxiliary networks to automatically learn how useful each neuron is however, they often do not take computational limitations into account. In this work, we propose a general methodology for pruning neural networks. Our proposed methodology can prune neural networks to respect pre-defined computational budgets on arbitrary, possibly non-differentiable, functions. Furthermore, we only assume the ability to be able to evaluate these functions for different inputs, and hence they do not need to be fully specified beforehand. We achieve this by proposing a novel pruning strategy via constrained reinforcement learning algorithms. We prove the effectiveness of our approach via comparison with state-of-the-art methods on standard image classification datasets. Specifically, we reduce 83-92.90 of total parameters on various variants of VGG while achieving comparable or better performance than that of original networks. We also achieved 75.09 reduction in parameters on ResNet18 without incurring any loss in accuracy.
Generative Adversarial Imitation Learning for End-to-End Autonomous Driving on Urban Environments
Venue: arXiv cs.RO 2021
Year: 2021

Autonomous driving is a complex task, which has been tackled since the first self-driving car ALVINN in 1989, with a supervised learning approach, or behavioral cloning (BC). In BC, a neural network is trained with state-action pairs that constitute the training set made by an expert, i.e., a human driver. However, this type of imitation learning does not take into account the temporal dependencies that might exist between actions taken in different moments of a navigation trajectory. These type of tasks are better handled by reinforcement learning (RL) algorithms, which need to define a reward function. On the other hand, more recent approaches to imitation learning, such as Generative Adversarial Imitation Learning (GAIL), can train policies without explicitly requiring to define a reward function, allowing an agent to learn by trial and error directly on a training set of expert trajectories. In this work, we propose two variations of GAIL for autonomous navigation of a vehicle in the realistic CARLA simulation environment for urban scenarios. Both of them use the same network architecture, which process high dimensional image input from three frontal cameras, and other nine continuous inputs representing the velocity, the next point from the sparse trajectory and a high-level driving command. We show that both of them are capable of imitating the expert trajectory from start to end after training ends, but the GAIL loss function that is augmented with BC outperforms the former in terms of convergence time and training stability.
MAAD: A Model and Dataset for "Attended Awareness" in Driving
Venue: arXiv cs.HC 2021
Year: 2021

We propose a computational model to estimate a person's attended awareness of their environment. We define attended awareness to be those parts of a potentially dynamic scene which a person has attended to in recent history and which they are still likely to be physically aware of. Our model takes as input scene information in the form of a video and noisy gaze estimates, and outputs visual saliency, a refined gaze estimate, and an estimate of the person's attended awareness. In order to test our model, we capture a new dataset with a high-precision gaze tracker including 24.5 hours of gaze sequences from 23 subjects attending to videos of driving scenes. The dataset also contains third-party annotations of the subjects' attended awareness based on observations of their scan path. Our results show that our model is able to reasonably estimate attended awareness in a controlled setting, and in the future could potentially be extended to real egocentric driving data to help enable more effective ahead-of-time warnings in safety systems and thereby augment driver performance. We also demonstrate our model's effectiveness on the tasks of saliency, gaze calibration, and denoising, using both our dataset and an existing saliency dataset. We make our model and dataset available at https://github.com/ToyotaResearchInstitute/att-aware/.
Partial Hierarchical Pose Graph Optimization for SLAM
Venue: arXiv cs.RO 2021
Year: 2021

In this paper we consider a hierarchical pose graph optimization (HPGO) for Simultaneous Localization and Mapping (SLAM). We propose a fast incremental procedure for building hierarchy levels in pose graphs. We study the properties of this procedure and show that our solution delivers high execution speed, high reduction rate and good flexibility. We propose a way to do partial hierarchical optimization and compare it to other optimization modes. We show that given a comparatively large amount of poses, partial HPGO gives a 10x speed up comparing to the original optimization, not sacrificing the quality.