OpenRaiser/Intern-Atlas huggingface dataset:
NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification
Venue: arXiv cs.LG 2023
Year: 2023

Gene-disease associations are fundamental for understanding disease etiology and developing effective interventions and treatments. Identifying genes not yet associated with a disease due to a lack of studies is a challenging task in which prioritization based on prior knowledge is an important element. The computational search for new candidate disease genes may be eased by positive-unlabeled learning, the machine learning setting in which only a subset of instances are labeled as positive while the rest of the data set is unlabeled. In this work, we propose a set of effective network-based features to be used in a novel Markov diffusion-based multi-class labeling strategy for putative disease gene discovery. The performances of the new labeling algorithm and the effectiveness of the proposed features have been tested on ten different disease data sets using three machine learning algorithms. The new features have been compared against classical topological and functional/ontological features and a set of network- and biological-derived features already used in gene discovery tasks. The predictive power of the integrated methodology in searching for new disease genes has been found to be competitive against state-of-the-art algorithms.
SamBaS: Sampling-Based Stochastic Block Partitioning
Venue: arXiv cs.SI 2023
Year: 2023

Community detection is a well-studied problem with applications in domains ranging from networking to bioinformatics. Due to the rapid growth in the volume of real-world data, there is growing interest in accelerating contemporary community detection algorithms. However, the more accurate and statistically robust methods tend to be hard to parallelize. One such method is stochastic block partitioning (SBP) - a community detection algorithm that works well on graphs with complex and heterogeneous community structure. In this paper, we present a sampling-based SBP (SamBaS) for accelerating SBP on sparse graphs. We characterize how various graph parameters affect the speedup and result quality of community detection with SamBaS and quantify the trade-offs therein. To evaluate SamBas on real-world web graphs without known ground-truth communities, we introduce partition quality score (PQS), an evaluation metric that outperforms modularity in terms of correlation with F1 score. Overall, SamBaS achieves speedups of up to 10X while maintaining result quality (and even improving result quality by over 150% on certain graphs, relative to F1 score).
FedChain: Chained Algorithms for Near-Optimal Communication Cost in Federated Learning
Venue: arXiv cs.LG 2023
Year: 2023

Federated learning (FL) aims to minimize the communication complexity of training a model over heterogeneous data distributed across many clients. A common approach is local methods, where clients take multiple optimization steps over local data before communicating with the server (e.g., FedAvg). Local methods can exploit similarity between clients' data. However, in existing analyses, this comes at the cost of slow convergence in terms of the dependence on the number of communication rounds R. On the other hand, global methods, where clients simply return a gradient vector in each round (e.g., SGD), converge faster in terms of R but fail to exploit the similarity between clients even when clients are homogeneous. We propose FedChain, an algorithmic framework that combines the strengths of local methods and global methods to achieve fast convergence in terms of R while leveraging the similarity between clients. Using FedChain, we instantiate algorithms that improve upon previously known rates in the general convex and PL settings, and are near-optimal (via an algorithm-independent lower bound that we show) for problems that satisfy strong convexity. Empirical results support this theoretical gain over existing methods.
Global Convergence of the ODE Limit for Online Actor-Critic Algorithms in Reinforcement Learning
Venue: arXiv cs.LG 2023
Year: 2023

Actor-critic algorithms are widely used in reinforcement learning, but are challenging to mathematically analyse due to the online arrival of non-i.i.d. data samples. The distribution of the data samples dynamically changes as the model is updated, introducing a complex feedback loop between the data distribution and the reinforcement learning algorithm. We prove that, under a time rescaling, the online actor-critic algorithm with tabular parametrization converges to an ordinary differential equation (ODE) as the number of updates becomes large. The proof first establishes the geometric ergodicity of the data samples under a fixed actor policy. Then, using a Poisson equation, we prove that the fluctuations of the data samples around a dynamic probability measure, which is a function of the evolving actor model, vanish as the number of updates become large. Once the ODE limit has been derived, we study its convergence properties using a two time-scale analysis which asymptotically de-couples the critic ODE from the actor ODE. The convergence of the critic to the solution of the Bellman equation and the actor to the optimal policy are proven. In addition, a convergence rate to this global minimum is also established. Our convergence analysis holds under specific choices for the learning rates and exploration rates in the actor-critic algorithm, which could provide guidance for the implementation of actor-critic algorithms in practice.
Quantization Backdoors to Deep Learning Commercial Frameworks
Venue: arXiv cs.CR 2023
Year: 2023

Currently, there is a burgeoning demand for deploying deep learning (DL) models on ubiquitous edge Internet of Things (IoT) devices attributed to their low latency and high privacy preservation. However, DL models are often large in size and require large-scale computation, which prevents them from being placed directly onto IoT devices, where resources are constrained and 32-bit floating-point (float-32) operations are unavailable. Commercial framework (i.e., a set of toolkits) empowered model quantization is a pragmatic solution that enables DL deployment on mobile devices and embedded systems by effortlessly post-quantizing a large high-precision model (e.g., float-32) into a small low-precision model (e.g., int-8) while retaining the model inference accuracy. However, their usability might be threatened by security vulnerabilities. This work reveals that the standard quantization toolkits can be abused to activate a backdoor. We demonstrate that a full-precision backdoored model which does not have any backdoor effect in the presence of a trigger -- as the backdoor is dormant -- can be activated by the default i) TensorFlow-Lite (TFLite) quantization, the only product-ready quantization framework to date, and ii) the beta released PyTorch Mobile framework. When each of the float-32 models is converted into an int-8 format model through the standard TFLite or Pytorch Mobile framework's post-training quantization, the backdoor is activated in the quantized model, which shows a stable attack success rate close to 100% upon inputs with the trigger, while it behaves normally upon non-trigger inputs. This work highlights that a stealthy security threat occurs when an end user utilizes the on-device post-training model quantization frameworks, informing security researchers of cross-platform overhaul of DL models post quantization even if these models pass front-end backdoor inspections.
Semantic-Preserving Adversarial Text Attacks
Venue: arXiv cs.CL 2023
Year: 2023

Deep neural networks (DNNs) are known to be vulnerable to adversarial images, while their robustness in text classification is rarely studied. Several lines of text attack methods have been proposed in the literature, including character-level, word-level, and sentence-level attacks. However, it is still a challenge to minimize the number of word changes necessary to induce misclassification, while simultaneously ensuring lexical correctness, syntactic soundness, and semantic similarity. In this paper, we propose a Bigram and Unigram based adaptive Semantic Preservation Optimization (BU-SPO) method to examine the vulnerability of deep models. Our method has four major merits. Firstly, we propose to attack text documents not only at the unigram word level but also at the bigram level which better keeps semantics and avoids producing meaningless outputs. Secondly, we propose a hybrid method to replace the input words with options among both their synonyms candidates and sememe candidates, which greatly enriches the potential substitutions compared to only using synonyms. Thirdly, we design an optimization algorithm, i.e., Semantic Preservation Optimization (SPO), to determine the priority of word replacements, aiming to reduce the modification cost. Finally, we further improve the SPO with a semantic Filter (named SPOF) to find the adversarial example with the highest semantic similarity. We evaluate the effectiveness of our BU-SPO and BU-SPOF on IMDB, AG's News, and Yahoo! Answers text datasets by attacking four popular DNNs models. Results show that our methods achieve the highest attack success rates and semantics rates by changing the smallest number of words compared with existing methods.
Growing Cosine Unit: A Novel Oscillatory Activation Function That Can Speedup Training and Reduce Parameters in Convolutional Neural Networks
Venue: arXiv cs.LG 2023
Year: 2023

Convolutional neural networks have been successful in solving many socially important and economically significant problems. This ability to learn complex high-dimensional functions hierarchically can be attributed to the use of nonlinear activation functions. A key discovery that made training deep networks feasible was the adoption of the Rectified Linear Unit (ReLU) activation function to alleviate the vanishing gradient problem caused by using saturating activation functions. Since then, many improved variants of the ReLU activation have been proposed. However, a majority of activation functions used today are non-oscillatory and monotonically increasing due to their biological plausibility. This paper demonstrates that oscillatory activation functions can improve gradient flow and reduce network size. Two theorems on limits of non-oscillatory activation functions are presented. A new oscillatory activation function called Growing Cosine Unit(GCU) defined as $C(z) = z\cos z$ that outperforms Sigmoids, Swish, Mish and ReLU on a variety of architectures and benchmarks is presented. The GCU activation has multiple zeros enabling single GCU neurons to have multiple hyperplanes in the decision boundary. This allows single GCU neurons to learn the XOR function without feature engineering. Experimental results indicate that replacing the activation function in the convolution layers with the GCU activation function significantly improves performance on CIFAR-10, CIFAR-100 and Imagenette.
Private Multi-Task Learning: Formulation and Applications to Federated Learning
Venue: arXiv cs.LG 2023
Year: 2023

Many problems in machine learning rely on multi-task learning (MTL), in which the goal is to solve multiple related machine learning tasks simultaneously. MTL is particularly relevant for privacy-sensitive applications in areas such as healthcare, finance, and IoT computing, where sensitive data from multiple, varied sources are shared for the purpose of learning. In this work, we formalize notions of client-level privacy for MTL via joint differential privacy (JDP), a relaxation of differential privacy for mechanism design and distributed optimization. We then propose an algorithm for mean-regularized MTL, an objective commonly used for applications in personalized federated learning, subject to JDP. We analyze our objective and solver, providing certifiable guarantees on both privacy and utility. Empirically, we find that our method provides improved privacy/utility trade-offs relative to global baselines across common federated learning benchmarks.
Phy-Q as a measure for physical reasoning intelligence
Venue: arXiv cs.AI 2023
Year: 2023

Humans are well-versed in reasoning about the behaviors of physical objects and choosing actions accordingly to accomplish tasks, while it remains a major challenge for AI. To facilitate research addressing this problem, we propose a new testbed that requires an agent to reason about physical scenarios and take an action appropriately. Inspired by the physical knowledge acquired in infancy and the capabilities required for robots to operate in real-world environments, we identify 15 essential physical scenarios. We create a wide variety of distinct task templates, and we ensure all the task templates within the same scenario can be solved by using one specific strategic physical rule. By having such a design, we evaluate two distinct levels of generalization, namely the local generalization and the broad generalization. We conduct an extensive evaluation with human players, learning agents with varying input types and architectures, and heuristic agents with different strategies. Inspired by how human IQ is calculated, we define the physical reasoning quotient (Phy-Q score) that reflects the physical reasoning intelligence of an agent using the physical scenarios we considered. Our evaluation shows that 1) all agents are far below human performance, and 2) learning agents, even with good local generalization ability, struggle to learn the underlying physical reasoning rules and fail to generalize broadly. We encourage the development of intelligent agents that can reach the human level Phy-Q score. Website: https://github.com/phy-q/benchmark
Coalgebras for Bisimulation of Weighted Automata over Semirings
Venue: arXiv cs.FL 2023
Year: 2023

Weighted automata are a generalization of nondeterministic automata that associate a weight drawn from a semiring $K$ with every transition and every state. Their behaviours can be formalized either as weighted language equivalence or weighted bisimulation. In this paper we explore the properties of weighted automata in the framework of coalgebras over (i) the category $\mathsf{SMod}$ of semimodules over a semiring $K$ and $K$-linear maps, and (ii) the category $\mathsf{Set}$ of sets and maps. We show that the behavioural equivalences defined by the corresponding final coalgebras in these two cases characterize weighted language equivalence and weighted bisimulation, respectively. These results extend earlier work by Bonchi et al. using the category $\mathsf{Vect}$ of vector spaces and linear maps as the underlying model for weighted automata with weights drawn from a field $K$. The key step in our work is generalizing the notions of linear relation and linear bisimulation of Boreale from vector spaces to semimodules using the concept of the kernel of a $K$-linear map in the sense of universal algebra. We also provide an abstract procedure for forward partition refinement for computing weighted language equivalence. Since for weighted automata defined over semirings the problem is undecidable in general, it is guaranteed to halt only in special cases. We provide sufficient conditions for the termination of our procedure. Although the results are similar to those of Bonchi et al., many of our proofs are new, especially those about the coalgebra in $\mathsf{SMod}$ characterizing weighted language equivalence.
A Review and Collation of Graphical Perception Knowledge for Visualization Recommendation
Venue: arXiv cs.HC 2023
Year: 2023

Selecting appropriate visual encodings is critical to designing effective visualization recommendation systems, yet few findings from graphical perception are typically applied within these systems. We observe two significant limitations in translating graphical perception knowledge into actionable visualization recommendation rules/constraints: inconsistent reporting of findings and a lack of shared data across studies. How can we translate the graphical perception literature into a knowledge base for visualization recommendation? We present a review of 59 papers that study user perception and performance across ten visual analysis tasks. Through this study, we contribute a JSON dataset that collates existing theoretical and experimental knowledge and summarizes key study outcomes in graphical perception. We illustrate how this dataset can inform automated encoding decisions with three representative visualization recommendation systems. Based on our findings, we highlight open challenges and opportunities for the community in collating graphical perception knowledge for a range of visualization recommendation scenarios.
AI Descartes: Combining Data and Theory for Derivable Scientific Discovery
Venue: arXiv cs.AI 2023
Year: 2023

Scientists have long aimed to discover meaningful formulae which accurately describe experimental data. A common approach is to manually create mathematical models of natural phenomena using domain knowledge, and then fit these models to data. In contrast, machine-learning algorithms automate the construction of accurate data-driven models while consuming large amounts of data. The problem of incorporating prior knowledge in the form of constraints on the functional form of a learned model (e.g., nonnegativity) has been explored in the literature. However, finding models that are consistent with prior knowledge expressed in the form of general logical axioms (e.g., conservation of energy) is an open problem. We develop a method to enable principled derivations of models of natural phenomena from axiomatic knowledge and experimental data by combining logical reasoning with symbolic regression. We demonstrate these concepts for Kepler's third law of planetary motion, Einstein's relativistic time-dilation law, and Langmuir's theory of adsorption, automatically connecting experimental data with background theory in each case. We show that laws can be discovered from few data points when using formal logical reasoning to distinguish the correct formula from a set of plausible formulas that have similar error on the data. The combination of reasoning with machine learning provides generalizeable insights into key aspects of natural phenomena. We envision that this combination will enable derivable discovery of fundamental laws of science and believe that our work is an important step towards automating the scientific method.
Detecting Inspiring Content on Social Media
Venue: arXiv cs.CL 2023
Year: 2023

Inspiration moves a person to see new possibilities and transforms the way they perceive their own potential. Inspiration has received little attention in psychology, and has not been researched before in the NLP community. To the best of our knowledge, this work is the first to study inspiration through machine learning methods. We aim to automatically detect inspiring content from social media data. To this end, we analyze social media posts to tease out what makes a post inspiring and what topics are inspiring. We release a dataset of 5,800 inspiring and 5,800 non-inspiring English-language public post unique ids collected from a dump of Reddit public posts made available by a third party and use linguistic heuristics to automatically detect which social media English-language posts are inspiring.
Learn2Agree: Fitting with Multiple Annotators without Objective Ground Truth
Venue: arXiv cs.LG 2023
Year: 2023

The annotation of domain experts is important for some medical applications where the objective ground truth is ambiguous to define, e.g., the rehabilitation for some chronic diseases, and the prescreening of some musculoskeletal abnormalities without further medical examinations. However, improper uses of the annotations may hinder developing reliable models. On one hand, forcing the use of a single ground truth generated from multiple annotations is less informative for the modeling. On the other hand, feeding the model with all the annotations without proper regularization is noisy given existing disagreements. For such issues, we propose a novel Learning to Agreement (Learn2Agree) framework to tackle the challenge of learning from multiple annotators without objective ground truth. The framework has two streams, with one stream fitting with the multiple annotators and the other stream learning agreement information between annotators. In particular, the agreement learning stream produces regularization information to the classifier stream, tuning its decision to be better in line with the agreement between annotators. The proposed method can be easily added to existing backbones, with experiments on two medical datasets showed better agreement levels with annotators.
Taming Self-Supervised Learning for Presentation Attack Detection: De-Folding and De-Mixing
Venue: arXiv cs.CV 2023
Year: 2023

Biometric systems are vulnerable to Presentation Attacks (PA) performed using various Presentation Attack Instruments (PAIs). Even though there are numerous Presentation Attack Detection (PAD) techniques based on both deep learning and hand-crafted features, the generalization of PAD for unknown PAI is still a challenging problem. In this work, we empirically prove that the initialization of the PAD model is a crucial factor for the generalization, which is rarely discussed in the community. Based on such observation, we proposed a self-supervised learning-based method, denoted as DF-DM. Specifically, DF-DM is based on a global-local view coupled with De-Folding and De-Mixing to derive the task-specific representation for PAD. During De-Folding, the proposed technique will learn region-specific features to represent samples in a local pattern by explicitly minimizing generative loss. While De-Mixing drives detectors to obtain the instance-specific features with global information for more comprehensive representation by minimizing interpolation-based consistency. Extensive experimental results show that the proposed method can achieve significant improvements in terms of both face and fingerprint PAD in more complicated and hybrid datasets when compared with state-of-the-art methods. When training in CASIA-FASD and Idiap Replay-Attack, the proposed method can achieve an 18.60% Equal Error Rate (EER) in OULU-NPU and MSU-MFSD, exceeding baseline performance by 9.54%. The source code of the proposed technique is available at https://github.com/kongzhecn/dfdm.
Privacy-Protecting Techniques for Behavioral Biometric Data: A Survey
Venue: arXiv cs.CR 2023
Year: 2023

Our behavior (the way we talk, walk, act or think) is unique and can be used as a biometric trait. It also correlates with sensitive attributes like emotions and health conditions. Hence, techniques to protect individuals privacy against unwanted inferences are required, if such data is planned to be processed. To consolidate knowledge in this area, we systematically review applicable anonymization techniques. We taxonomize and compare existing solutions regarding privacy goals, conceptual operation, advantages, and limitations. We review anonymization techniques for the behavioral biometric traits of voice, gait, hand motions, eye-gaze, heartbeat (ECG), and brain activity (EEG). Our analysis shows that some behavioral traits (e.g., voice) have received much attention, while others (e.g., eye-gaze, brain activity) are mostly neglected. We also find that the evaluation methodology of behavioral anonymization techniques can be further improved.