Despite the success of CNNs, selecting the optimal architecture for a given task remains an open problem. Instead of aiming to select a single optimal architecture, we propose a ``fabric'' that embeds an exponentially large number of architectures. The fabric consists of a 3D trellis that connects response maps at different layers, scales, and channels with a sparse homogeneous local connectivity pattern.

Recent neural architecture search (NAS) frameworks have been successful in finding optimal architectures for given conditions (e.g., performance or latency). However, they search for optimal architectures in terms of their performance on clean images only, while robustness against various types of perturbations or corruptions is crucial in practice. Although there exist several robust NAS frameworks that tackle this issue by integrating adversarial training into one-shot NAS, however, they are limited in that they only consider robustness against adversarial attacks and require significant computational resources to discover optimal architectures for a single task, which makes them impractical in real-world scenarios. To address these challenges, we propose a novel lightweight robust zero-cost proxy that considers the consistency across features, parameters, and gradients of both clean and perturbed images at the initialization state.

Foundation models have revolutionized various fields such as natural language processing (NLP) and computer vision (CV). While efforts have been made to transfer the success of the foundation models in general AI domains to biology, existing works focus on directly adopting the existing foundation model architectures from general machine learning domains without a systematic design considering the unique physicochemical and structural properties of each biological data modality. This leads to suboptimal performance, as these repurposed architectures struggle to capture the long-range dependencies, sparse information, and complex underlying ``grammars'' inherent to biological data. To address this gap, we introduce BioArc, a novel framework designed to move beyond intuition-driven architecture design towards principled, automated architecture discovery for biological foundation models. Leveraging Neural Architecture Search (NAS), BioArc systematically explores a vast architecture design space, evaluating architectures across multiple biological modalities while rigorously analyzing the interplay between architecture, tokenization, and training strategies. This large-scale analysis identifies novel, high-performance architectures, allowing us to distill a set of empirical design principles to guide future model development. Furthermore, to make the best of this set of discovered principled architectures, we propose and compare several architecture prediction methods that effectively and efficiently predict optimal architectures for new biological tasks. Overall, our work provides a foundational resource and a principled methodology to guide the creation of the next generation of task-specific and foundation models for biology.

Deep neural networks have received a considerable attention due to the success of their training for real world machine learning applications. They are also of great interest to the understanding of sensory processing in cortical sensory hierarchies. The purpose of this work is to advance our theoretical understanding of the computational benefits of these architectures. Using a simple model of clustered noisy inputs and a simple learning rule, we provide analytically derived recursion relations describing the propagation of the signals along the deep network. By analysis of these equations, and defining performance measures, we show that these model networks have optimal depths. We further explore the dependence of the optimal architecture on the system parameters.

Despite the success of CNNs, selecting the optimal architecture for a given task remains an open problem. Instead of aiming to select a single optimal architecture, we propose a ``fabric'' that embeds an exponentially large number of architectures. The fabric consists of a 3D trellis that connects response maps at different layers, scales, and channels with a sparse homogeneous local connectivity pattern.

Deep neural networks have received a considerable attention due to the success of their training for real world machine learning applications.

Time series forecasting plays a pivotal role in a wide range of applications, including weather prediction, healthcare, structural health monitoring, predictive maintenance, energy systems, and financial markets. While models such as LSTM, GRU, Transformers, and State-Space Models (SSMs) have become standard tools in this domain, selecting the optimal architecture remains a challenge. Performance comparisons often depend on evaluation metrics and the datasets under analysis, making the choice of a universally optimal model controversial. In this work, we introduce a flexible automated framework for time series forecasting that systematically designs and evaluates diverse network architectures by integrating LSTM, GRU, multi-head Attention, and SSM blocks. Using a multi-objective optimization approach, our framework determines the number, sequence, and combination of blocks to align with specific requirements and evaluation objectives. From the resulting Pareto-optimal architectures, the best model for a given context is selected via a user-defined preference function. We validate our framework across four distinct real-world applications. Results show that a single-layer GRU or LSTM is usually optimal when minimizing training time alone. However, when maximizing accuracy or balancing multiple objectives, the best architectures are often composite designs incorporating multiple block types in specific configurations. By employing a weighted preference function, users can resolve trade-offs between objectives, revealing novel, context-specific optimal architectures. Our findings underscore that no single neural architecture is universally optimal for time series forecasting. Instead, the best-performing model emerges as a data-driven composite architecture tailored to user-defined criteria and evaluation objectives.

While this work attempts to elucidate a theoretical understanding of deep networks, the model they analyze diverges substantially from models which have been successful.

Recent neural architecture search (NAS) frameworks have been successful in finding optimal architectures for given conditions (e.g., performance or latency). However, they search for optimal architectures in terms of their performance on clean images only, while robustness against various types of perturbations or corruptions is crucial in practice. Although there exist several robust NAS frameworks that tackle this issue by integrating adversarial training into one-shot NAS, however, they are limited in that they only consider robustness against adversarial attacks and require significant computational resources to discover optimal architectures for a single task, which makes them impractical in real-world scenarios. To address these challenges, we propose a novel lightweight robust zero-cost proxy that considers the consistency across features, parameters, and gradients of both clean and perturbed images at the initialization state. The experimental results demonstrate that our proxy can rapidly and efficiently search for neural architectures that are consistently robust against various perturbations on multiple benchmark datasets and diverse search spaces, largely outperforming existing clean zero-shot NAS and robust NAS with reduced search cost.

One-shot methods have significantly advanced the field of neural architecture search (NAS) by adopting weight-sharing strategy to reduce search costs. However, the accuracy of performance estimation can be compromised by co-adaptation. Few-shot methods divide the entire supernet into individual sub-supernets by splitting edge by edge to alleviate this issue, yet neglect relationships among edges and result in performance degradation on huge search space. In this paper, we introduce HEP-NAS, a hierarchy-wise partition algorithm designed to further enhance accuracy. To begin with, HEP-NAS treats edges sharing the same end node as a hierarchy, permuting and splitting edges within the same hierarchy to directly search for the optimal operation combination for each intermediate node. This approach aligns more closely with the ultimate goal of NAS. Furthermore, HEP-NAS selects the most promising sub-supernet after each segmentation, progressively narrowing the search space in which the optimal architecture may exist. To improve performance evaluation of sub-supernets, HEP-NAS employs search space mutual distillation, stabilizing the training process and accelerating the convergence of each individual sub-supernet. Within a given budget, HEP-NAS enables the splitting of all edges and gradually searches for architectures with higher accuracy. Experimental results across various datasets and search spaces demonstrate the superiority of HEP-NAS compared to state-of-the-art methods.