Knowledge-Guided Biomarker Identification for Label-Free Single-Cell RNA-Seq Data: A Reinforcement Learning Perspective

Gene panel selection aims to identify the most informative genomic biomarkers in label-free genomic datasets. Traditional approaches, which rely on domain expertise, embedded machine learning models, or heuristic-based iterative optimization, often introduce biases and inefficiencies, potentially obscuring critical biological signals. To address these challenges, we present an iterative gene panel selection strategy that harnesses ensemble knowledge from existing gene selection algorithms to establish preliminary boundaries or prior knowledge, which guide the initial search space. Subsequently, we incorporate reinforcement learning through a reward function shaped by expert behavior, enabling dynamic refinement and targeted selection of gene panels. This integration mitigates biases stemming from initial boundaries while capitalizing on RL's stochastic adaptability. Comprehensive comparative experiments, case studies, and downstream analyses demonstrate the effectiveness of our method, highlighting its improved precision and efficiency for label-free biomarker discovery. Our results underscore the potential of this approach to advance single-cell genomics data analysis.

Augmented Contrastive Clustering with Uncertainty-Aware Prototyping for Time Series Test Time Adaptation

Test-time adaptation aims to adapt pre-trained deep neural networks using solely online unlabelled test data during inference. Although TTA has shown promise in visual applications, its potential in time series contexts remains largely unexplored. Existing TTA methods, originally designed for visual tasks, may not effectively handle the complex temporal dynamics of real-world time series data, resulting in suboptimal adaptation performance. To address this gap, we propose Augmented Contrastive Clustering with Uncertainty-aware Prototyping (ACCUP), a straightforward yet effective TTA method for time series data. Initially, our approach employs augmentation ensemble on the time series data to capture diverse temporal information and variations, incorporating uncertainty-aware prototypes to distill essential characteristics. Additionally, we introduce an entropy comparison scheme to selectively acquire more confident predictions, enhancing the reliability of pseudo labels. Furthermore, we utilize augmented contrastive clustering to enhance feature discriminability and mitigate error accumulation from noisy pseudo labels, promoting cohesive clustering within the same class while facilitating clear separation between different classes. Extensive experiments conducted on three real-world time series datasets and an additional visual dataset demonstrate the effectiveness and generalization potential of the proposed method, advancing the underexplored realm of TTA for time series data.

Atomic Fact Decomposition Helps Attributed Question Answering

Attributed Question Answering (AQA) aims to provide both a trustworthy answer and a reliable attribution report for a given question. Retrieval is a widely adopted approach, including two general paradigms: Retrieval-Then-Read (RTR) and post-hoc retrieval. Recently, Large Language Models (LLMs) have shown remarkable proficiency, prompting growing interest in AQA among researchers. However, RTR-based AQA often suffers from irrelevant knowledge and rapidly changing information, even when LLMs are adopted, while post-hoc retrieval-based AQA struggles with comprehending long-form answers with complex logic, and precisely identifying the content needing revision and preserving the original intent. To tackle these problems, this paper proposes an Atomic fact decomposition-based Retrieval and Editing (ARE) framework, which decomposes the generated long-form answers into molecular clauses and atomic facts by the instruction-tuned LLMs. Notably, the instruction-tuned LLMs are fine-tuned using a well-constructed dataset, generated from large scale Knowledge Graphs (KGs). This process involves extracting one-hop neighbors from a given set of entities and transforming the result into coherent long-form text. Subsequently, ARE leverages a search engine to retrieve evidences related to atomic facts, inputting these evidences into an LLM-based verifier to determine whether the facts require expansion for re-retrieval or editing. Furthermore, the edited facts are backtracked into the original answer, with evidence aggregated based on the relationship between molecular clauses and atomic facts. Extensive evaluations demonstrate the superior performance of our proposed method over the state-of-the-arts on several datasets, with an additionally proposed new metric $Attr_{p}$ for evaluating the precision of evidence attribution.

Context-Aware Adapter Tuning for Few-Shot Relation Learning in Knowledge Graphs

Knowledge graphs (KGs) are instrumental in various real-world applications, yet they often suffer from incompleteness due to missing relations. To predict instances for novel relations with limited training examples, few-shot relation learning approaches have emerged, utilizing techniques such as meta-learning. However, the assumption is that novel relations in meta-testing and base relations in meta-training are independently and identically distributed, which may not hold in practice. To address the limitation, we propose RelAdapter, a context-aware adapter for few-shot relation learning in KGs designed to enhance the adaptation process in meta-learning. First, RelAdapter is equipped with a lightweight adapter module that facilitates relation-specific, tunable adaptation of meta-knowledge in a parameter-efficient manner. Second, RelAdapter is enriched with contextual information about the target relation, enabling enhanced adaptation to each distinct relation. Extensive experiments on three benchmark KGs validate the superiority of RelAdapter over state-of-the-art methods.

Diversified and Adaptive Negative Sampling on Knowledge Graphs

In knowledge graph embedding, aside from positive triplets (ie: facts in the knowledge graph), the negative triplets used for training also have a direct influence on the model performance. In reality, since knowledge graphs are sparse and incomplete, negative triplets often lack explicit labels, and thus they are often obtained from various sampling strategies (eg: randomly replacing an entity in a positive triplet). An ideal sampled negative triplet should be informative enough to help the model train better. However, existing methods often ignore diversity and adaptiveness in their sampling process, which harms the informativeness of negative triplets. As such, we propose a generative adversarial approach called Diversified and Adaptive Negative Sampling DANS on knowledge graphs. DANS is equipped with a two-way generator that generates more diverse negative triplets through two pathways, and an adaptive mechanism that produces more fine-grained examples by localizing the global generator for different entities and relations. On the one hand, the two-way generator increase the overall informativeness with more diverse negative examples; on the other hand, the adaptive mechanism increases the individual sample-wise informativeness with more fine-grained sampling. Finally, we evaluate the performance of DANS on three benchmark knowledge graphs to demonstrate its effectiveness through quantitative and qualitative experiments.

Double Oracle Neural Architecture Search for Game Theoretic Deep Learning Models

In this paper, we propose a new approach to train deep learning models using game theory concepts including Generative Adversarial Networks (GANs) and Adversarial Training (AT) where we deploy a double-oracle framework using best response oracles. GAN is essentially a two-player zero-sum game between the generator and the discriminator. The same concept can be applied to AT with attacker and classifier as players. Training these models is challenging as a pure Nash equilibrium may not exist and even finding the mixed Nash equilibrium is difficult as training algorithms for both GAN and AT have a large-scale strategy space. Extending our preliminary model DO-GAN, we propose the methods to apply the double oracle framework concept to Adversarial Neural Architecture Search (NAS for GAN) and Adversarial Training (NAS for AT) algorithms. We first generalize the players' strategies as the trained models of generator and discriminator from the best response oracles. We then compute the meta-strategies using a linear program. For scalability of the framework where multiple network models of best responses are stored in the memory, we prune the weakly-dominated players' strategies to keep the oracles from becoming intractable. Finally, we conduct experiments on MNIST, CIFAR-10 and TinyImageNet for DONAS-GAN. We also evaluate the robustness under FGSM and PGD attacks on CIFAR-10, SVHN and TinyImageNet for DONAS-AT. We show that all our variants have significant improvements in both subjective qualitative evaluation and quantitative metrics, compared with their respective base architectures.

Temporal Source Recovery for Time-Series Source-Free Unsupervised Domain Adaptation

Source-Free Unsupervised Domain Adaptation (SFUDA) has gained popularity for its ability to adapt pretrained models to target domains without accessing source domains, ensuring source data privacy. While SFUDA is well-developed in visual tasks, its application to Time-Series SFUDA (TS-SFUDA) remains limited due to the challenge of transferring crucial temporal dependencies across domains. Although a few researchers begin to explore this area, they rely on specific source domain designs, which are impractical as source data owners cannot be expected to follow particular pretraining protocols. To solve this, we propose Temporal Source Recovery (TemSR), a framework that transfers temporal dependencies for effective TS-SFUDA without requiring source-specific designs. TemSR features a recovery process that leverages masking, recovery, and optimization to generate a source-like distribution with recovered source temporal dependencies. To ensure effective recovery, we further design segment-based regularization to restore local dependencies and anchor-based recovery diversity maximization to enhance the diversity of the source-like distribution. The source-like distribution is then adapted to the target domain using traditional UDA techniques. Extensive experiments across multiple TS tasks demonstrate the effectiveness of TemSR, even surpassing existing TS-SFUDA method that requires source domain designs. Code is available in https://github.com/Frank-Wang-oss/TemSR.

EverAdapt: Continuous Adaptation for Dynamic Machine Fault Diagnosis Environments

Unsupervised Domain Adaptation (UDA) has emerged as a key solution in data-driven fault diagnosis, addressing domain shift where models underperform in changing environments. However, under the realm of continually changing environments, UDA tends to underperform on previously seen domains when adapting to new ones - a problem known as catastrophic forgetting. To address this limitation, we introduce the EverAdapt framework, specifically designed for continuous model adaptation in dynamic environments. Central to EverAdapt is a novel Continual Batch Normalization (CBN), which leverages source domain statistics as a reference point to standardize feature representations across domains. EverAdapt not only retains statistical information from previous domains but also adapts effectively to new scenarios. Complementing CBN, we design a class-conditional domain alignment module for effective integration of target domains, and a Sample-efficient Replay strategy to reinforce memory retention. Experiments on real-world datasets demonstrate EverAdapt superiority in maintaining robust fault diagnosis in dynamic environments. Our code is available: https://github.com/mohamedr002/EverAdapt

LPViT: Low-Power Semi-structured Pruning for Vision Transformers

Vision transformers have emerged as a promising alternative to convolutional neural networks for various image analysis tasks, offering comparable or superior performance. However, one significant drawback of ViTs is their resource-intensive nature, leading to increased memory footprint, computation complexity, and power consumption. To democratize this high-performance technology and make it more environmentally friendly, it is essential to compress ViT models, reducing their resource requirements while maintaining high performance. In this paper, we introduce a new block-structured pruning to address the resource-intensive issue for ViTs, offering a balanced trade-off between accuracy and hardware acceleration. Unlike unstructured pruning or channel-wise structured pruning, block pruning leverages the block-wise structure of linear layers, resulting in more efficient matrix multiplications. To optimize this pruning scheme, our paper proposes a novel hardware-aware learning objective that simultaneously maximizes speedup and minimizes power consumption during inference, tailored to the block sparsity structure. This objective eliminates the need for empirical look-up tables and focuses solely on reducing parametrized layer connections. Moreover, our paper provides a lightweight algorithm to achieve post-training pruning for ViTs, utilizing second-order Taylor approximation and empirical optimization to solve the proposed hardware-aware objective. Extensive experiments on ImageNet are conducted across various ViT architectures, including DeiT-B and DeiT-S, demonstrating competitive performance with other pruning methods and achieving a remarkable balance between accuracy preservation and power savings. Especially, we achieve up to 3.93x and 1.79x speedups on dedicated hardware and GPUs respectively for DeiT-B, and also observe an inference power reduction by 1.4x on real-world GPUs.

DM3D: Distortion-Minimized Weight Pruning for Lossless 3D Object Detection

Applying deep neural networks to 3D point cloud processing has attracted increasing attention due to its advanced performance in many areas, such as AR/VR, autonomous driving, and robotics. However, as neural network models and 3D point clouds expand in size, it becomes a crucial challenge to reduce the computational and memory overhead to meet latency and energy constraints in real-world applications. Although existing approaches have proposed to reduce both computational cost and memory footprint, most of them only address the spatial redundancy in inputs, i.e. removing the redundancy of background points in 3D data. In this paper, we propose a novel post-training weight pruning scheme for 3D object detection that is (1) orthogonal to all existing point cloud sparsifying methods, which determines redundant parameters in the pretrained model that lead to minimal distortion in both locality and confidence (detection distortion); and (2) a universal plug-and-play pruning framework that works with arbitrary 3D detection model. This framework aims to minimize detection distortion of network output to maximally maintain detection precision, by identifying layer-wise sparsity based on second-order Taylor approximation of the distortion. Albeit utilizing second-order information, we introduced a lightweight scheme to efficiently acquire Hessian information, and subsequently perform dynamic programming to solve the layer-wise sparsity. Extensive experiments on KITTI, Nuscenes and ONCE datasets demonstrate that our approach is able to maintain and even boost the detection precision on pruned model under noticeable computation reduction (FLOPs). Noticeably, we achieve over 3.89x, 3.72x FLOPs reduction on CenterPoint and PVRCNN model, respectively, without mAP decrease, significantly improving the state-of-the-art.