Many applications such as recommendation systems or sports tournaments involve pairwise comparisons within a collection of $n$ items, the goal being to aggregate the binary outcomes of the comparisons in order to recover the latent strength and/or global ranking of the items. In recent years, this problem has received significant interest from a theoretical perspective with a number of methods being proposed, along with associated statistical guarantees under the assumption of a suitable generative model. While these results typically collect the pairwise comparisons as one comparison graph $G$, however in many applications - such as the outcomes of soccer matches during a tournament - the nature of pairwise outcomes can evolve with time. Theoretical results for such a dynamic setting are relatively limited compared to the aforementioned static setting. We study in this paper an extension of the classic BTL (Bradley-Terry-Luce) model for the static setting to our dynamic setup under the assumption that the probabilities of the pairwise outcomes evolve smoothly over the time domain $[0,1]$. Given a sequence of comparison graphs $(G_{t'})_{t' \in \mathcal{T}}$ on a regular grid $\mathcal{T} \subset [0,1]$, we aim at recovering the latent strengths of the items $w_t^* \in \mathbb{R}^n$ at any time $t \in [0,1]$. To this end, we adapt the Rank Centrality method - a popular spectral approach for ranking in the static case - by locally averaging the available data on a suitable neighborhood of $t$. When $(G_{t'})_{t' \in \mathcal{T}}$ is a sequence of Erd\"os-Renyi graphs, we provide non-asymptotic $\ell_2$ and $\ell_{\infty}$ error bounds for estimating $w_t^*$ which in particular establishes the consistency of this method in terms of $n$, and the grid size $\lvert\mathcal{T}\rvert$. We also complement our theoretical analysis with experiments on real and synthetic data.
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During Automated Program Repair (APR), it can be challenging to synthesize correct patches for real-world systems in general-purpose programming languages. Recent Large Language Models (LLMs) have been shown to be helpful "copilots" in assisting developers with various coding tasks, and have also been directly applied for patch synthesis. However, most LLMs treat programs as sequences of tokens, meaning that they are ignorant of the underlying semantics constraints of the target programming language. This results in plenty of statically invalid generated patches, impeding the practicality of the technique. Therefore, we propose Repilot, a framework to further copilot the AI "copilots" (i.e., LLMs) by synthesizing more valid patches during the repair process. Our key insight is that many LLMs produce outputs autoregressively (i.e., token by token), resembling human writing programs, which can be significantly boosted and guided through a Completion Engine. Repilot synergistically synthesizes a candidate patch through the interaction between an LLM and a Completion Engine, which 1) prunes away infeasible tokens suggested by the LLM and 2) proactively completes the token based on the suggestions provided by the Completion Engine. Our evaluation on a subset of the widely-used Defects4j 1.2 and 2.0 datasets shows that Repilot fixes 66 and 50 bugs, respectively, surpassing the best-performing baseline by 14 and 16 bugs fixed. More importantly, Repilot is capable of producing more valid and correct patches than the base LLM when given the same generation budget.
This note explores in more details instabilities of explicit super-time-stepping schemes, such as the Runge-Kutta-Chebyshev or Runge-Kutta-Legendre schemes, noticed in the litterature, when applied to the Heston stochastic volatility model. The stability remarks are relevant beyond the scope of super-time-stepping schemes.
Due to the proliferation of malware, defenders are increasingly turning to automation and machine learning as part of the malware detection tool-chain. However, machine learning models are susceptible to adversarial attacks, requiring the testing of model and product robustness. Meanwhile, attackers also seek to automate malware generation and evasion of antivirus systems, and defenders try to gain insight into their methods. This work proposes a new algorithm that combines Malware Evasion and Model Extraction (MEME) attacks. MEME uses model-based reinforcement learning to adversarially modify Windows executable binary samples while simultaneously training a surrogate model with a high agreement with the target model to evade. To evaluate this method, we compare it with two state-of-the-art attacks in adversarial malware creation, using three well-known published models and one antivirus product as targets. Results show that MEME outperforms the state-of-the-art methods in terms of evasion capabilities in almost all cases, producing evasive malware with an evasion rate in the range of 32-73%. It also produces surrogate models with a prediction label agreement with the respective target models between 97-99%. The surrogate could be used to fine-tune and improve the evasion rate in the future.
Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at //github.com/gersteinlab/biocoder.
This paper addresses the tradeoff between standard accuracy on clean examples and robustness against adversarial examples in deep neural networks (DNNs). Although adversarial training (AT) improves robustness, it degrades the standard accuracy, thus yielding the tradeoff. To mitigate this tradeoff, we propose a novel AT method called ARREST, which comprises three components: (i) adversarial finetuning (AFT), (ii) representation-guided knowledge distillation (RGKD), and (iii) noisy replay (NR). AFT trains a DNN on adversarial examples by initializing its parameters with a DNN that is standardly pretrained on clean examples. RGKD and NR respectively entail a regularization term and an algorithm to preserve latent representations of clean examples during AFT. RGKD penalizes the distance between the representations of the standardly pretrained and AFT DNNs. NR switches input adversarial examples to nonadversarial ones when the representation changes significantly during AFT. By combining these components, ARREST achieves both high standard accuracy and robustness. Experimental results demonstrate that ARREST mitigates the tradeoff more effectively than previous AT-based methods do.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query. Although the most common formulation of text ranking is search, instances of the task can also be found in many natural language processing applications. This survey provides an overview of text ranking with neural network architectures known as transformers, of which BERT is the best-known example. The combination of transformers and self-supervised pretraining has, without exaggeration, revolutionized the fields of natural language processing (NLP), information retrieval (IR), and beyond. In this survey, we provide a synthesis of existing work as a single point of entry for practitioners who wish to gain a better understanding of how to apply transformers to text ranking problems and researchers who wish to pursue work in this area. We cover a wide range of modern techniques, grouped into two high-level categories: transformer models that perform reranking in multi-stage ranking architectures and learned dense representations that attempt to perform ranking directly. There are two themes that pervade our survey: techniques for handling long documents, beyond the typical sentence-by-sentence processing approaches used in NLP, and techniques for addressing the tradeoff between effectiveness (result quality) and efficiency (query latency). Although transformer architectures and pretraining techniques are recent innovations, many aspects of how they are applied to text ranking are relatively well understood and represent mature techniques. However, there remain many open research questions, and thus in addition to laying out the foundations of pretrained transformers for text ranking, this survey also attempts to prognosticate where the field is heading.
Sampling methods (e.g., node-wise, layer-wise, or subgraph) has become an indispensable strategy to speed up training large-scale Graph Neural Networks (GNNs). However, existing sampling methods are mostly based on the graph structural information and ignore the dynamicity of optimization, which leads to high variance in estimating the stochastic gradients. The high variance issue can be very pronounced in extremely large graphs, where it results in slow convergence and poor generalization. In this paper, we theoretically analyze the variance of sampling methods and show that, due to the composite structure of empirical risk, the variance of any sampling method can be decomposed into \textit{embedding approximation variance} in the forward stage and \textit{stochastic gradient variance} in the backward stage that necessities mitigating both types of variance to obtain faster convergence rate. We propose a decoupled variance reduction strategy that employs (approximate) gradient information to adaptively sample nodes with minimal variance, and explicitly reduces the variance introduced by embedding approximation. We show theoretically and empirically that the proposed method, even with smaller mini-batch sizes, enjoys a faster convergence rate and entails a better generalization compared to the existing methods.
We propose a novel single shot object detection network named Detection with Enriched Semantics (DES). Our motivation is to enrich the semantics of object detection features within a typical deep detector, by a semantic segmentation branch and a global activation module. The segmentation branch is supervised by weak segmentation ground-truth, i.e., no extra annotation is required. In conjunction with that, we employ a global activation module which learns relationship between channels and object classes in a self-supervised manner. Comprehensive experimental results on both PASCAL VOC and MS COCO detection datasets demonstrate the effectiveness of the proposed method. In particular, with a VGG16 based DES, we achieve an mAP of 81.7 on VOC2007 test and an mAP of 32.8 on COCO test-dev with an inference speed of 31.5 milliseconds per image on a Titan Xp GPU. With a lower resolution version, we achieve an mAP of 79.7 on VOC2007 with an inference speed of 13.0 milliseconds per image.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
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