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In recent years, significant progress has been made in the field of protein function prediction with the development of various machine-learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e. assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein's function in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including protein sequence, structure, and textual annotation and description. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate functional descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate function prediction of existing as well as first-to-see proteins.
We present a deep Graph Convolutional Kernel Machine (GCKM) for semi-supervised node classification in graphs. The method is built of two main types of blocks: (i) We introduce unsupervised kernel machine layers propagating the node features in a one-hop neighborhood, using implicit node feature mappings. (ii) We specify a semi-supervised classification kernel machine through the lens of the Fenchel-Young inequality. We derive an effective initialization scheme and efficient end-to-end training algorithm in the dual variables for the full architecture. The main idea underlying GCKM is that, because of the unsupervised core, the final model can achieve higher performance in semi-supervised node classification when few labels are available for training. Experimental results demonstrate the effectiveness of the proposed framework.
Ensuring fairness in Recommendation Systems (RSs) across demographic groups is critical due to the increased integration of RSs in applications such as personalized healthcare, finance, and e-commerce. Graph-based RSs play a crucial role in capturing intricate higher-order interactions among entities. However, integrating these graph models into the Federated Learning (FL) paradigm with fairness constraints poses formidable challenges as this requires access to the entire interaction graph and sensitive user information (such as gender, age, etc.) at the central server. This paper addresses the pervasive issue of inherent bias within RSs for different demographic groups without compromising the privacy of sensitive user attributes in FL environment with the graph-based model. To address the group bias, we propose F2PGNN (Fair Federated Personalized Graph Neural Network), a novel framework that leverages the power of Personalized Graph Neural Network (GNN) coupled with fairness considerations. Additionally, we use differential privacy techniques to fortify privacy protection. Experimental evaluation on three publicly available datasets showcases the efficacy of F2PGNN in mitigating group unfairness by 47% ∼ 99% compared to the state-of-the-art while preserving privacy and maintaining the utility. The results validate the significance of our framework in achieving equitable and personalized recommendations using GNN within the FL landscape. Source code is at: https://github.com/nimeshagrawal/F2PGNN-AAAI24
We consider the problem of multi-objective optimization (MOO) of expensive black-box functions with the goal of discovering high-quality and diverse Pareto fronts where we are allowed to evaluate a batch of inputs. This problem arises in many real-world applications including penicillin production where diversity of solutions is critical. We solve this problem in the framework of Bayesian optimization (BO) and propose a novel approach referred to as Pareto front-Diverse Batch Multi-Objective BO (PDBO). PDBO tackles two important challenges: 1) How to automatically select the best acquisition function in each BO iteration, and 2) How to select a diverse batch of inputs by considering multiple objectives. We propose principled solutions to address these two challenges. First, PDBO employs a multi-armed bandit approach to select one acquisition function from a given library. We solve a cheap MOO problem by assigning the selected acquisition function for each expensive objective function to obtain a candidate set of inputs for evaluation. Second, it utilizes Determinantal Point Processes (DPPs) to choose a Pareto-front-diverse batch of inputs for evaluation from the candidate set obtained from the first step. The key parameters for the methods behind these two steps are updated after each round of function evaluations. Experiments on multiple MOO benchmarks demonstrate that PDBO outperforms prior methods in terms of both the quality and diversity of Pareto solutions.
Continual Learning is a step towards lifelong intelligence where models continuously learn from recently collected data without forgetting previous knowledge. Existing continual learning approaches mostly focus on image classification in the class-incremental setup with clear task boundaries and unlimited computational budget. This work explores the problem of Online Domain-Incremental Continual Segmentation (ODICS), where the model is continually trained over batches of densely labeled images from different domains, with limited computation and no information about the task boundaries. ODICS arises in many practical applications. In autonomous driving, this may correspond to the realistic scenario of training a segmentation model over time on a sequence of cities. We analyze several existing continual learning methods and show that they perform poorly in this setting despite working well in class-incremental segmentation. We propose SimCS, a parameter-free method complementary to existing ones that uses simulated data to regularize continual learning. Experiments show that SimCS provides consistent improvements when combined with different CL methods.
The problem of sample complexity of online reinforcement learning is often studied in the literature without taking into account any partial knowledge about the system dynamics that could potentially accelerate the learning process. In this paper, we study the sample complexity of online Q-learning methods when some prior knowledge about the dynamics is available or can be learned efficiently. We focus on systems that evolve according to an additive disturbance model of the form S_{h+1} = ƒ(S_h, A_h) + W_h, where ƒ represents the underlying system dynamics, and W_h are unknown disturbances independent of states and actions. In the setting of finite episodic Markov decision processes with S states, A actions, and episode length H, we present an optimistic Q-learning algorithm that achieves Õ(Poly(H)√T) regret under perfect knowledge of ƒ, where T is the total number of interactions with the system. This is in contrast to the typical Õ(Poly(H)√SAT) regret for existing Q-learning methods. Further, if only a noisy estimate ƒ_hat of ƒ is available, our method can learn an approximately optimal policy in a number of samples that is independent of the cardinalities of state and action spaces. The sub-optimality gap depends on the approximation error ƒ_hat − ƒ, as well as the Lipschitz constant of the corresponding optimal value function. Our approach does not require modeling of the transition probabilities and enjoys the same memory complexity as model-free methods.
Backpropagation (BP), the standard learning algorithm for artificial neural networks, is often considered biologically implausible. In contrast, the standard learning algorithm for predictive coding (PC) models in neuroscience, known as the inference learning algorithm (IL), is a promising, bio-plausible alternative. However, several challenges and questions hinder IL's application to real-world problems. For example, IL is computationally demanding, and without memory-intensive optimizers like Adam, IL may converge to poor local minima. Moreover, although IL can reduce loss more quickly than BP, the reasons for these speedups or their robustness remains unclear. In this paper, we tackle these challenges by 1) altering the standard implementation of PC circuits to substantially reduce computation, 2) developing a novel optimizer that improves the convergence of IL without increasing memory usage, and 3) establishing theoretical results that help elucidate the conditions under which IL is sensitive to second and higher-order information.
Pairwise learning, an important domain within machine learning, addresses loss functions defined on pairs of training examples, including those in metric learning and AUC maximization. Acknowledging the quadratic growth in computation complexity accompanying pairwise loss as the sample size grows, researchers have turned to online gradient descent (OGD) methods for enhanced scalability. Recently, an OGD algorithm emerged, employing gradient computation involving prior and most recent examples, a step that effectively reduces algorithmic complexity to O(T), with T being the number of received examples. This approach, however, confines itself to linear models while assuming the independence of example arrivals. We introduce a lightweight OGD algorithm that does not require the independence of examples and generalizes to kernel pairwise learning. Our algorithm builds the gradient based on a random example and a moving average representing the past data, which results in a sub-linear regret bound with a complexity of O(T). Furthermore, through the integration of O(√T logT) random Fourier features, the complexity of kernel calculations is effectively minimized. Several experiments with real-world datasets show that the proposed technique outperforms kernel and linear algorithms in offline and online scenarios.
Counterfactual explanations offer an intuitive and straightforward way to explain black-box models and offer algorithmic recourse to individuals. To address the need for plausible explanations, existing work has primarily relied on surrogate models to learn how the input data is distributed. This effectively reallocates the task of learning realistic explanations for the data from the model itself to the surrogate. Consequently, the generated explanations may seem plausible to humans but need not necessarily describe the behaviour of the black-box model faithfully. We formalise this notion of faithfulness through the introduction of a tailored evaluation metric and propose a novel algorithmic framework for generating Energy-Constrained Conformal Counterfactuals that are only as plausible as the model permits. Through extensive empirical studies, we demonstrate that ECCCo reconciles the need for faithfulness and plausibility. In particular, we show that for models with gradient access, it is possible to achieve state-of-the-art performance without the need for surrogate models. To do so, our framework relies solely on properties defining the black-box model itself by leveraging recent advances in energy-based modelling and conformal prediction. To our knowledge, this is the first venture in this direction for generating faithful counterfactual explanations. Thus, we anticipate that ECCCo can serve as a baseline for future research. We believe that our work opens avenues for researchers and practitioners seeking tools to better distinguish trustworthy from unreliable models.
In the field of optimal transport, two prominent subfields face each other: (i) unregularized optimal transport, ``a-la-Kantorovich'', which leads to extremely sparse plans but with algorithms that scale poorly, and (ii) entropic-regularized optimal transport, ``a-la-Sinkhorn-Cuturi'', which gets near-linear approximation algorithms but leads to maximally un-sparse plans. In this paper, we show that an extension of the latter to tempered exponential measures, a generalization of exponential families with indirect measure normalization, gets to a very convenient middle ground, with both very fast approximation algorithms and sparsity, which is under control up to sparsity patterns. In addition, our formulation fits naturally in the unbalanced optimal transport problem setting.
Diffusion models (DM) have become state-of-the-art generative models because of their capability of generating high-quality images from noises without adversarial training. However, they are vulnerable to backdoor attacks as reported by recent studies. When a data input (e.g., some Gaussian noise) is stamped with a trigger (e.g., a white patch), the backdoored model always generates the target image (e.g., an improper photo). However, effective defense strategies to mitigate backdoors from DMs are underexplored. To bridge this gap, we propose the first backdoor detection and removal framework for DMs. We evaluate our framework Elijah on over hundreds of DMs of 3 types including DDPM, NCSN and LDM, with 13 samplers against 3 existing backdoor attacks. Extensive experiments show that our approach can have close to 100% detection accuracy and reduce the backdoor effects to close to zero without significantly sacrificing the model utility.
Generalized Category Discovery (GCD) is a crucial real-world task that aims to recognize both known and novel categories from an unlabeled dataset by leveraging another labeled dataset with only known categories. Despite the improved performance on known categories, current methods perform poorly on novel categories. We attribute the poor performance to two reasons: biased knowledge transfer between labeled and unlabeled data and noisy representation learning on the unlabeled data. The former leads to unreliable estimation of learning targets for novel categories and the latter hinders models from learning discriminative features. To mitigate these two issues, we propose a Transfer and Alignment Network (TAN), which incorporates two knowledge transfer mechanisms to calibrate the biased knowledge and two feature alignment mechanisms to learn discriminative features. Specifically, we model different categories with prototypes and transfer the prototypes in labeled data to correct model bias towards known categories. On the one hand, we pull instances with known categories in unlabeled data closer to these prototypes to form more compact clusters and avoid boundary overlap between known and novel categories. On the other hand, we use these prototypes to calibrate noisy prototypes estimated from unlabeled data based on category similarities, which allows for more accurate estimation of prototypes for novel categories that can be used as reliable learning targets later. After knowledge transfer, we further propose two feature alignment mechanisms to acquire both instance- and category-level knowledge from unlabeled data by aligning instance features with both augmented features and the calibrated prototypes, which can boost model performance on both known and novel categories with less noise. Experiments on three benchmark datasets show that our model outperforms SOTA methods, especially on novel categories. Theoretical analysis is provided for an in-depth understanding of our model in general. Our code and data are available at https://github.com/Lackel/TAN.
Network Pruning is a promising way to address the huge computing resource demands of the deployment and inference of Large Language Models (LLMs). Retraining-free is important for LLMs' pruning methods. However, almost all of the existing retraining-free pruning approaches for LLMs focus on unstructured pruning, which requires specific hardware support for acceleration. In this paper, we propose a novel retraining-free structured pruning framework for LLMs, named FLAP (FLuctuation-based Adaptive Structured Pruning). It is hardware-friendly by effectively reducing storage and enhancing inference speed. For effective structured pruning of LLMs, we highlight three critical elements that demand the utmost attention: formulating structured importance metrics, adaptively searching the global compressed model, and implementing compensation mechanisms to mitigate performance loss. First, FLAP determines whether the output feature map is easily recoverable when a column of weight is removed, based on the fluctuation pruning metric. Then it standardizes the importance scores to adaptively determine the global compressed model structure. At last, FLAP adds additional bias terms to recover the output feature maps using the baseline values. We thoroughly evaluate our approach on a variety of language benchmarks. Without any retraining, our method significantly outperforms the state-of-the-art methods, including LLM-Pruner and the extension of Wanda in structured pruning. The code is released at https://github.com/CASIA-IVA-Lab/FLAP.
Re-training a deep learning model each time a single data point receives a new label is impractical due to the inherent complexity of the training process. Consequently, existing active learning (AL) algorithms tend to adopt a batch-based approach where, during each AL iteration, a set of data points is collectively chosen for annotation. However, this strategy frequently leads to redundant sampling, ultimately eroding the efficacy of the labeling procedure. In this paper, we introduce a new AL algorithm that harnesses the power of a Gaussian process surrogate in conjunction with the neural network principal learner. Our proposed model adeptly updates the surrogate learner for every new data instance, enabling it to emulate and capitalize on the continuous learning dynamics of the neural network without necessitating a complete retraining of the principal model for each individual label. Experiments on four benchmark datasets demonstrate that this approach yields significant enhancements, either rivaling or aligning with the performance of state-of-the-art techniques.
Recent advancements in federated learning (FL) have greatly facilitated the development of decentralized collaborative applications, particularly in the domain of Artificial Intelligence of Things (AIoT). However, a critical aspect missing from the current research landscape is the ability to enable data-driven client models with symbolic reasoning capabilities. Specifically, the inherent heterogeneity of participating client devices poses a significant challenge, as each client exhibits unique logic reasoning properties. Failing to consider these device-specific specifications can result in critical properties being missed in the client predictions, leading to suboptimal performance. In this work, we propose a new training paradigm that leverages temporal logic reasoning to address this issue. Our approach involves enhancing the training process by incorporating mechanically generated logic expressions for each FL client. Additionally, we introduce the concept of aggregation clusters and develop a partitioning algorithm to effectively group clients based on the alignment of their temporal reasoning properties. We evaluate the proposed method on two tasks: a real-world traffic volume prediction task consisting of sensory data from fifteen states and a smart city multi-task prediction utilizing synthetic data. The evaluation results exhibit clear improvements, with performance accuracy improved by up to 54% across all sequential prediction models.
Quantum Machine Learning (QML) has emerged as a promising field of research, aiming to leverage the capabilities of quantum computing to enhance existing machine learning methodologies. Recent studies have revealed that, like their classical counterparts, QML models based on Parametrized Quantum Circuits (PQCs) are also vulnerable to adversarial attacks. Moreover, the existence of Universal Adversarial Perturbations (UAPs) in the quantum domain has been demonstrated theoretically in the context of quantum classifiers. In this work, we introduce QuGAP: a novel framework for generating UAPs for quantum classifiers. We conceptualize the notion of additive UAPs for PQC-based classifiers and theoretically demonstrate their existence. We then utilize generative models (QuGAP-A) to craft additive UAPs and experimentally show that quantum classifiers are susceptible to such attacks. Moreover, we formulate a new method for generating unitary UAPs (QuGAP-U) using quantum generative models and a novel loss function based on fidelity constraints. We evaluate the performance of the proposed framework and show that our method achieves state-of-the-art misclassification rates, while maintaining high fidelity between legitimate and adversarial samples.
Spiking neural networks (SNNs) have garnered significant attention for their low power consumption when deployed on neuromorphic hardware that operates in orders of magnitude lower power than general-purpose hardware. Direct training methods for SNNs come with an inherent latency for which the SNNs are optimized, and in general, the higher the latency, the better the predictive powers of the models, but at the same time, the higher the energy consumption during training and inference. Furthermore, an SNN model optimized for one particular latency does not necessarily perform well in lower latencies, which becomes relevant in scenarios where it is necessary to switch to a lower latency because of the depletion of onboard energy or other operational requirements. In this work, we propose Stochastic Latency Training (SLT), a direct training method for SNNs that optimizes the model for the given latency but simultaneously offers a minimum reduction of predictive accuracy when shifted to lower inference latencies. We provide heuristics for our approach with partial theoretical justification and experimental evidence showing the state-of-the-art performance of our models on datasets such as CIFAR-10, DVS-CIFAR-10, CIFAR-100, and DVS-Gesture. Our code is available at https://github.com/srinuvaasu/SLT
Federated learning (FL) has been widely studied recently due to its property to collaboratively train data from different devices without sharing the raw data. Nevertheless, recent studies show that an adversary can still be possible to infer private information about devices' data, e.g., sensitive attributes such as income, race, and sexual orientation. To mitigate the attribute inference attacks, various existing privacy-preserving FL methods can be adopted/adapted. However, all these existing methods have key limitations: they need to know the FL task in advance, or have intolerable computational overheads or utility losses, or do not have provable privacy guarantees. We address these issues and design a task-agnostic privacy-preserving presentation learning method for FL (TAPPFL) against attribute inference attacks. TAPPFL is formulated via information theory. Specifically, TAPPFL has two mutual information goals, where one goal learns task-agnostic data representations that contain the least information about the private attribute in each device's data, and the other goal ensures the learnt data representations include as much information as possible about the device data to maintain FL utility. We also derive privacy guarantees of TAPPFL against worst-case attribute inference attacks, as well as the inherent tradeoff between utility preservation and privacy protection. Extensive results on multiple datasets and applications validate the effectiveness of TAPPFL to protect data privacy, maintain the FL utility, and be efficient as well. Experimental results also show that TAPPFL outperforms the existing defenses.
Probabilistic circuits (PCs) such as sum-product networks efficiently represent large multi-variate probability distributions. They are preferred in practice over other probabilistic representations, such as Bayesian and Markov networks, because PCs can solve marginal inference (MAR) tasks in time that scales linearly in the size of the network. Unfortunately, the most probable explanation (MPE) task and its generalization, the marginal maximum-a-posteriori (MMAP) inference task remain NP-hard in these models. Inspired by the recent work on using neural networks for generating near-optimal solutions to optimization problems such as integer linear programming, we propose an approach that uses neural networks to approximate MMAP inference in PCs. The key idea in our approach is to approximate the cost of an assignment to the query variables using a continuous multilinear function and then use the latter as a loss function. The two main benefits of our new method are that it is self-supervised, and after the neural network is learned, it requires only linear time to output a solution. We evaluate our new approach on several benchmark datasets and show that it outperforms three competing linear time approximations: max-product inference, max-marginal inference, and sequential estimation, which are used in practice to solve MMAP tasks in PCs.
Given a set of observations, feature acquisition is about finding the subset of unobserved features which would enhance accuracy. Such problems has been explored in a sequential setting in prior work. Here, the model receives feedback from every new feature acquireed and chooses to explore more features or to predict. However, sequential acquisition is not feasible in some settings where time is of essence. We consider the problem of feature acquisition in batch, where the subset of features to be queried in batch is chosen based on the currently observed features, and then acquired as a batch, followed by prediction. We solve this problem using several technical innovations. First, we use a feature generator to draw a subset of the synthetic features for some examples, which reduces the cost of oracle queries. Second, to make the feature acquisition problem tractable for the large heterogeneous observed features, we partition the data into buckets, by borrowing tools from locality sensitive hashing and then train a mixture of experts model. Third, we design a tractable lower bound of the original objective. We use a greedy algorithm combined with model training to solve the underlying problem. Experiments with four datasets shows that our approach outperforms these methods in terms of trade off between accuracy and feature acquisition cost.
There has been a great deal of recent interest in binarized neural networks, especially because of their explainability. At the same time, automatic differentiation algorithms such as backpropagation fail for binarized neural networks, which limits their applicability. We show that binarized neural networks admit a tame representation by reformulating the problem of training binarized neural networks as a subadditive dual of a mixed-integer program, which we show to have nice properties. This makes it possible to use the framework of Bolte et al. for implicit differentiation, which offers the possibility for practical implementation of backpropagation in the context of binarized neural networks. This approach could also be used for a broader class of mixed-integer programs, beyond the training of binarized neural networks, as encountered in symbolic approaches to AI and beyond.
Pandora’s Box is a fundamental stochastic optimization problem, where the decision-maker must find a good alternative, while minimizing the search cost of exploring the value of each alternative. In the original formulation, it is assumed that accurate distributions are given for the values of all the alternatives, while recent work studies the online variant of Pandora’s Box where the distributions are originally unknown. In this work, we study Pandora’s Box in the online setting, while incorporating context. At each round, we are presented with a number of alternatives each having a context, an exploration cost and an unknown value drawn from an unknown distribution that may change at every round. Our main result is a no-regret algorithm that performs comparably well against the optimal algorithm which knows all prior distributions exactly. Our algorithm works even in the bandit setting where the algorithm never learns the values of the alternatives that were not explored. The key technique that enables our result is a novel modification of the realizability condition in contextual bandits that connects a context to a sufficient statistic of each alternative’s distribution (its reservation value) rather than its mean.
Recent studies show that deep reinforcement learning (DRL) agents tend to overfit to the task on which they were trained and fail to adapt to minor environment changes. To expedite learning when transferring to unseen tasks, we propose a novel approach to representing the current task using reward machines (RMs), state machine abstractions that induce subtasks based on the current task’s rewards and dynamics. Our method provides agents with symbolic representations of optimal transitions from their current abstract state and rewards them for achieving these transitions. These representations are shared across tasks, allowing agents to exploit knowledge of previously encountered symbols and transitions, thus enhancing transfer. Empirical results show that our representations improve sample efficiency and few-shot transfer in a variety of domains.
As Federated Learning (FL) gains prominence in distributed machine learning applications, achieving fairness without compromising predictive performance becomes paramount. The data being gathered from distributed clients in an FL environment often leads to class imbalance. In such scenarios, balanced accuracy rather than accuracy is the true representation of model performance. However, most state-of-the-art fair FL methods report accuracy as the measure of performance, which can lead to misguided interpretations of the model's effectiveness to mitigate discrimination. To the best of our knowledge, this work presents the first attempt towards achieving Pareto-optimal trade-offs between balanced accuracy and fairness in a federated environment (FairTrade). By utilizing multi-objective optimization, the framework negotiates the intricate balance between model's balanced accuracy and fairness. The framework's agnostic design adeptly accommodates both statistical and causal fairness notions, ensuring its adaptability across diverse FL contexts. We provide empirical evidence of our framework's efficacy through extensive experiments on five real-world datasets and comparisons with six baselines. The empirical results underscore the potential of our framework in improving the trade-off between fairness and balanced accuracy in FL applications.
Quantization has emerged as a promising direction for model compression. Recently, data-free quantization has been widely studied as a promising method to avoid privacy concerns, which synthesizes images as an alternative to real training data. Existing methods use classification loss to ensure the reliability of the synthesized images. Unfortunately, even if these images are well-classified by the pre-trained model, they still suffer from low semantics and homogenization issues. Intuitively, these low-semantic images are sensitive to perturbations, and the pre-trained model tends to have inconsistent output when the generator synthesizes an image with low semantics. To this end, we propose Robustness-Guided Image Synthesis (RIS), a simple but effective method to enrich the semantics of synthetic images and improve image diversity, further boosting the performance of data-free compression tasks. Concretely, we first introduce perturbations on input and model weight, then define the inconsistency metrics at feature and prediction levels before and after perturbations. On the basis of inconsistency on two levels, we design a robustness optimization objective to eliminate low-semantic images. Moreover, we also make our approach diversity-aware by forcing the generator to synthesize images with small correlations. With RIS, we achieve state-of-the-art performance for various settings on data-free quantization and can be extended to other data-free compression tasks.