Do Protein Transformers Have Biological Intelligence?

Deep neural networks, particularly Transformers, have been widely adopted for predicting the functional properties of proteins. In this work, we focus on exploring whether Protein Transformers can capture biological intelligence among protein sequences. To achieve our goal, we first introduce a protein function dataset, namely Protein-FN, providing over 9000 protein data with meaningful labels. Second, we devise a new Transformer architecture, namely Sequence Protein Transformers (SPT), for computationally efficient protein function predictions. Third, we develop a novel Explainable Artificial Intelligence (XAI) technique called Sequence Score, which can efficiently interpret the decision-making processes of protein models, thereby overcoming the difficulty of deciphering biological intelligence bided in Protein Transformers. Remarkably, even our smallest SPT-Tiny model, which contains only 5.4M parameters, demonstrates impressive predictive accuracy, achieving 94.3% on the Antibiotic Resistance (AR) dataset and 99.6% on the Protein-FN dataset, all accomplished by training from scratch. Besides, our Sequence Score technique helps reveal that our SPT models can discover several meaningful patterns underlying the sequence structures of protein data, with these patterns aligning closely with the domain knowledge in the biology community. We have officially released our Protein-FN dataset on Hugging Face Datasets https://huggingface.co/datasets/Protein-FN/Protein-FN. Our code is available at https://github.com/fudong03/BioIntelligence.

Budget-Adaptive Adapter Tuning in Orthogonal Subspaces for Continual Learning in LLMs

Large language models (LLMs) often suffer from catastrophic forgetting in continual learning (CL) scenarios, where performance on previously learned tasks degrades severely while training on sequentially arriving tasks. Although pioneering CL approaches using orthogonal subspaces can mitigate task interference, they typically employ fixed budget allocation, neglecting the varying complexity across tasks and layers. Besides, recent budget-adaptive tuning methods for LLMs often adopt multi-stage paradigms that decouple optimization and budget allocation. Such decoupling results in potential misalignment, which hinders those approaches' practical application in CL scenarios. To address these limitations, we propose OA-Adapter, a novel parameter-efficient approach for continual learning in LLMs that unifies dynamic budget adaptation with orthogonal subspace learning in a single end-to-end training stage. Specifically, OA-Adapter introduces a dynamic bottleneck dimension adaptation mechanism that simultaneously allocates an efficient parameter budget and optimizes task objectives without misalignment. To effectively preserve previously acquired knowledge while coordinating with the dynamic budget allocation, orthogonal constraints are applied specifically between the parameter subspace of the current task and the dynamically allocated parameter subspaces of historical tasks. Experimental results on continual learning benchmarks demonstrate that OA-Adapter outperforms state-of-the-art methods in both accuracy and parameter efficiency, achieving higher average accuracy while using 58.5% fewer parameters on the standard CL benchmark.

NeRFCom: Feature Transform Coding Meets Neural Radiance Field for Free-View 3D Scene Semantic Transmission

We introduce NeRFCom, a novel communication system designed for end-to-end 3D scene transmission. Compared to traditional systems relying on handcrafted NeRF semantic feature decomposition for compression and well-adaptive channel coding for transmission error correction, our NeRFCom employs a nonlinear transform and learned probabilistic models, enabling flexible variable-rate joint source-channel coding and efficient bandwidth allocation aligned with the NeRF semantic feature's different contribution to the 3D scene synthesis fidelity. Experimental results demonstrate that NeRFCom achieves free-view 3D scene efficient transmission while maintaining robustness under adverse channel conditions.

Rate-Distortion-Perception Controllable Joint Source-Channel Coding for High-Fidelity Generative Communications

End-to-end image transmission has recently become a crucial trend in intelligent wireless communications, driven by the increasing demand for high bandwidth efficiency. However, existing methods primarily optimize the trade-off between bandwidth cost and objective distortion, often failing to deliver visually pleasing results aligned with human perception. In this paper, we propose a novel rate-distortion-perception (RDP) jointly optimized joint source-channel coding (JSCC) framework to enhance perception quality in human communications. Our RDP-JSCC framework integrates a flexible plug-in conditional Generative Adversarial Networks (GANs) to provide detailed and realistic image reconstructions at the receiver, overcoming the limitations of traditional rate-distortion optimized solutions that typically produce blurry or poorly textured images. Based on this framework, we introduce a distortion-perception controllable transmission (DPCT) model, which addresses the variation in the perception-distortion trade-off. DPCT uses a lightweight spatial realism embedding module (SREM) to condition the generator on a realism map, enabling the customization of appearance realism for each image region at the receiver from a single transmission. Furthermore, for scenarios with scarce bandwidth, we propose an interest-oriented content-controllable transmission (CCT) model. CCT prioritizes the transmission of regions that attract user attention and generates other regions from an instance label map, ensuring both content consistency and appearance realism for all regions while proportionally reducing channel bandwidth costs. Comprehensive experiments demonstrate the superiority of our RDP-optimized image transmission framework over state-of-the-art engineered image transmission systems and advanced perceptual methods.

FedEx: Expediting Federated Learning over Heterogeneous Mobile Devices by Overlapping and Participant Selection

Training latency is critical for the success of numerous intrigued applications ignited by federated learning (FL) over heterogeneous mobile devices. By revolutionarily overlapping local gradient transmission with continuous local computing, FL can remarkably reduce its training latency over homogeneous clients, yet encounter severe model staleness, model drifts, memory cost and straggler issues in heterogeneous environments. To unleash the full potential of overlapping, we propose, FedEx, a novel \underline{fed}erated learning approach to \underline{ex}pedite FL training over mobile devices under data, computing and wireless heterogeneity. FedEx redefines the overlapping procedure with staleness ceilings to constrain memory consumption and make overlapping compatible with participation selection (PS) designs. Then, FedEx characterizes the PS utility function by considering the latency reduced by overlapping, and provides a holistic PS solution to address the straggler issue. FedEx also introduces a simple but effective metric to trigger overlapping, in order to avoid model drifts. Experimental results show that compared with its peer designs, FedEx demonstrates substantial reductions in FL training latency over heterogeneous mobile devices with limited memory cost.

DiffCom: Channel Received Signal is a Natural Condition to Guide Diffusion Posterior Sampling

End-to-end visual communication systems typically optimize a trade-off between channel bandwidth costs and signal-level distortion metrics. However, under challenging physical conditions, this traditional discriminative communication paradigm often results in unrealistic reconstructions with perceptible blurring and aliasing artifacts, despite the inclusion of perceptual or adversarial losses for optimizing. This issue primarily stems from the receiver's limited knowledge about the underlying data manifold and the use of deterministic decoding mechanisms. To address these limitations, this paper introduces DiffCom, a novel end-to-end generative communication paradigm that utilizes off-the-shelf generative priors and probabilistic diffusion models for decoding, thereby improving perceptual quality without heavily relying on bandwidth costs and received signal quality. Unlike traditional systems that rely on deterministic decoders optimized solely for distortion metrics, our DiffCom leverages raw channel-received signal as a fine-grained condition to guide stochastic posterior sampling. Our approach ensures that reconstructions remain on the manifold of real data with a novel confirming constraint, enhancing the robustness and reliability of the generated outcomes. Furthermore, DiffCom incorporates a blind posterior sampling technique to address scenarios with unknown forward transmission characteristics. Extensive experimental validations demonstrate that DiffCom not only produces realistic reconstructions with details faithful to the original data but also achieves superior robustness against diverse wireless transmission degradations. Collectively, these advancements establish DiffCom as a new benchmark in designing generative communication systems that offer enhanced robustness and generalization superiorities.

Deep Generative Modeling Reshapes Compression and Transmission: From Efficiency to Resiliency

Information theory and machine learning are inextricably linked and have even been referred to as "two sides of the same coin". One particularly elegant connection is the essential equivalence between probabilistic generative modeling and data compression or transmission. In this article, we reveal the dual-functionality of deep generative models that reshapes both data compression for efficiency and transmission error concealment for resiliency. We present how the contextual predictive capabilities of powerful generative models can be well positioned to be strong compressors and estimators. In this sense, we advocate for viewing the deep generative modeling problem through the lens of end-to-end communications, and evaluate the compression and error restoration capabilities of foundation generative models. We show that the kernel of many large generative models is powerful predictor that can capture complex relationships among semantic latent variables, and the communication viewpoints provide novel insights into semantic feature tokenization, contextual learning, and usage of deep generative models. In summary, our article highlights the essential connections of generative AI to source and channel coding techniques, and motivates researchers to make further explorations in this emerging topic.

WHALE-FL: Wireless and Heterogeneity Aware Latency Efficient Federated Learning over Mobile Devices via Adaptive Subnetwork Scheduling

As a popular distributed learning paradigm, federated learning (FL) over mobile devices fosters numerous applications, while their practical deployment is hindered by participating devices' computing and communication heterogeneity. Some pioneering research efforts proposed to extract subnetworks from the global model, and assign as large a subnetwork as possible to the device for local training based on its full computing and communications capacity. Although such fixed size subnetwork assignment enables FL training over heterogeneous mobile devices, it is unaware of (i) the dynamic changes of devices' communication and computing conditions and (ii) FL training progress and its dynamic requirements of local training contributions, both of which may cause very long FL training delay. Motivated by those dynamics, in this paper, we develop a wireless and heterogeneity aware latency efficient FL (WHALE-FL) approach to accelerate FL training through adaptive subnetwork scheduling. Instead of sticking to the fixed size subnetwork, WHALE-FL introduces a novel subnetwork selection utility function to capture device and FL training dynamics, and guides the mobile device to adaptively select the subnetwork size for local training based on (a) its computing and communication capacity, (b) its dynamic computing and/or communication conditions, and (c) FL training status and its corresponding requirements for local training contributions. Our evaluation shows that, compared with peer designs, WHALE-FL effectively accelerates FL training without sacrificing learning accuracy.

Pragmatic Communication in Multi-Agent Collaborative Perception

Collaborative perception allows each agent to enhance its perceptual abilities by exchanging messages with others. It inherently results in a trade-off between perception ability and communication costs. Previous works transmit complete full-frame high-dimensional feature maps among agents, resulting in substantial communication costs. To promote communication efficiency, we propose only transmitting the information needed for the collaborator's downstream task. This pragmatic communication strategy focuses on three key aspects: i) pragmatic message selection, which selects task-critical parts from the complete data, resulting in spatially and temporally sparse feature vectors; ii) pragmatic message representation, which achieves pragmatic approximation of high-dimensional feature vectors with a task-adaptive dictionary, enabling communicating with integer indices; iii) pragmatic collaborator selection, which identifies beneficial collaborators, pruning unnecessary communication links. Following this strategy, we first formulate a mathematical optimization framework for the perception-communication trade-off and then propose PragComm, a multi-agent collaborative perception system with two key components: i) single-agent detection and tracking and ii) pragmatic collaboration. The proposed PragComm promotes pragmatic communication and adapts to a wide range of communication conditions. We evaluate PragComm for both collaborative 3D object detection and tracking tasks in both real-world, V2V4Real, and simulation datasets, OPV2V and V2X-SIM2.0. PragComm consistently outperforms previous methods with more than 32.7K times lower communication volume on OPV2V. Code is available at github.com/PhyllisH/PragComm.

Fundamental Limitation of Semantic Communications: Neural Estimation for Rate-Distortion

This paper studies the fundamental limit of semantic communications over the discrete memoryless channel. We consider the scenario to send a semantic source consisting of an observation state and its corresponding semantic state, both of which are recovered at the receiver. To derive the performance limitation, we adopt the semantic rate-distortion function (SRDF) to study the relationship among the minimum compression rate, observation distortion, semantic distortion, and channel capacity. For the case with unknown semantic source distribution, while only a set of the source samples is available, we propose a neural-network-based method by leveraging the generative networks to learn the semantic source distribution. Furthermore, for a special case where the semantic state is a deterministic function of the observation, we design a cascade neural network to estimate the SRDF. For the case with perfectly known semantic source distribution, we propose a general Blahut-Arimoto algorithm to effectively compute the SRDF. Finally, experimental results validate our proposed algorithms for the scenarios with ideal Gaussian semantic source and some practical datasets.