OpenRaiser/Intern-Atlas huggingface dataset:
SafeDrug: Dual Molecular Graph Encoders for Recommending Effective and Safe Drug Combinations
Venue: arXiv cs.LG 2022
Year: 2022

Medication recommendation is an essential task of AI for healthcare. Existing works focused on recommending drug combinations for patients with complex health conditions solely based on their electronic health records. Thus, they have the following limitations: (1) some important data such as drug molecule structures have not been utilized in the recommendation process. (2) drug-drug interactions (DDI) are modeled implicitly, which can lead to sub-optimal results. To address these limitations, we propose a DDI-controllable drug recommendation model named SafeDrug to leverage drugs' molecule structures and model DDIs explicitly. SafeDrug is equipped with a global message passing neural network (MPNN) module and a local bipartite learning module to fully encode the connectivity and functionality of drug molecules. SafeDrug also has a controllable loss function to control DDI levels in the recommended drug combinations effectively. On a benchmark dataset, our SafeDrug is relatively shown to reduce DDI by 19.43% and improves 2.88% on Jaccard similarity between recommended and actually prescribed drug combinations over previous approaches. Moreover, SafeDrug also requires much fewer parameters than previous deep learning-based approaches, leading to faster training by about 14% and around 2x speed-up in inference.
Meta-Learning-Based Deep Reinforcement Learning for Multiobjective Optimization Problems
Venue: arXiv cs.AI 2022
Year: 2022

Deep reinforcement learning (DRL) has recently shown its success in tackling complex combinatorial optimization problems. When these problems are extended to multiobjective ones, it becomes difficult for the existing DRL approaches to flexibly and efficiently deal with multiple subproblems determined by weight decomposition of objectives. This paper proposes a concise meta-learning-based DRL approach. It first trains a meta-model by meta-learning. The meta-model is fine-tuned with a few update steps to derive submodels for the corresponding subproblems. The Pareto front is then built accordingly. Compared with other learning-based methods, our method can greatly shorten the training time of multiple submodels. Due to the rapid and excellent adaptability of the meta-model, more submodels can be derived so as to increase the quality and diversity of the found solutions. The computational experiments on multiobjective traveling salesman problems and multiobjective vehicle routing problem with time windows demonstrate the superiority of our method over most of learning-based and iteration-based approaches.
Multi-FR: A Multi-objective Optimization Framework for Multi-stakeholder Fairness-aware Recommendation
Venue: arXiv cs.IR 2022
Year: 2022

Nowadays, most online services are hosted on multi-stakeholder marketplaces, where consumers and producers may have different objectives. Conventional recommendation systems, however, mainly focus on maximizing consumers' satisfaction by recommending the most relevant items to each individual. This may result in unfair exposure of items, thus jeopardizing producer benefits. Additionally, they do not care whether consumers from diverse demographic groups are equally satisfied. To address these limitations, we propose a multi-objective optimization framework for fairness-aware recommendation, Multi-FR, that adaptively balances accuracy and fairness for various stakeholders with Pareto optimality guarantee. We first propose four fairness constraints on consumers and producers. In order to train the whole framework in an end-to-end way, we utilize the smooth rank and stochastic ranking policy to make these fairness criteria differentiable and friendly to back-propagation. Then, we adopt the multiple gradient descent algorithm to generate a Pareto set of solutions, from which the most appropriate one is selected by the Least Misery Strategy. The experimental results demonstrate that Multi-FR largely improves recommendation fairness on multiple stakeholders over the state-of-the-art approaches while maintaining almost the same recommendation accuracy. The training efficiency study confirms our model's ability to simultaneously optimize different fairness constraints for many stakeholders efficiently.
Laplace Matching for fast Approximate Inference in Latent Gaussian Models
Venue: arXiv cs.LG 2022
Year: 2022

Bayesian inference on non-Gaussian data is often non-analytic and requires computationally expensive approximations such as sampling or variational inference. We propose an approximate inference framework primarily designed to be computationally cheap while still achieving high approximation quality. The concept, which we call Laplace Matching, involves closed-form, approximate, bi-directional transformations between the parameter spaces of exponential families. These are constructed from Laplace approximations under custom-designed basis transformations. The mappings can then be leveraged to effectively turn a latent Gaussian distribution into an approximate conjugate prior to a rich class of observable variables. This allows us to train latent Gaussian models such as Gaussian Processes on non-Gaussian data at nearly no additional cost. The method can be thought of as a pre-processing step which can be implemented in <5 lines of code and runs in less than a second. Furthermore, Laplace Matching yields a simple way to group similar data points together, e.g. to produce inducing points for GPs. We empirically evaluate the method with experiments for four different exponential distributions, namely the Beta, Gamma, Dirichlet and inverse Wishart, showing approximation quality comparable to state-of-the-art approximate inference techniques at a drastic reduction in computational cost.
Duplex Sequence-to-Sequence Learning for Reversible Machine Translation
Venue: arXiv cs.CL 2022
Year: 2022

Sequence-to-sequence learning naturally has two directions. How to effectively utilize supervision signals from both directions? Existing approaches either require two separate models, or a multitask-learned model but with inferior performance. In this paper, we propose REDER (Reversible Duplex Transformer), a parameter-efficient model and apply it to machine translation. Either end of REDER can simultaneously input and output a distinct language. Thus REDER enables reversible machine translation by simply flipping the input and output ends. Experiments verify that REDER achieves the first success of reversible machine translation, which helps outperform its multitask-trained baselines by up to 1.3 BLEU.
Mental Models of Adversarial Machine Learning
Venue: arXiv cs.CR 2022
Year: 2022

Although machine learning is widely used in practice, little is known about practitioners' understanding of potential security challenges. In this work, we close this substantial gap and contribute a qualitative study focusing on developers' mental models of the machine learning pipeline and potentially vulnerable components. Similar studies have helped in other security fields to discover root causes or improve risk communication. Our study reveals two \facets of practitioners' mental models of machine learning security. Firstly, practitioners often confuse machine learning security with threats and defences that are not directly related to machine learning. Secondly, in contrast to most academic research, our participants perceive security of machine learning as not solely related to individual models, but rather in the context of entire workflows that consist of multiple components. Jointly with our additional findings, these two facets provide a foundation to substantiate mental models for machine learning security and have implications for the integration of adversarial machine learning into corporate workflows, \new{decreasing practitioners' reported uncertainty}, and appropriate regulatory frameworks for machine learning security.
Separations for Estimating Large Frequency Moments on Data Streams
Venue: arXiv cs.DS 2022
Year: 2022

We study the classical problem of moment estimation of an underlying vector whose $n$ coordinates are implicitly defined through a series of updates in a data stream. We show that if the updates to the vector arrive in the random-order insertion-only model, then there exist space efficient algorithms with improved dependencies on the approximation parameter $\varepsilon$. In particular, for any real $p > 2$, we first obtain an algorithm for $F_p$ moment estimation using $\tilde{\mathcal{O}}\left(\frac{1}{\varepsilon^{4/p}}\cdot n^{1-2/p}\right)$ bits of memory. Our techniques also give algorithms for $F_p$ moment estimation with $p>2$ on arbitrary order insertion-only and turnstile streams, using $\tilde{\mathcal{O}}\left(\frac{1}{\varepsilon^{4/p}}\cdot n^{1-2/p}\right)$ bits of space and two passes, which is the first optimal multi-pass $F_p$ estimation algorithm up to $\log n$ factors. Finally, we give an improved lower bound of $Ω\left(\frac{1}{\varepsilon^2}\cdot n^{1-2/p}\right)$ for one-pass insertion-only streams. Our results separate the complexity of this problem both between random and non-random orders, as well as one-pass and multi-pass streams.
Neural Program Repair with Execution-based Backpropagation
Venue: arXiv cs.SE 2022
Year: 2022

Neural machine translation (NMT) architectures have achieved promising results for automatic program repair. Yet, they have the limitation of generating low-quality patches (e.g., not compilable patches). This is because the existing works only optimize a purely syntactic loss function based on characters and tokens without incorporating program-specific information during neural network weight optimization. In this paper, we propose a novel program repair model called RewardRepair. The core novelty of RewardRepair is to improve NMT-based program repair with a loss function based on program compilation and test execution information, rewarding the network to produce patches that compile and that do not overfit. We conduct several experiments to evaluate RewardRepair showing that it is feasible and effective to use compilation and test execution results to optimize the underlying neural repair model. RewardRepair correctly repairs 207 bugs over four benchmarks. we report on repair success for 121 bugs that are fixed for the first time in the literature. Also, RewardRepair produces up to 45.3% of compilable patches, an improvement over the 39% by the state-of-the-art.
Partitioning H-Free Graphs of Bounded Diameter
Venue: arXiv cs.DS 2022
Year: 2022

A natural way of increasing our understanding of NP-complete graph problems is to restrict the input to a special graph class. Classes of $H$-free graphs, that is, graphs that do not contain some graph $H$ as an induced subgraph, have proven to be an ideal testbed for such a complexity study. However, if the forbidden graph $H$ contains a cycle or claw, then these problems often stay NP-complete. A recent complexity study on the $k$-Colouring problem shows that we may still obtain tractable results if we also bound the diameter of the $H$-free input graph. We continue this line of research by initiating a complexity study on the impact of bounding the diameter for a variety of classical vertex partitioning problems restricted to $H$-free graphs. We prove that bounding the diameter does not help for Independent Set, but leads to new tractable cases for problems closely related to 3-Colouring. That is, we show that Near-Bipartiteness, Independent Feedback Vertex Set, Independent Odd Cycle Transversal, Acyclic 3-Colouring and Star 3-Colouring are all polynomial-time solvable for chair-free graphs of bounded diameter. To obtain these results we exploit a new structural property of 3-colourable chair-free graphs.
SUPR-GAN: SUrgical PRediction GAN for Event Anticipation in Laparoscopic and Robotic Surgery
Venue: arXiv cs.CV 2022
Year: 2022

Comprehension of surgical workflow is the foundation upon which artificial intelligence (AI) and machine learning (ML) holds the potential to assist intraoperative decision-making and risk mitigation. In this work, we move beyond mere identification of past surgical phases, into the prediction of future surgical steps and specification of the transitions between them. We use a novel Generative Adversarial Network (GAN) formulation to sample future surgical phases trajectories conditioned on past video frames from laparoscopic cholecystectomy (LC) videos and compare it to state-of-the-art approaches for surgical video analysis and alternative prediction methods. We demonstrate the GAN formulation's effectiveness through inferring and predicting the progress of LC videos. We quantify the horizon-accuracy trade-off and explored average performance, as well as the performance on the more challenging, and clinically relevant transitions between phases. Furthermore, we conduct a survey, asking 16 surgeons of different specialties and educational levels to qualitatively evaluate predicted surgery phases.
Survey and Taxonomy of Adversarial Reconnaissance Techniques
Venue: arXiv cs.CR 2022
Year: 2022

Adversaries are often able to penetrate networks and compromise systems by exploiting vulnerabilities in people and systems. The key to the success of these attacks is information that adversaries collect throughout the phases of the cyber kill chain. We summarize and analyze the methods, tactics, and tools that adversaries use to conduct reconnaissance activities throughout the attack process. First, we discuss what types of information adversaries seek, and how and when they can obtain this information. Then, we provide a taxonomy and detailed overview of adversarial reconnaissance techniques. The taxonomy introduces a categorization of reconnaissance techniques based on the source as third-party, human-, and system-based information gathering. This paper provides a comprehensive view of adversarial reconnaissance that can help in understanding and modeling this complex but vital aspect of cyber attacks as well as insights that can improve defensive strategies, such as cyber deception.
TAG: Task-based Accumulated Gradients for Lifelong learning
Venue: arXiv cs.LG 2022
Year: 2022

When an agent encounters a continual stream of new tasks in the lifelong learning setting, it leverages the knowledge it gained from the earlier tasks to help learn the new tasks better. In such a scenario, identifying an efficient knowledge representation becomes a challenging problem. Most research works propose to either store a subset of examples from the past tasks in a replay buffer, dedicate a separate set of parameters to each task or penalize excessive updates over parameters by introducing a regularization term. While existing methods employ the general task-agnostic stochastic gradient descent update rule, we propose a task-aware optimizer that adapts the learning rate based on the relatedness among tasks. We utilize the directions taken by the parameters during the updates by accumulating the gradients specific to each task. These task-based accumulated gradients act as a knowledge base that is maintained and updated throughout the stream. We empirically show that our proposed adaptive learning rate not only accounts for catastrophic forgetting but also allows positive backward transfer. We also show that our method performs better than several state-of-the-art methods in lifelong learning on complex datasets with a large number of tasks.
Restoring Hebrew Diacritics Without a Dictionary
Venue: arXiv cs.CL 2022
Year: 2022

We demonstrate that it is feasible to diacritize Hebrew script without any human-curated resources other than plain diacritized text. We present NAKDIMON, a two-layer character level LSTM, that performs on par with much more complicated curation-dependent systems, across a diverse array of modern Hebrew sources.
Object-Based Augmentation Improves Quality of Remote Sensing Semantic Segmentation
Venue: arXiv cs.CV 2022
Year: 2022

Today deep convolutional neural networks (CNNs) push the limits for most computer vision problems, define trends, and set state-of-the-art results. In remote sensing tasks such as object detection and semantic segmentation, CNNs reach the SotA performance. However, for precise performance, CNNs require much high-quality training data. Rare objects and the variability of environmental conditions strongly affect prediction stability and accuracy. To overcome these data restrictions, it is common to consider various approaches including data augmentation techniques. This study focuses on the development and testing of object-based augmentation. The practical usefulness of the developed augmentation technique is shown in the remote sensing domain, being one of the most demanded ineffective augmentation techniques. We propose a novel pipeline for georeferenced image augmentation that enables a significant increase in the number of training samples. The presented pipeline is called object-based augmentation (OBA) and exploits objects' segmentation masks to produce new realistic training scenes using target objects and various label-free backgrounds. We test the approach on the buildings segmentation dataset with six different CNN architectures and show that the proposed method benefits for all the tested models. We also show that further augmentation strategy optimization can improve the results. The proposed method leads to the meaningful improvement of U-Net model predictions from 0.78 to 0.83 F1-score.
Joint Optimization for RIS-Assisted Wireless Communications: From Physical and Electromagnetic Perspectives
Venue: arXiv cs.IT 2022
Year: 2022

Reconfigurable intelligent surfaces (RISs) are envisioned to be a disruptive wireless communication technique that is capable of reconfiguring the wireless propagation environment. In this paper, we study a free-space RIS-assisted multiple-input single-output (MISO) communication system in far-field operation. To maximize the received power from the physical and electromagnetic nature point of view, a comprehensive optimization, including beamforming of the transmitter, phase shifts of the RIS, orientation and position of the RIS is formulated and addressed. After exploiting the property of line-of-sight (LoS) links, we derive closed-form solutions of beamforming and phase shifts. For the non-trivial RIS position optimization problem in arbitrary three-dimensional space, a dimensional-reducing theory is proved. The simulation results show that the proposed closed-form beamforming and phase shifts approach the upper bound of the received power. The robustness of our proposed solutions in terms of the perturbation is also verified. Moreover, the RIS significantly enhances the performance of the mmWave/THz communication system.
Automating Data Science: Prospects and Challenges
Venue: arXiv cs.DB 2022
Year: 2022

Given the complexity of typical data science projects and the associated demand for human expertise, automation has the potential to transform the data science process. Key insights: * Automation in data science aims to facilitate and transform the work of data scientists, not to replace them. * Important parts of data science are already being automated, especially in the modeling stages, where techniques such as automated machine learning (AutoML) are gaining traction. * Other aspects are harder to automate, not only because of technological challenges, but because open-ended and context-dependent tasks require human interaction.
DEEMD: Drug Efficacy Estimation against SARS-CoV-2 based on cell Morphology with Deep multiple instance learning
Venue: arXiv cs.LG 2022
Year: 2022

Drug repurposing can accelerate the identification of effective compounds for clinical use against SARS-CoV-2, with the advantage of pre-existing clinical safety data and an established supply chain. RNA viruses such as SARS-CoV-2 manipulate cellular pathways and induce reorganization of subcellular structures to support their life cycle. These morphological changes can be quantified using bioimaging techniques. In this work, we developed DEEMD: a computational pipeline using deep neural network models within a multiple instance learning framework, to identify putative treatments effective against SARS-CoV-2 based on morphological analysis of the publicly available RxRx19a dataset. This dataset consists of fluorescence microscopy images of SARS-CoV-2 non-infected cells and infected cells, with and without drug treatment. DEEMD first extracts discriminative morphological features to generate cell morphological profiles from the non-infected and infected cells. These morphological profiles are then used in a statistical model to estimate the applied treatment efficacy on infected cells based on similarities to non-infected cells. DEEMD is capable of localizing infected cells via weak supervision without any expensive pixel-level annotations. DEEMD identifies known SARS-CoV-2 inhibitors, such as Remdesivir and Aloxistatin, supporting the validity of our approach. DEEMD can be explored for use on other emerging viruses and datasets to rapidly identify candidate antiviral treatments in the future}. Our implementation is available online at https://www.github.com/Sadegh-Saberian/DEEMD
Fairness in Information Access Systems
Venue: arXiv cs.IR 2022
Year: 2022

Recommendation, information retrieval, and other information access systems pose unique challenges for investigating and applying the fairness and non-discrimination concepts that have been developed for studying other machine learning systems. While fair information access shares many commonalities with fair classification, the multistakeholder nature of information access applications, the rank-based problem setting, the centrality of personalization in many cases, and the role of user response complicate the problem of identifying precisely what types and operationalizations of fairness may be relevant, let alone measuring or promoting them. In this monograph, we present a taxonomy of the various dimensions of fair information access and survey the literature to date on this new and rapidly-growing topic. We preface this with brief introductions to information access and algorithmic fairness, to facilitate use of this work by scholars with experience in one (or neither) of these fields who wish to learn about their intersection. We conclude with several open problems in fair information access, along with some suggestions for how to approach research in this space.
SimNet: Accurate and High-Performance Computer Architecture Simulation using Deep Learning
Venue: arXiv cs.AR 2022
Year: 2022

While discrete-event simulators are essential tools for architecture research, design, and development, their practicality is limited by an extremely long time-to-solution for realistic applications under investigation. This work describes a concerted effort, where machine learning (ML) is used to accelerate discrete-event simulation. First, an ML-based instruction latency prediction framework that accounts for both static instruction properties and dynamic processor states is constructed. Then, a GPU-accelerated parallel simulator is implemented based on the proposed instruction latency predictor, and its simulation accuracy and throughput are validated and evaluated against a state-of-the-art simulator. Leveraging modern GPUs, the ML-based simulator outperforms traditional simulators significantly.