Daily Papers

In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one of the first major DNAS methods. In contrast with previous works based on Reinforcement Learning or Evolutionary Algorithms, DNAS is faster by several orders of magnitude and uses fewer computational resources. In this comprehensive survey, we focus specifically on DNAS and review recent approaches in this field. Furthermore, we propose a novel challenge-based taxonomy to classify DNAS methods. We also discuss the contributions brought to DNAS in the past few years and its impact on the global NAS field. Finally, we conclude by giving some insights into future research directions for the DNAS field.

Designing accurate and efficient ConvNets for mobile devices is challenging because the design space is combinatorially large. Due to this, previous neural architecture search (NAS) methods are computationally expensive. ConvNet architecture optimality depends on factors such as input resolution and target devices. However, existing approaches are too expensive for case-by-case redesigns. Also, previous work focuses primarily on reducing FLOPs, but FLOP count does not always reflect actual latency. To address these, we propose a differentiable neural architecture search (DNAS) framework that uses gradient-based methods to optimize ConvNet architectures, avoiding enumerating and training individual architectures separately as in previous methods. FBNets, a family of models discovered by DNAS surpass state-of-the-art models both designed manually and generated automatically. FBNet-B achieves 74.1% top-1 accuracy on ImageNet with 295M FLOPs and 23.1 ms latency on a Samsung S8 phone, 2.4x smaller and 1.5x faster than MobileNetV2-1.3 with similar accuracy. Despite higher accuracy and lower latency than MnasNet, we estimate FBNet-B's search cost is 420x smaller than MnasNet's, at only 216 GPU-hours. Searched for different resolutions and channel sizes, FBNets achieve 1.5% to 6.4% higher accuracy than MobileNetV2. The smallest FBNet achieves 50.2% accuracy and 2.9 ms latency (345 frames per second) on a Samsung S8. Over a Samsung-optimized FBNet, the iPhone-X-optimized model achieves a 1.4x speedup on an iPhone X.

Designing domain specific neural networks is a time-consuming, error-prone, and expensive task. Neural Architecture Search (NAS) exists to simplify domain-specific model development but there is a gap in the literature for time series classification on microcontrollers. Therefore, we adapt the concept of differentiable neural architecture search (DNAS) to solve the time-series classification problem on resource-constrained microcontrollers (MCUs). We introduce MicroNAS, a domain-specific HW-NAS system integration of DNAS, Latency Lookup Tables, dynamic convolutions and a novel search space specifically designed for time-series classification on MCUs. The resulting system is hardware-aware and can generate neural network architectures that satisfy user-defined limits on the execution latency and peak memory consumption. Our extensive studies on different MCUs and standard benchmark datasets demonstrate that MicroNAS finds MCU-tailored architectures that achieve performance (F1-score) near to state-of-the-art desktop models. We also show that our approach is superior in adhering to memory and latency constraints compared to domain-independent NAS baselines such as DARTS.

The COVID-19 pandemic has spread globally for several months. Because its transmissibility and high pathogenicity seriously threaten people's lives, it is crucial to accurately and quickly detect COVID-19 infection. Many recent studies have shown that deep learning (DL) based solutions can help detect COVID-19 based on chest CT scans. However, most existing work focuses on 2D datasets, which may result in low quality models as the real CT scans are 3D images. Besides, the reported results span a broad spectrum on different datasets with a relatively unfair comparison. In this paper, we first use three state-of-the-art 3D models (ResNet3D101, DenseNet3D121, and MC3\_18) to establish the baseline performance on the three publicly available chest CT scan datasets. Then we propose a differentiable neural architecture search (DNAS) framework to automatically search for the 3D DL models for 3D chest CT scans classification with the Gumbel Softmax technique to improve the searching efficiency. We further exploit the Class Activation Mapping (CAM) technique on our models to provide the interpretability of the results. The experimental results show that our automatically searched models (CovidNet3D) outperform the baseline human-designed models on the three datasets with tens of times smaller model size and higher accuracy. Furthermore, the results also verify that CAM can be well applied in CovidNet3D for COVID-19 datasets to provide interpretability for medical diagnosis.

We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can traverse any series of modules in any order. DNAs are a natural generalization of the sparse methods such as Mixture-of-Experts, Mixture-of-Depths, parameter sharing, etc. Computation and communication patterns of DNA modules are learnt end-to-end during training and depend on the content and context of each token (or patch). These patterns can be shaped by further requirements added to the optimization objective such as compute/memory efficiency or load balancing. We empirically show that (i) trained DNAs are competitive with the dense baselines in both domains and (ii) compute efficiency/parameter sharing can be learnt from data. Next, we analyze the emergent connectivity and computation patterns in the trained DNAs. We find that the paths that tokens take through the models are themselves distributed according to a power-law. We show that some paths (or, equivalently, groups of modules) show emergent specialization. Finally, we demonstrate that models learn to allocate compute and active parameters in an interpretable way.

Selecting appropriate datasets is critical in modern computer vision. However, no general-purpose tools exist to evaluate the extent to which two datasets differ. For this, we propose representing images - and by extension datasets - using Distributions of Neuron Activations (DNAs). DNAs fit distributions, such as histograms or Gaussians, to activations of neurons in a pre-trained feature extractor through which we pass the image(s) to represent. This extractor is frozen for all datasets, and we rely on its generally expressive power in feature space. By comparing two DNAs, we can evaluate the extent to which two datasets differ with granular control over the comparison attributes of interest, providing the ability to customise the way distances are measured to suit the requirements of the task at hand. Furthermore, DNAs are compact, representing datasets of any size with less than 15 megabytes. We demonstrate the value of DNAs by evaluating their applicability on several tasks, including conditional dataset comparison, synthetic image evaluation, and transfer learning, and across diverse datasets, ranging from synthetic cat images to celebrity faces and urban driving scenes.

Differentiable ARchiTecture Search (DARTS) is one of the most trending Neural Architecture Search (NAS) methods. It drastically reduces search cost by resorting to weight-sharing. However, it also dramatically reduces the search space, thus excluding potential promising architectures. In this article, we propose D-DARTS, a solution that addresses this problem by nesting neural networks at the cell level instead of using weight-sharing to produce more diversified and specialized architectures. Moreover, we introduce a novel algorithm that can derive deeper architectures from a few trained cells, increasing performance and saving computation time. In addition, we also present an alternative search space (DARTOpti) in which we optimize existing handcrafted architectures (e.g., ResNet) rather than starting from scratch. This approach is accompanied by a novel metric that measures the distance between architectures inside our custom search space. Our solution reaches competitive performance on multiple computer vision tasks. Code and pretrained models can be accessed at https://github.com/aheuillet/D-DARTS.

This paper addresses the scalability challenge of architecture search by formulating the task in a differentiable manner. Unlike conventional approaches of applying evolution or reinforcement learning over a discrete and non-differentiable search space, our method is based on the continuous relaxation of the architecture representation, allowing efficient search of the architecture using gradient descent. Extensive experiments on CIFAR-10, ImageNet, Penn Treebank and WikiText-2 show that our algorithm excels in discovering high-performance convolutional architectures for image classification and recurrent architectures for language modeling, while being orders of magnitude faster than state-of-the-art non-differentiable techniques. Our implementation has been made publicly available to facilitate further research on efficient architecture search algorithms.

Differentiable Neural Architecture Search is one of the most popular Neural Architecture Search (NAS) methods for its search efficiency and simplicity, accomplished by jointly optimizing the model weight and architecture parameters in a weight-sharing supernet via gradient-based algorithms. At the end of the search phase, the operations with the largest architecture parameters will be selected to form the final architecture, with the implicit assumption that the values of architecture parameters reflect the operation strength. While much has been discussed about the supernet's optimization, the architecture selection process has received little attention. We provide empirical and theoretical analysis to show that the magnitude of architecture parameters does not necessarily indicate how much the operation contributes to the supernet's performance. We propose an alternative perturbation-based architecture selection that directly measures each operation's influence on the supernet. We re-evaluate several differentiable NAS methods with the proposed architecture selection and find that it is able to extract significantly improved architectures from the underlying supernets consistently. Furthermore, we find that several failure modes of DARTS can be greatly alleviated with the proposed selection method, indicating that much of the poor generalization observed in DARTS can be attributed to the failure of magnitude-based architecture selection rather than entirely the optimization of its supernet.

There has been a large literature of neural architecture search, but most existing work made use of heuristic rules that largely constrained the search flexibility. In this paper, we first relax these manually designed constraints and enlarge the search space to contain more than 10^{160} candidates. In the new space, most existing differentiable search methods can fail dramatically. We then propose a novel algorithm named Gradual One-Level Differentiable Neural Architecture Search (GOLD-NAS) which introduces a variable resource constraint to one-level optimization so that the weak operators are gradually pruned out from the super-network. In standard image classification benchmarks, GOLD-NAS can find a series of Pareto-optimal architectures within a single search procedure. Most of the discovered architectures were never studied before, yet they achieve a nice tradeoff between recognition accuracy and model complexity. We believe the new space and search algorithm can advance the search of differentiable NAS.

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and complexity of the problem, this manual architecture exploration likely exceeds human design abilities. In this paper, we propose a principled approach, rooted in differentiable neural architecture search, to automatically define branching (tree-like) structures in the encoding stage of a multi-task neural network. To allow flexibility within resource-constrained environments, we introduce a proxyless, resource-aware loss that dynamically controls the model size. Evaluations across a variety of dense prediction tasks show that our approach consistently finds high-performing branching structures within limited resource budgets.

Differentiable neural architecture search methods became popular in recent years, mainly due to their low search costs and flexibility in designing the search space. However, these methods suffer the difficulty in optimizing network, so that the searched network is often unfriendly to hardware. This paper deals with this problem by adding a differentiable latency loss term into optimization, so that the search process can tradeoff between accuracy and latency with a balancing coefficient. The core of latency prediction is to encode each network architecture and feed it into a multi-layer regressor, with the training data which can be easily collected from randomly sampling a number of architectures and evaluating them on the hardware. We evaluate our approach on NVIDIA Tesla-P100 GPUs. With 100K sampled architectures (requiring a few hours), the latency prediction module arrives at a relative error of lower than 10%. Equipped with this module, the search method can reduce the latency by 20% meanwhile preserving the accuracy. Our approach also enjoys the ability of being transplanted to a wide range of hardware platforms with very few efforts, or being used to optimizing other non-differentiable factors such as power consumption.

Neural Architecture Search (NAS) has been a source of dramatic improvements in neural network design, with recent results meeting or exceeding the performance of hand-tuned architectures. However, our understanding of how to represent the search space for neural net architectures and how to search that space efficiently are both still in their infancy. We have performed an in-depth analysis to identify limitations in a widely used search space and a recent architecture search method, Differentiable Architecture Search (DARTS). These findings led us to introduce novel network blocks with a more general, balanced, and consistent design; a better-optimized Cosine Power Annealing learning rate schedule; and other improvements. Our resulting sharpDARTS search is 50% faster with a 20-30% relative improvement in final model error on CIFAR-10 when compared to DARTS. Our best single model run has 1.93% (1.98+/-0.07) validation error on CIFAR-10 and 5.5% error (5.8+/-0.3) on the recently released CIFAR-10.1 test set. To our knowledge, both are state of the art for models of similar size. This model also generalizes competitively to ImageNet at 25.1% top-1 (7.8% top-5) error. We found improvements for existing search spaces but does DARTS generalize to new domains? We propose Differentiable Hyperparameter Grid Search and the HyperCuboid search space, which are representations designed to leverage DARTS for more general parameter optimization. Here we find that DARTS fails to generalize when compared against a human's one shot choice of models. We look back to the DARTS and sharpDARTS search spaces to understand why, and an ablation study reveals an unusual generalization gap. We finally propose Max-W regularization to solve this problem, which proves significantly better than the handmade design. Code will be made available.

Differentiable architecture search (DARTS) yields highly efficient gradient-based neural architecture search (NAS) by relaxing the discrete operation selection to optimize continuous architecture parameters that maps NAS from the discrete optimization to a continuous problem. DARTS then remaps the relaxed supernet back to the discrete space by one-off post-search pruning to obtain the final architecture (finalnet). Some emerging works argue that this remap is inherently prone to mismatch the network between training and evaluation which leads to performance discrepancy and even model collapse in extreme cases. We propose to close the gap between the relaxed supernet in training and the pruned finalnet in evaluation through utilizing small temperature to sparsify the continuous distribution in the training phase. To this end, we first formulate sparse-noisy softmax to get around gradient saturation. We then propose an exponential temperature schedule to better control the outbound distribution and elaborate an entropy-based adaptive scheme to finally achieve the enhancement. We conduct extensive experiments to verify the efficiency and efficacy of our method.

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

We explore efficient neural architecture search methods and show that a simple yet powerful evolutionary algorithm can discover new architectures with excellent performance. Our approach combines a novel hierarchical genetic representation scheme that imitates the modularized design pattern commonly adopted by human experts, and an expressive search space that supports complex topologies. Our algorithm efficiently discovers architectures that outperform a large number of manually designed models for image classification, obtaining top-1 error of 3.6% on CIFAR-10 and 20.3% when transferred to ImageNet, which is competitive with the best existing neural architecture search approaches. We also present results using random search, achieving 0.3% less top-1 accuracy on CIFAR-10 and 0.1% less on ImageNet whilst reducing the search time from 36 hours down to 1 hour.

Current neural architecture search (NAS) strategies focus only on finding a single, good, architecture. They offer little insight into why a specific network is performing well, or how we should modify the architecture if we want further improvements. We propose a Bayesian optimisation (BO) approach for NAS that combines the Weisfeiler-Lehman graph kernel with a Gaussian process surrogate. Our method optimises the architecture in a highly data-efficient manner: it is capable of capturing the topological structures of the architectures and is scalable to large graphs, thus making the high-dimensional and graph-like search spaces amenable to BO. More importantly, our method affords interpretability by discovering useful network features and their corresponding impact on the network performance. Indeed, we demonstrate empirically that our surrogate model is capable of identifying useful motifs which can guide the generation of new architectures. We finally show that our method outperforms existing NAS approaches to achieve the state of the art on both closed- and open-domain search spaces.

Neural architecture search (NAS) is a hard computationally expensive optimization problem with a discrete, vast, and spiky search space. One of the key research efforts dedicated to this space focuses on accelerating NAS via certain proxy evaluations of neural architectures. Different from the prevalent predictor-based methods using surrogate models and differentiable architecture search via supernetworks, we propose an optimization proxy to streamline the NAS as an end-to-end optimization framework, named OptiProxy-NAS. In particular, using a proxy representation, the NAS space is reformulated to be continuous, differentiable, and smooth. Thereby, any differentiable optimization method can be applied to the gradient-based search of the relaxed architecture parameters. Our comprehensive experiments on 12 NAS tasks of 4 search spaces across three different domains including computer vision, natural language processing, and resource-constrained NAS fully demonstrate the superior search results and efficiency. Further experiments on low-fidelity scenarios verify the flexibility.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Logic synthesis, a critical stage in electronic design automation (EDA), optimizes gate-level circuits to minimize power consumption and area occupancy in integrated circuits (ICs). Traditional logic synthesis tools rely on human-designed heuristics, often yielding suboptimal results. Although differentiable architecture search (DAS) has shown promise in generating circuits from truth tables, it faces challenges such as high computational complexity, convergence to local optima, and extensive hyperparameter tuning. Consequently, we propose a novel approach integrating conditional generative models with DAS for circuit generation. Our approach first introduces CircuitVQ, a circuit tokenizer trained based on our Circuit AutoEncoder We then develop CircuitAR, a masked autoregressive model leveraging CircuitVQ as the tokenizer. CircuitAR can generate preliminary circuit structures from truth tables, which guide DAS in producing functionally equivalent circuits. Notably, we observe the scalability and emergent capability in generating complex circuit structures of our CircuitAR models. Extensive experiments also show the superior performance of our method. This research bridges the gap between probabilistic generative models and precise circuit generation, offering a robust solution for logic synthesis.

Neural architecture search (NAS), the study of automating the discovery of optimal deep neural network architectures for tasks in domains such as computer vision and natural language processing, has seen rapid growth in the machine learning research community. While there have been many recent advancements in NAS, there is still a significant focus on reducing the computational cost incurred when validating discovered architectures by making search more efficient. Evolutionary algorithms, specifically genetic algorithms, have a history of usage in NAS and continue to gain popularity versus other optimization approaches as a highly efficient way to explore the architecture objective space. Most NAS research efforts have centered around computer vision tasks and only recently have other modalities, such as the rapidly growing field of natural language processing, been investigated in depth. In this work, we show how genetic algorithms can be paired with lightly trained objective predictors in an iterative cycle to accelerate multi-objective architectural exploration in a way that works in the modalities of both machine translation and image classification.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

Recent advances in Neural Architecture Search (NAS) such as one-shot NAS offer the ability to extract specialized hardware-aware sub-network configurations from a task-specific super-network. While considerable effort has been employed towards improving the first stage, namely, the training of the super-network, the search for derivative high-performing sub-networks is still under-explored. Popular methods decouple the super-network training from the sub-network search and use performance predictors to reduce the computational burden of searching on different hardware platforms. We propose a flexible search framework that automatically and efficiently finds optimal sub-networks that are optimized for different performance metrics and hardware configurations. Specifically, we show how evolutionary algorithms can be paired with lightly trained objective predictors in an iterative cycle to accelerate architecture search in a multi-objective setting for various modalities including machine translation and image classification.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

Neural Architecture Search (NAS) has garnered significant research interest due to its capability to discover architectures superior to manually designed ones. Learning text representation is crucial for text classification and other language-related tasks. The NAS model used in text classification does not have a Hybrid hierarchical structure, and there is no restriction on the architecture structure, due to which the search space becomes very large and mostly redundant, so the existing RL models are not able to navigate the search space effectively. Also, doing a flat architecture search leads to an unorganised search space, which is difficult to traverse. For this purpose, we propose HHNAS-AM (Hierarchical Hybrid Neural Architecture Search with Adaptive Mutation Policies), a novel approach that efficiently explores diverse architectural configurations. We introduce a few architectural templates to search on which organise the search spaces, where search spaces are designed on the basis of domain-specific cues. Our method employs mutation strategies that dynamically adapt based on performance feedback from previous iterations using Q-learning, enabling a more effective and accelerated traversal of the search space. The proposed model is fully probabilistic, enabling effective exploration of the search space. We evaluate our approach on the database id (db_id) prediction task, where it consistently discovers high-performing architectures across multiple experiments. On the Spider dataset, our method achieves an 8% improvement in test accuracy over existing baselines.

Neural architecture search (NAS) has achieved breakthrough success in a great number of applications in the past few years. It could be time to take a step back and analyze the good and bad aspects in the field of NAS. A variety of algorithms search architectures under different search space. These searched architectures are trained using different setups, e.g., hyper-parameters, data augmentation, regularization. This raises a comparability problem when comparing the performance of various NAS algorithms. NAS-Bench-101 has shown success to alleviate this problem. In this work, we propose an extension to NAS-Bench-101: NAS-Bench-201 with a different search space, results on multiple datasets, and more diagnostic information. NAS-Bench-201 has a fixed search space and provides a unified benchmark for almost any up-to-date NAS algorithms. The design of our search space is inspired from the one used in the most popular cell-based searching algorithms, where a cell is represented as a DAG. Each edge here is associated with an operation selected from a predefined operation set. For it to be applicable for all NAS algorithms, the search space defined in NAS-Bench-201 includes all possible architectures generated by 4 nodes and 5 associated operation options, which results in 15,625 candidates in total. The training log and the performance for each architecture candidate are provided for three datasets. This allows researchers to avoid unnecessary repetitive training for selected candidate and focus solely on the search algorithm itself. The training time saved for every candidate also largely improves the efficiency of many methods. We provide additional diagnostic information such as fine-grained loss and accuracy, which can give inspirations to new designs of NAS algorithms. In further support, we have analyzed it from many aspects and benchmarked 10 recent NAS algorithms.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Deep neural networks have recently become a popular solution to keyword spotting systems, which enable the control of smart devices via voice. In this paper, we apply neural architecture search to search for convolutional neural network models that can help boost the performance of keyword spotting based on features extracted from acoustic signals while maintaining an acceptable memory footprint. Specifically, we use differentiable architecture search techniques to search for operators and their connections in a predefined cell search space. The found cells are then scaled up in both depth and width to achieve competitive performance. We evaluated the proposed method on Google's Speech Commands Dataset and achieved a state-of-the-art accuracy of over 97% on the setting of 12-class utterance classification commonly reported in the literature.

Differentiable Architecture Search (DARTS) is a simple yet efficient Neural Architecture Search (NAS) method. During the search stage, DARTS trains a supernet by jointly optimizing architecture parameters and network parameters. During the evaluation stage, DARTS discretizes the supernet to derive the optimal architecture based on architecture parameters. However, recent research has shown that during the training process, the supernet tends to converge towards sharp minima rather than flat minima. This is evidenced by the higher sharpness of the loss landscape of the supernet, which ultimately leads to a performance gap between the supernet and the optimal architecture. In this paper, we propose Self-Distillation Differentiable Neural Architecture Search (SD-DARTS) to alleviate the discretization gap. We utilize self-distillation to distill knowledge from previous steps of the supernet to guide its training in the current step, effectively reducing the sharpness of the supernet's loss and bridging the performance gap between the supernet and the optimal architecture. Furthermore, we introduce the concept of voting teachers, where multiple previous supernets are selected as teachers, and their output probabilities are aggregated through voting to obtain the final teacher prediction. Experimental results on real datasets demonstrate the advantages of our novel self-distillation-based NAS method compared to state-of-the-art alternatives.

Differentiable architecture search (DARTS) is an effective method for data-driven neural network design based on solving a bilevel optimization problem. Despite its success in many architecture search tasks, there are still some concerns about the accuracy of first-order DARTS and the efficiency of the second-order DARTS. In this paper, we formulate a single level alternative and a relaxed architecture search (RARTS) method that utilizes the whole dataset in architecture learning via both data and network splitting, without involving mixed second derivatives of the corresponding loss functions like DARTS. In our formulation of network splitting, two networks with different but related weights cooperate in search of a shared architecture. The advantage of RARTS over DARTS is justified by a convergence theorem and an analytically solvable model. Moreover, RARTS outperforms DARTS and its variants in accuracy and search efficiency, as shown in adequate experimental results. For the task of searching topological architecture, i.e., the edges and the operations, RARTS obtains a higher accuracy and 60\% reduction of computational cost than second-order DARTS on CIFAR-10. RARTS continues to out-perform DARTS upon transfer to ImageNet and is on par with recent variants of DARTS even though our innovation is purely on the training algorithm without modifying search space. For the task of searching width, i.e., the number of channels in convolutional layers, RARTS also outperforms the traditional network pruning benchmarks. Further experiments on the public architecture search benchmark like NATS-Bench also support the preeminence of RARTS.

Recent advances show that Neural Architectural Search (NAS) method is able to find state-of-the-art image classification deep architectures. In this paper, we consider the one-shot NAS problem for resource constrained applications. This problem is of great interest because it is critical to choose different architectures according to task complexity when the resource is constrained. Previous techniques are either too slow for one-shot learning or does not take the resource constraint into consideration. In this paper, we propose the resource constrained differentiable architecture search (RC-DARTS) method to learn architectures that are significantly smaller and faster while achieving comparable accuracy. Specifically, we propose to formulate the RC-DARTS task as a constrained optimization problem by adding the resource constraint. An iterative projection method is proposed to solve the given constrained optimization problem. We also propose a multi-level search strategy to enable layers at different depths to adaptively learn different types of neural architectures. Through extensive experiments on the Cifar10 and ImageNet datasets, we show that the RC-DARTS method learns lightweight neural architectures which have smaller model size and lower computational complexity while achieving comparable or better performances than the state-of-the-art methods.

Neural Architecture Search (NAS) algorithms automate the task of finding optimal deep learning architectures given an initial search space of possible operations. Developing these search spaces is usually a manual affair with pre-optimized search spaces being more efficient, rather than searching from scratch. In this paper we present a new framework called Neural Architecture Type System (NeuralArTS) that categorizes the infinite set of network operations in a structured type system. We further demonstrate how NeuralArTS can be applied to convolutional layers and propose several future directions.

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

Neural Architecture Search (NAS) is an exciting new field which promises to be as much as a game-changer as Convolutional Neural Networks were in 2012. Despite many great works leading to substantial improvements on a variety of tasks, comparison between different methods is still very much an open issue. While most algorithms are tested on the same datasets, there is no shared experimental protocol followed by all. As such, and due to the under-use of ablation studies, there is a lack of clarity regarding why certain methods are more effective than others. Our first contribution is a benchmark of 8 NAS methods on 5 datasets. To overcome the hurdle of comparing methods with different search spaces, we propose using a method's relative improvement over the randomly sampled average architecture, which effectively removes advantages arising from expertly engineered search spaces or training protocols. Surprisingly, we find that many NAS techniques struggle to significantly beat the average architecture baseline. We perform further experiments with the commonly used DARTS search space in order to understand the contribution of each component in the NAS pipeline. These experiments highlight that: (i) the use of tricks in the evaluation protocol has a predominant impact on the reported performance of architectures; (ii) the cell-based search space has a very narrow accuracy range, such that the seed has a considerable impact on architecture rankings; (iii) the hand-designed macro-structure (cells) is more important than the searched micro-structure (operations); and (iv) the depth-gap is a real phenomenon, evidenced by the change in rankings between 8 and 20 cell architectures. To conclude, we suggest best practices, that we hope will prove useful for the community and help mitigate current NAS pitfalls. The code used is available at https://github.com/antoyang/NAS-Benchmark.

Neural architecture search (NAS) finds high performing networks for a given task. Yet the results of NAS are fairly prosaic; they did not e.g. create a shift from convolutional structures to transformers. This is not least because the search spaces in NAS often aren't diverse enough to include such transformations a priori. Instead, for NAS to provide greater potential for fundamental design shifts, we need a novel expressive search space design which is built from more fundamental operations. To this end, we introduce einspace, a search space based on a parameterised probabilistic context-free grammar. Our space is versatile, supporting architectures of various sizes and complexities, while also containing diverse network operations which allow it to model convolutions, attention components and more. It contains many existing competitive architectures, and provides flexibility for discovering new ones. Using this search space, we perform experiments to find novel architectures as well as improvements on existing ones on the diverse Unseen NAS datasets. We show that competitive architectures can be obtained by searching from scratch, and we consistently find large improvements when initialising the search with strong baselines. We believe that this work is an important advancement towards a transformative NAS paradigm where search space expressivity and strategic search initialisation play key roles.

Neural architecture search (NAS) has achieved remarkable results in deep neural network design. Differentiable architecture search converts the search over discrete architectures into a hyperparameter optimization problem which can be solved by gradient descent. However, questions have been raised regarding the effectiveness and generalizability of gradient methods for solving non-convex architecture hyperparameter optimization problems. In this paper, we propose L^{2}NAS, which learns to intelligently optimize and update architecture hyperparameters via an actor neural network based on the distribution of high-performing architectures in the search history. We introduce a quantile-driven training procedure which efficiently trains L^{2}NAS in an actor-critic framework via continuous-action reinforcement learning. Experiments show that L^{2}NAS achieves state-of-the-art results on NAS-Bench-201 benchmark as well as DARTS search space and Once-for-All MobileNetV3 search space. We also show that search policies generated by L^{2}NAS are generalizable and transferable across different training datasets with minimal fine-tuning.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Neural Architecture Search (NAS) has gained significant popularity as an effective tool for designing high performance deep neural networks (DNNs). NAS can be performed via policy gradient, evolutionary algorithms, differentiable architecture search or tree-search methods. While significant progress has been made for both policy gradient and differentiable architecture search, tree-search methods have so far failed to achieve comparable accuracy or search efficiency. In this paper, we formulate NAS as a Combinatorial Multi-Armed Bandit (CMAB) problem (CMAB-NAS). This allows the decomposition of a large search space into smaller blocks where tree-search methods can be applied more effectively and efficiently. We further leverage a tree-based method called Nested Monte-Carlo Search to tackle the CMAB-NAS problem. On CIFAR-10, our approach discovers a cell structure that achieves a low error rate that is comparable to the state-of-the-art, using only 0.58 GPU days, which is 20 times faster than current tree-search methods. Moreover, the discovered structure transfers well to large-scale datasets such as ImageNet.

Differentiable architecture search (DARTS) provided a fast solution in finding effective network architectures, but suffered from large memory and computing overheads in jointly training a super-network and searching for an optimal architecture. In this paper, we present a novel approach, namely, Partially-Connected DARTS, by sampling a small part of super-network to reduce the redundancy in exploring the network space, thereby performing a more efficient search without comprising the performance. In particular, we perform operation search in a subset of channels while bypassing the held out part in a shortcut. This strategy may suffer from an undesired inconsistency on selecting the edges of super-net caused by sampling different channels. We alleviate it using edge normalization, which adds a new set of edge-level parameters to reduce uncertainty in search. Thanks to the reduced memory cost, PC-DARTS can be trained with a larger batch size and, consequently, enjoys both faster speed and higher training stability. Experimental results demonstrate the effectiveness of the proposed method. Specifically, we achieve an error rate of 2.57% on CIFAR10 with merely 0.1 GPU-days for architecture search, and a state-of-the-art top-1 error rate of 24.2% on ImageNet (under the mobile setting) using 3.8 GPU-days for search. Our code has been made available at: https://github.com/yuhuixu1993/PC-DARTS.

Neural architecture search (NAS) automates the design process of high-performing architectures, but remains bottlenecked by expensive performance evaluation. Most existing studies that achieve faster evaluation are mostly tied to cell-based search spaces and graph encodings tailored to those individual search spaces, limiting their flexibility and scalability when applied to more expressive search spaces. In this work, we aim to close the gap of individual search space restrictions and search space dependent network representations. We present ONNX-Bench, a benchmark consisting of a collection of neural networks in a unified format based on ONNX files. ONNX-Bench includes all open-source NAS-bench-based neural networks, resulting in a total size of more than 600k {architecture, accuracy} pairs. This benchmark allows creating a shared neural network representation, ONNX-Net, able to represent any neural architecture using natural language descriptions acting as an input to a performance predictor. This text-based encoding can accommodate arbitrary layer types, operation parameters, and heterogeneous topologies, enabling a single surrogate to generalise across all neural architectures rather than being confined to cell-based search spaces. Experiments show strong zero-shot performance across disparate search spaces using only a small amount of pretraining samples, enabling the unprecedented ability to evaluate any neural network architecture instantly.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Neural architecture search (NAS) can have a significant impact in computer vision by automatically designing optimal neural network architectures for various tasks. A variant, binarized neural architecture search (BNAS), with a search space of binarized convolutions, can produce extremely compressed models. Unfortunately, this area remains largely unexplored. BNAS is more challenging than NAS due to the learning inefficiency caused by optimization requirements and the huge architecture space. To address these issues, we introduce channel sampling and operation space reduction into a differentiable NAS to significantly reduce the cost of searching. This is accomplished through a performance-based strategy used to abandon less potential operations. Two optimization methods for binarized neural networks are used to validate the effectiveness of our BNAS. Extensive experiments demonstrate that the proposed BNAS achieves a performance comparable to NAS on both CIFAR and ImageNet databases. An accuracy of 96.53% vs. 97.22% is achieved on the CIFAR-10 dataset, but with a significantly compressed model, and a 40% faster search than the state-of-the-art PC-DARTS.

Realistic human-centric rendering plays a key role in both computer vision and computer graphics. Rapid progress has been made in the algorithm aspect over the years, yet existing human-centric rendering datasets and benchmarks are rather impoverished in terms of diversity, which are crucial for rendering effect. Researchers are usually constrained to explore and evaluate a small set of rendering problems on current datasets, while real-world applications require methods to be robust across different scenarios. In this work, we present DNA-Rendering, a large-scale, high-fidelity repository of human performance data for neural actor rendering. DNA-Rendering presents several alluring attributes. First, our dataset contains over 1500 human subjects, 5000 motion sequences, and 67.5M frames' data volume. Second, we provide rich assets for each subject -- 2D/3D human body keypoints, foreground masks, SMPLX models, cloth/accessory materials, multi-view images, and videos. These assets boost the current method's accuracy on downstream rendering tasks. Third, we construct a professional multi-view system to capture data, which contains 60 synchronous cameras with max 4096 x 3000 resolution, 15 fps speed, and stern camera calibration steps, ensuring high-quality resources for task training and evaluation. Along with the dataset, we provide a large-scale and quantitative benchmark in full-scale, with multiple tasks to evaluate the existing progress of novel view synthesis, novel pose animation synthesis, and novel identity rendering methods. In this manuscript, we describe our DNA-Rendering effort as a revealing of new observations, challenges, and future directions to human-centric rendering. The dataset, code, and benchmarks will be publicly available at https://dna-rendering.github.io/

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.

Designing architectures for deep neural networks requires expert knowledge and substantial computation time. We propose a technique to accelerate architecture selection by learning an auxiliary HyperNet that generates the weights of a main model conditioned on that model's architecture. By comparing the relative validation performance of networks with HyperNet-generated weights, we can effectively search over a wide range of architectures at the cost of a single training run. To facilitate this search, we develop a flexible mechanism based on memory read-writes that allows us to define a wide range of network connectivity patterns, with ResNet, DenseNet, and FractalNet blocks as special cases. We validate our method (SMASH) on CIFAR-10 and CIFAR-100, STL-10, ModelNet10, and Imagenet32x32, achieving competitive performance with similarly-sized hand-designed networks. Our code is available at https://github.com/ajbrock/SMASH

Differentiable Architecture Search (DARTS) has attracted a lot of attention due to its simplicity and small search costs achieved by a continuous relaxation and an approximation of the resulting bi-level optimization problem. However, DARTS does not work robustly for new problems: we identify a wide range of search spaces for which DARTS yields degenerate architectures with very poor test performance. We study this failure mode and show that, while DARTS successfully minimizes validation loss, the found solutions generalize poorly when they coincide with high validation loss curvature in the architecture space. We show that by adding one of various types of regularization we can robustify DARTS to find solutions with less curvature and better generalization properties. Based on these observations, we propose several simple variations of DARTS that perform substantially more robustly in practice. Our observations are robust across five search spaces on three image classification tasks and also hold for the very different domains of disparity estimation (a dense regression task) and language modelling.

Turing machine and decision tree have developed independently for a long time. With the recent development of differentiable models, there is an intersection between them. Neural turing machine(NTM) opens door for the memory network. It use differentiable attention mechanism to read/write external memory bank. Differentiable forest brings differentiable properties to classical decision tree. In this short note, we show the deep connection between these two models. That is: differentiable forest is a special case of NTM. Differentiable forest is actually decision tree based neural turing machine. Based on this deep connection, we propose a response augmented differential forest (RaDF). The controller of RaDF is differentiable forest, the external memory of RaDF are response vectors which would be read/write by leaf nodes.

Feature selection in deep learning remains a critical challenge, particularly for high-dimensional tabular data where interpretability and computational efficiency are paramount. We present GFSNetwork, a novel neural architecture that performs differentiable feature selection through temperature-controlled Gumbel-Sigmoid sampling. Unlike traditional methods, where the user has to define the requested number of features, GFSNetwork selects it automatically during an end-to-end process. Moreover, GFSNetwork maintains constant computational overhead regardless of the number of input features. We evaluate GFSNetwork on a series of classification and regression benchmarks, where it consistently outperforms recent methods including DeepLasso, attention maps, as well as traditional feature selectors, while using significantly fewer features. Furthermore, we validate our approach on real-world metagenomic datasets, demonstrating its effectiveness in high-dimensional biological data. Concluding, our method provides a scalable solution that bridges the gap between neural network flexibility and traditional feature selection interpretability. We share our python implementation of GFSNetwork at https://github.com/wwydmanski/GFSNetwork, as well as a PyPi package (gfs_network).

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

Neural architecture search (NAS) has a great impact by automatically designing effective neural network architectures. However, the prohibitive computational demand of conventional NAS algorithms (e.g. 10^4 GPU hours) makes it difficult to directly search the architectures on large-scale tasks (e.g. ImageNet). Differentiable NAS can reduce the cost of GPU hours via a continuous representation of network architecture but suffers from the high GPU memory consumption issue (grow linearly w.r.t. candidate set size). As a result, they need to utilize~proxy tasks, such as training on a smaller dataset, or learning with only a few blocks, or training just for a few epochs. These architectures optimized on proxy tasks are not guaranteed to be optimal on the target task. In this paper, we present ProxylessNAS that can directly learn the architectures for large-scale target tasks and target hardware platforms. We address the high memory consumption issue of differentiable NAS and reduce the computational cost (GPU hours and GPU memory) to the same level of regular training while still allowing a large candidate set. Experiments on CIFAR-10 and ImageNet demonstrate the effectiveness of directness and specialization. On CIFAR-10, our model achieves 2.08\% test error with only 5.7M parameters, better than the previous state-of-the-art architecture AmoebaNet-B, while using 6times fewer parameters. On ImageNet, our model achieves 3.1\% better top-1 accuracy than MobileNetV2, while being 1.2times faster with measured GPU latency. We also apply ProxylessNAS to specialize neural architectures for hardware with direct hardware metrics (e.g. latency) and provide insights for efficient CNN architecture design.

Differentiable architecture search (DARTS) is successfully applied in many vision tasks. However, directly using DARTS for Transformers is memory-intensive, which renders the search process infeasible. To this end, we propose a multi-split reversible network and combine it with DARTS. Specifically, we devise a backpropagation-with-reconstruction algorithm so that we only need to store the last layer's outputs. By relieving the memory burden for DARTS, it allows us to search with larger hidden size and more candidate operations. We evaluate the searched architecture on three sequence-to-sequence datasets, i.e., WMT'14 English-German, WMT'14 English-French, and WMT'14 English-Czech. Experimental results show that our network consistently outperforms standard Transformers across the tasks. Moreover, our method compares favorably with big-size Evolved Transformers, reducing search computation by an order of magnitude.

Neural Architecture Search (NAS) yields state-of-the-art neural networks that outperform their best manually-designed counterparts. However, previous NAS methods search for architectures under one set of training hyper-parameters (i.e., a training recipe), overlooking superior architecture-recipe combinations. To address this, we present Neural Architecture-Recipe Search (NARS) to search both (a) architectures and (b) their corresponding training recipes, simultaneously. NARS utilizes an accuracy predictor that scores architecture and training recipes jointly, guiding both sample selection and ranking. Furthermore, to compensate for the enlarged search space, we leverage "free" architecture statistics (e.g., FLOP count) to pretrain the predictor, significantly improving its sample efficiency and prediction reliability. After training the predictor via constrained iterative optimization, we run fast evolutionary searches in just CPU minutes to generate architecture-recipe pairs for a variety of resource constraints, called FBNetV3. FBNetV3 makes up a family of state-of-the-art compact neural networks that outperform both automatically and manually-designed competitors. For example, FBNetV3 matches both EfficientNet and ResNeSt accuracy on ImageNet with up to 2.0x and 7.1x fewer FLOPs, respectively. Furthermore, FBNetV3 yields significant performance gains for downstream object detection tasks, improving mAP despite 18% fewer FLOPs and 34% fewer parameters than EfficientNet-based equivalents.

Neural architecture search (NAS) has shown great success in the automatic design of deep neural networks (DNNs). However, the best way to use data to search network architectures is still unclear and under exploration. Previous work has analyzed the necessity of having ground-truth labels in NAS and inspired broad interest. In this work, we take a further step to question whether real data is necessary for NAS to be effective. The answer to this question is important for applications with limited amount of accessible data, and can help people improve NAS by leveraging the extra flexibility of data generation. To explore if NAS needs real data, we construct three types of unreal datasets using: 1) randomly labeled real images; 2) generated images and labels; and 3) generated Gaussian noise with random labels. These datasets facilitate to analyze the generalization and expressivity of the searched architectures. We study the performance of architectures searched on these constructed datasets using popular differentiable NAS methods. Extensive experiments on CIFAR, ImageNet and CheXpert show that the searched architectures can achieve promising results compared with those derived from the conventional NAS pipeline with real labeled data, suggesting the feasibility of performing NAS with unreal data.

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Neural architecture search (NAS) faces a challenge in balancing the exploration of expressive, broad search spaces that enable architectural innovation with the need for efficient evaluation of architectures to effectively search such spaces. We investigate surrogate model training for improving search in highly expressive NAS search spaces based on context-free grammars. We show that i) surrogate models trained either using zero-cost-proxy metrics and neural graph features (GRAF) or by fine-tuning an off-the-shelf LM have high predictive power for the performance of architectures both within and across datasets, ii) these surrogates can be used to filter out bad architectures when searching on novel datasets, thereby significantly speeding up search and achieving better final performances, and iii) the surrogates can be further used directly as the search objective for huge speed-ups.

Recent advances in Neural Architecture Search (NAS) which extract specialized hardware-aware configurations (a.k.a. "sub-networks") from a hardware-agnostic "super-network" have become increasingly popular. While considerable effort has been employed towards improving the first stage, namely, the training of the super-network, the search for derivative high-performing sub-networks is still largely under-explored. For example, some recent network morphism techniques allow a super-network to be trained once and then have hardware-specific networks extracted from it as needed. These methods decouple the super-network training from the sub-network search and thus decrease the computational burden of specializing to different hardware platforms. We propose a comprehensive system that automatically and efficiently finds sub-networks from a pre-trained super-network that are optimized to different performance metrics and hardware configurations. By combining novel search tactics and algorithms with intelligent use of predictors, we significantly decrease the time needed to find optimal sub-networks from a given super-network. Further, our approach does not require the super-network to be refined for the target task a priori, thus allowing it to interface with any super-network. We demonstrate through extensive experiments that our system works seamlessly with existing state-of-the-art super-network training methods in multiple domains. Moreover, we show how novel search tactics paired with evolutionary algorithms can accelerate the search process for ResNet50, MobileNetV3 and Transformer while maintaining objective space Pareto front diversity and demonstrate an 8x faster search result than the state-of-the-art Bayesian optimization WeakNAS approach.

Deep learning has proven to be a highly effective problem-solving tool for object detection and image segmentation across various domains such as healthcare and autonomous driving. At the heart of this performance lies neural architecture design which relies heavily on domain knowledge and prior experience on the researchers' behalf. More recently, this process of finding the most optimal architectures, given an initial search space of possible operations, was automated by Neural Architecture Search (NAS). In this paper, we evaluate the robustness of one such algorithm known as Efficient NAS (ENAS) against data agnostic poisoning attacks on the original search space with carefully designed ineffective operations. By evaluating algorithm performance on the CIFAR-10 dataset, we empirically demonstrate how our novel search space poisoning (SSP) approach and multiple-instance poisoning attacks exploit design flaws in the ENAS controller to result in inflated prediction error rates for child networks. Our results provide insights into the challenges to surmount in using NAS for more adversarially robust architecture search.

Neural Architecture Search (NAS) has demonstrated its power on various AI accelerating platforms such as Field Programmable Gate Arrays (FPGAs) and Graphic Processing Units (GPUs). However, it remains an open problem, how to integrate NAS with Application-Specific Integrated Circuits (ASICs), despite them being the most powerful AI accelerating platforms. The major bottleneck comes from the large design freedom associated with ASIC designs. Moreover, with the consideration that multiple DNNs will run in parallel for different workloads with diverse layer operations and sizes, integrating heterogeneous ASIC sub-accelerators for distinct DNNs in one design can significantly boost performance, and at the same time further complicate the design space. To address these challenges, in this paper we build ASIC template set based on existing successful designs, described by their unique dataflows, so that the design space is significantly reduced. Based on the templates, we further propose a framework, namely NASAIC, which can simultaneously identify multiple DNN architectures and the associated heterogeneous ASIC accelerator design, such that the design specifications (specs) can be satisfied, while the accuracy can be maximized. Experimental results show that compared with successive NAS and ASIC design optimizations which lead to design spec violations, NASAIC can guarantee the results to meet the design specs with 17.77%, 2.49x, and 2.32x reductions on latency, energy, and area and with 0.76% accuracy loss. To the best of the authors' knowledge, this is the first work on neural architecture and ASIC accelerator design co-exploration.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Albeit being a prevalent architecture searching approach, differentiable architecture search (DARTS) is largely hindered by its substantial memory cost since the entire supernet resides in the memory. This is where the single-path DARTS comes in, which only chooses a single-path submodel at each step. While being memory-friendly, it also comes with low computational costs. Nonetheless, we discover a critical issue of single-path DARTS that has not been primarily noticed. Namely, it also suffers from severe performance collapse since too many parameter-free operations like skip connections are derived, just like DARTS does. In this paper, we propose a new algorithm called RObustifying Memory-Efficient NAS (ROME) to give a cure. First, we disentangle the topology search from the operation search to make searching and evaluation consistent. We then adopt Gumbel-Top2 reparameterization and gradient accumulation to robustify the unwieldy bi-level optimization. We verify ROME extensively across 15 benchmarks to demonstrate its effectiveness and robustness.

Neural Architecture Search (NAS) aims to automatically excavate the optimal network architecture with superior test performance. Recent neural architecture search (NAS) approaches rely on validation loss or accuracy to find the superior network for the target data. In this paper, we investigate a new neural architecture search measure for excavating architectures with better generalization. We demonstrate that the flatness of the loss surface can be a promising proxy for predicting the generalization capability of neural network architectures. We evaluate our proposed method on various search spaces, showing similar or even better performance compared to the state-of-the-art NAS methods. Notably, the resultant architecture found by flatness measure generalizes robustly to various shifts in data distribution (e.g. ImageNet-V2,-A,-O), as well as various tasks such as object detection and semantic segmentation. Code is available at https://github.com/clovaai/GeNAS.

Neural architecture search automates neural network design and has achieved state-of-the-art results in many deep learning applications. While recent literature has focused on designing networks to maximize accuracy, little work has been conducted to understand the compatibility of architecture design spaces to varying hardware. In this paper, we analyze the neural blocks used to build Once-for-All (MobileNetV3), ProxylessNAS and ResNet families, in order to understand their predictive power and inference latency on various devices, including Huawei Kirin 9000 NPU, RTX 2080 Ti, AMD Threadripper 2990WX, and Samsung Note10. We introduce a methodology to quantify the friendliness of neural blocks to hardware and the impact of their placement in a macro network on overall network performance via only end-to-end measurements. Based on extensive profiling results, we derive design insights and apply them to hardware-specific search space reduction. We show that searching in the reduced search space generates better accuracy-latency Pareto frontiers than searching in the original search spaces, customizing architecture search according to the hardware. Moreover, insights derived from measurements lead to notably higher ImageNet top-1 scores on all search spaces investigated.

Recently, there has been a growing interest in automating the process of neural architecture design, and the Differentiable Architecture Search (DARTS) method makes the process available within a few GPU days. However, the performance of DARTS is often observed to collapse when the number of search epochs becomes large. Meanwhile, lots of "{\em skip-connect}s" are found in the selected architectures. In this paper, we claim that the cause of the collapse is that there exists overfitting in the optimization of DARTS. Therefore, we propose a simple and effective algorithm, named "DARTS+", to avoid the collapse and improve the original DARTS, by "early stopping" the search procedure when meeting a certain criterion. We also conduct comprehensive experiments on benchmark datasets and different search spaces and show the effectiveness of our DARTS+ algorithm, and DARTS+ achieves 2.32% test error on CIFAR10, 14.87% on CIFAR100, and 23.7% on ImageNet. We further remark that the idea of "early stopping" is implicitly included in some existing DARTS variants by manually setting a small number of search epochs, while we give an {\em explicit} criterion for "early stopping".

Neural networks surround us, in the form of large language models, speech transcription systems, molecular discovery algorithms, robotics, and much more. Stripped of anything else, neural networks are compositions of differentiable primitives, and studying them means learning how to program and how to interact with these models, a particular example of what is called differentiable programming. This primer is an introduction to this fascinating field imagined for someone, like Alice, who has just ventured into this strange differentiable wonderland. I overview the basics of optimizing a function via automatic differentiation, and a selection of the most common designs for handling sequences, graphs, texts, and audios. The focus is on a intuitive, self-contained introduction to the most important design techniques, including convolutional, attentional, and recurrent blocks, hoping to bridge the gap between theory and code (PyTorch and JAX) and leaving the reader capable of understanding some of the most advanced models out there, such as large language models (LLMs) and multimodal architectures.

While existing work on neural architecture search (NAS) tunes hyperparameters in a separate post-processing step, we demonstrate that architectural choices and other hyperparameter settings interact in a way that can render this separation suboptimal. Likewise, we demonstrate that the common practice of using very few epochs during the main NAS and much larger numbers of epochs during a post-processing step is inefficient due to little correlation in the relative rankings for these two training regimes. To combat both of these problems, we propose to use a recent combination of Bayesian optimization and Hyperband for efficient joint neural architecture and hyperparameter search.

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier---AmoebaNet-A---that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-the-art 83.9% / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

We investigate the potential of GPT-4~gpt4 to perform Neural Architecture Search (NAS) -- the task of designing effective neural architectures. Our proposed approach, GPT-4 Enhanced Neural archItectUre Search (GENIUS), leverages the generative capabilities of GPT-4 as a black-box optimiser to quickly navigate the architecture search space, pinpoint promising candidates, and iteratively refine these candidates to improve performance. We assess GENIUS across several benchmarks, comparing it with existing state-of-the-art NAS techniques to illustrate its effectiveness. Rather than targeting state-of-the-art performance, our objective is to highlight GPT-4's potential to assist research on a challenging technical problem through a simple prompting scheme that requires relatively limited domain expertiseCode available at \href{https://github.com/mingkai-zheng/GENIUS{https://github.com/mingkai-zheng/GENIUS}.}. More broadly, we believe our preliminary results point to future research that harnesses general purpose language models for diverse optimisation tasks. We also highlight important limitations to our study, and note implications for AI safety.

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Recently, interest has grown in exploring the hypothesis that neural activity conveys information through precise spiking motifs. To investigate this phenomenon, various algorithms have been proposed to detect such motifs in Single Unit Activity (SUA) recorded from populations of neurons. In this study, we present a novel detection model based on the inversion of a generative model of raster plot synthesis. Using this generative model, we derive an optimal detection procedure that takes the form of logistic regression combined with temporal convolution. A key advantage of this model is its differentiability, which allows us to formulate a supervised learning approach using a gradient descent on the binary cross-entropy loss. To assess the model's ability to detect spiking motifs in synthetic data, we first perform numerical evaluations. This analysis highlights the advantages of using spiking motifs over traditional firing rate based population codes. We then successfully demonstrate that our learning method can recover synthetically generated spiking motifs, indicating its potential for further applications. In the future, we aim to extend this method to real neurobiological data, where the ground truth is unknown, to explore and detect spiking motifs in a more natural and biologically relevant context.

Storing information in DNA molecules is of great interest because of its advantages in longevity, high storage density, and low maintenance cost. A key step in the DNA storage pipeline is to efficiently cluster the retrieved DNA sequences according to their similarities. Levenshtein distance is the most suitable metric on the similarity between two DNA sequences, but it is inferior in terms of computational complexity and less compatible with mature clustering algorithms. In this work, we propose a novel deep squared Euclidean embedding for DNA sequences using Siamese neural network, squared Euclidean embedding, and chi-squared regression. The Levenshtein distance is approximated by the squared Euclidean distance between the embedding vectors, which is fast calculated and clustering algorithm friendly. The proposed approach is analyzed theoretically and experimentally. The results show that the proposed embedding is efficient and robust.

This paper addresses the difficult problem of finding an optimal neural architecture design for a given image classification task. We propose a method that aggregates two main results of the previous state-of-the-art in neural architecture search. These are, appealing to the strong sampling efficiency of a search scheme based on sequential model-based optimization (SMBO), and increasing training efficiency by sharing weights among sampled architectures. Sequential search has previously demonstrated its capabilities to find state-of-the-art neural architectures for image classification. However, its computational cost remains high, even unreachable under modest computational settings. Affording SMBO with weight-sharing alleviates this problem. On the other hand, progressive search with SMBO is inherently greedy, as it leverages a learned surrogate function to predict the validation error of neural architectures. This prediction is directly used to rank the sampled neural architectures. We propose to attenuate the greediness of the original SMBO method by relaxing the role of the surrogate function so it predicts architecture sampling probability instead. We demonstrate with experiments on the CIFAR-10 dataset that our method, denominated Efficient progressive neural architecture search (EPNAS), leads to increased search efficiency, while retaining competitiveness of found architectures.

Graph neural networks (GNNs) have been successfully applied to learning representation on graphs in many relational tasks. Recently, researchers study neural architecture search (NAS) to reduce the dependence of human expertise and explore better GNN architectures, but they over-emphasize entity features and ignore latent relation information concealed in the edges. To solve this problem, we incorporate edge features into graph search space and propose Edge-featured Graph Neural Architecture Search to find the optimal GNN architecture. Specifically, we design rich entity and edge updating operations to learn high-order representations, which convey more generic message passing mechanisms. Moreover, the architecture topology in our search space allows to explore complex feature dependence of both entities and edges, which can be efficiently optimized by differentiable search strategy. Experiments at three graph tasks on six datasets show EGNAS can search better GNNs with higher performance than current state-of-the-art human-designed and searched-based GNNs.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Understanding biodiversity is a global challenge, in which DNA barcodes - short snippets of DNA that cluster by species - play a pivotal role. In particular, invertebrates, a highly diverse and under-explored group, pose unique taxonomic complexities. We explore machine learning approaches, comparing supervised CNNs, fine-tuned foundation models, and a DNA barcode-specific masking strategy across datasets of varying complexity. While simpler datasets and tasks favor supervised CNNs or fine-tuned transformers, challenging species-level identification demands a paradigm shift towards self-supervised pretraining. We propose BarcodeBERT, the first self-supervised method for general biodiversity analysis, leveraging a 1.5 M invertebrate DNA barcode reference library. This work highlights how dataset specifics and coverage impact model selection, and underscores the role of self-supervised pretraining in achieving high-accuracy DNA barcode-based identification at the species and genus level. Indeed, without the fine-tuning step, BarcodeBERT pretrained on a large DNA barcode dataset outperforms DNABERT and DNABERT-2 on multiple downstream classification tasks. The code repository is available at https://github.com/Kari-Genomics-Lab/BarcodeBERT

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

Realistic use of neural networks often requires adhering to multiple constraints on latency, energy and memory among others. A popular approach to find fitting networks is through constrained Neural Architecture Search (NAS), however, previous methods enforce the constraint only softly. Therefore, the resulting networks do not exactly adhere to the resource constraint and their accuracy is harmed. In this work we resolve this by introducing Hard Constrained diffeRentiable NAS (HardCoRe-NAS), that is based on an accurate formulation of the expected resource requirement and a scalable search method that satisfies the hard constraint throughout the search. Our experiments show that HardCoRe-NAS generates state-of-the-art architectures, surpassing other NAS methods, while strictly satisfying the hard resource constraints without any tuning required.

Fully automating machine learning pipelines is one of the key challenges of current artificial intelligence research, since practical machine learning often requires costly and time-consuming human-powered processes such as model design, algorithm development, and hyperparameter tuning. In this paper, we verify that automated architecture search synergizes with the effect of gradient-based meta learning. We adopt the progressive neural architecture search liu:pnas_google:DBLP:journals/corr/abs-1712-00559 to find optimal architectures for meta-learners. The gradient based meta-learner whose architecture was automatically found achieved state-of-the-art results on the 5-shot 5-way Mini-ImageNet classification problem with 74.65% accuracy, which is 11.54% improvement over the result obtained by the first gradient-based meta-learner called MAML finn:maml:DBLP:conf/icml/FinnAL17. To our best knowledge, this work is the first successful neural architecture search implementation in the context of meta learning.

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Predictor-based methods have substantially enhanced Neural Architecture Search (NAS) optimization. The efficacy of these predictors is largely influenced by the method of encoding neural network architectures. While traditional encodings used an adjacency matrix describing the graph structure of a neural network, novel encodings embrace a variety of approaches from unsupervised pretraining of latent representations to vectors of zero-cost proxies. In this paper, we categorize and investigate neural encodings from three main types: structural, learned, and score-based. Furthermore, we extend these encodings and introduce unified encodings, that extend NAS predictors to multiple search spaces. Our analysis draws from experiments conducted on over 1.5 million neural network architectures on NAS spaces such as NASBench-101 (NB101), NB201, NB301, Network Design Spaces (NDS), and TransNASBench-101. Building on our study, we present our predictor FLAN: Flow Attention for NAS. FLAN integrates critical insights on predictor design, transfer learning, and unified encodings to enable more than an order of magnitude cost reduction for training NAS accuracy predictors. Our implementation and encodings for all neural networks are open-sourced at https://github.com/abdelfattah-lab/flan_nas{https://github.com/abdelfattah-lab/flan\_nas}.

Neural architecture search (NAS) methods rely on a search strategy for deciding which architectures to evaluate next and a performance estimation strategy for assessing their performance (e.g., using full evaluations, multi-fidelity evaluations, or the one-shot model). In this paper, we focus on the search strategy. We introduce the simple yet powerful evolutionary algorithm of differential evolution to the NAS community. Using the simplest performance evaluation strategy of full evaluations, we comprehensively compare this search strategy to regularized evolution and Bayesian optimization and demonstrate that it yields improved and more robust results for 13 tabular NAS benchmarks based on NAS-Bench-101, NAS-Bench-1Shot1, NAS-Bench-201 and NAS-HPO bench.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

Neural architecture search (NAS) automatically finds the best task-specific neural network topology, outperforming many manual architecture designs. However, it can be prohibitively expensive as the search requires training thousands of different networks, while each can last for hours. In this work, we propose the Graph HyperNetwork (GHN) to amortize the search cost: given an architecture, it directly generates the weights by running inference on a graph neural network. GHNs model the topology of an architecture and therefore can predict network performance more accurately than regular hypernetworks and premature early stopping. To perform NAS, we randomly sample architectures and use the validation accuracy of networks with GHN generated weights as the surrogate search signal. GHNs are fast -- they can search nearly 10 times faster than other random search methods on CIFAR-10 and ImageNet. GHNs can be further extended to the anytime prediction setting, where they have found networks with better speed-accuracy tradeoff than the state-of-the-art manual designs.

Neural architecture search (NAS) has become a key component of AutoML and a standard tool to automate the design of deep neural networks. Recently, training-free NAS as an emerging paradigm has successfully reduced the search costs of standard training-based NAS by estimating the true architecture performance with only training-free metrics. Nevertheless, the estimation ability of these metrics typically varies across different tasks, making it challenging to achieve robust and consistently good search performance on diverse tasks with only a single training-free metric. Meanwhile, the estimation gap between training-free metrics and the true architecture performances limits training-free NAS to achieve superior performance. To address these challenges, we propose the robustifying and boosting training-free NAS (RoBoT) algorithm which (a) employs the optimized combination of existing training-free metrics explored from Bayesian optimization to develop a robust and consistently better-performing metric on diverse tasks, and (b) applies greedy search, i.e., the exploitation, on the newly developed metric to bridge the aforementioned gap and consequently to boost the search performance of standard training-free NAS further. Remarkably, the expected performance of our RoBoT can be theoretically guaranteed, which improves over the existing training-free NAS under mild conditions with additional interesting insights. Our extensive experiments on various NAS benchmark tasks yield substantial empirical evidence to support our theoretical results.

Developing neural network image classification models often requires significant architecture engineering. In this paper, we study a method to learn the model architectures directly on the dataset of interest. As this approach is expensive when the dataset is large, we propose to search for an architectural building block on a small dataset and then transfer the block to a larger dataset. The key contribution of this work is the design of a new search space (the "NASNet search space") which enables transferability. In our experiments, we search for the best convolutional layer (or "cell") on the CIFAR-10 dataset and then apply this cell to the ImageNet dataset by stacking together more copies of this cell, each with their own parameters to design a convolutional architecture, named "NASNet architecture". We also introduce a new regularization technique called ScheduledDropPath that significantly improves generalization in the NASNet models. On CIFAR-10 itself, NASNet achieves 2.4% error rate, which is state-of-the-art. On ImageNet, NASNet achieves, among the published works, state-of-the-art accuracy of 82.7% top-1 and 96.2% top-5 on ImageNet. Our model is 1.2% better in top-1 accuracy than the best human-invented architectures while having 9 billion fewer FLOPS - a reduction of 28% in computational demand from the previous state-of-the-art model. When evaluated at different levels of computational cost, accuracies of NASNets exceed those of the state-of-the-art human-designed models. For instance, a small version of NASNet also achieves 74% top-1 accuracy, which is 3.1% better than equivalently-sized, state-of-the-art models for mobile platforms. Finally, the learned features by NASNet used with the Faster-RCNN framework surpass state-of-the-art by 4.0% achieving 43.1% mAP on the COCO dataset.

Automatic algorithm-hardware co-design for DNN has shown great success in improving the performance of DNNs on FPGAs. However, this process remains challenging due to the intractable search space of neural network architectures and hardware accelerator implementation. Differing from existing hardware-aware neural architecture search (NAS) algorithms that rely solely on the expensive learning-based approaches, our work incorporates integer programming into the search algorithm to prune the design space. Given a set of hardware resource constraints, our integer programming formulation directly outputs the optimal accelerator configuration for mapping a DNN subgraph that minimizes latency. We use an accuracy predictor for different DNN subgraphs with different quantization schemes and generate accuracy-latency pareto frontiers. With low computational cost, our algorithm can generate quantized networks that achieve state-of-the-art accuracy and hardware performance on Xilinx Zynq (ZU3EG) FPGA for image classification on ImageNet dataset. The solution searched by our algorithm achieves 72.5% top-1 accuracy on ImageNet at framerate 50, which is 60% faster than MnasNet and 135% faster than FBNet with comparable accuracy.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

DARTS is a popular algorithm for neural architecture search (NAS). Despite its great advantage in search efficiency, DARTS often suffers weak stability, which reflects in the large variation among individual trials as well as the sensitivity to the hyper-parameters of the search process. This paper owes such instability to an optimization gap between the super-network and its sub-networks, namely, improving the validation accuracy of the super-network does not necessarily lead to a higher expectation on the performance of the sampled sub-networks. Then, we point out that the gap is due to the inaccurate estimation of the architectural gradients, based on which we propose an amended estimation method. Mathematically, our method guarantees a bounded error from the true gradients while the original estimation does not. Our approach bridges the gap from two aspects, namely, amending the estimation on the architectural gradients, and unifying the hyper-parameter settings in the search and re-training stages. Experiments on CIFAR10 and ImageNet demonstrate that our approach largely improves search stability and, more importantly, enables DARTS-based approaches to explore much larger search spaces that have not been investigated before.

Deep learning has revolutionized computer vision, but it achieved its tremendous success using deep network architectures which are mostly hand-crafted and therefore likely suboptimal. Neural Architecture Search (NAS) aims to bridge this gap by following a well-defined optimization paradigm which systematically looks for the best architecture, given objective criterion such as maximal classification accuracy. The main limitation of NAS is however its astronomical computational cost, as it typically requires training each candidate network architecture from scratch. In this paper, we aim to alleviate this limitation by proposing a novel training-free proxy for image classification accuracy based on Fisher Information. The proposed proxy has a strong theoretical background in statistics and it allows estimating expected image classification accuracy of a given deep network without training the network, thus significantly reducing computational cost of standard NAS algorithms. Our training-free proxy achieves state-of-the-art results on three public datasets and in two search spaces, both when evaluated using previously proposed metrics, as well as using a new metric that we propose which we demonstrate is more informative for practical NAS applications. The source code is publicly available at http://www.github.com/ondratybl/VKDNW

Neural networks have become an increasingly popular tool for solving many real-world problems. They are a general framework for differentiable optimization which includes many other machine learning approaches as special cases. In this thesis we build a category-theoretic formalism around a class of neural networks exemplified by CycleGAN. CycleGAN is a collection of neural networks, closed under composition, whose inductive bias is increased by enforcing composition invariants, i.e. cycle-consistencies. Inspired by Functorial Data Migration, we specify the interconnection of these networks using a categorical schema, and network instances as set-valued functors on this schema. We also frame neural network architectures, datasets, models, and a number of other concepts in a categorical setting and thus show a special class of functors, rather than functions, can be learned using gradient descent. We use the category-theoretic framework to conceive a novel neural network architecture whose goal is to learn the task of object insertion and object deletion in images with unpaired data. We test the architecture on three different datasets and obtain promising results.

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

Architecture optimization, which is a technique for finding an efficient neural network that meets certain requirements, generally reduces to a set of multiple-choice selection problems among alternative sub-structures or parameters. The discrete nature of the selection problem, however, makes this optimization difficult. To tackle this problem we introduce a novel concept of a trainable gate function. The trainable gate function, which confers a differentiable property to discretevalued variables, allows us to directly optimize loss functions that include non-differentiable discrete values such as 0-1 selection. The proposed trainable gate can be applied to pruning. Pruning can be carried out simply by appending the proposed trainable gate functions to each intermediate output tensor followed by fine-tuning the overall model, using any gradient-based training methods. So the proposed method can jointly optimize the selection of the pruned channels while fine-tuning the weights of the pruned model at the same time. Our experimental results demonstrate that the proposed method efficiently optimizes arbitrary neural networks in various tasks such as image classification, style transfer, optical flow estimation, and neural machine translation.

Large Language Models (LLMs) have emerged as powerful tools capable of accomplishing a broad spectrum of tasks. Their abilities span numerous areas, and one area where they have made a significant impact is in the domain of code generation. In this context, we view LLMs as mutation and crossover tools. Meanwhile, Quality-Diversity (QD) algorithms are known to discover diverse and robust solutions. By merging the code-generating abilities of LLMs with the diversity and robustness of QD solutions, we introduce LLMatic, a Neural Architecture Search (NAS) algorithm. While LLMs struggle to conduct NAS directly through prompts, LLMatic uses a procedural approach, leveraging QD for prompts and network architecture to create diverse and highly performant networks. We test LLMatic on the CIFAR-10 image classification benchmark, demonstrating that it can produce competitive networks with just 2,000 searches, even without prior knowledge of the benchmark domain or exposure to any previous top-performing models for the benchmark.

The deployment of Deep Neural Networks (DNNs) on edge devices is hindered by the substantial gap between performance requirements and available processing power. While recent research has made significant strides in developing pruning methods to build a sparse network for reducing the computing overhead of DNNs, there remains considerable accuracy loss, especially at high pruning ratios. We find that the architectures designed for dense networks by differentiable architecture search methods are ineffective when pruning mechanisms are applied to them. The main reason is that the current method does not support sparse architectures in their search space and uses a search objective that is made for dense networks and does not pay any attention to sparsity. In this paper, we propose a new method to search for sparsity-friendly neural architectures. We do this by adding two new sparse operations to the search space and modifying the search objective. We propose two novel parametric SparseConv and SparseLinear operations in order to expand the search space to include sparse operations. In particular, these operations make a flexible search space due to using sparse parametric versions of linear and convolution operations. The proposed search objective lets us train the architecture based on the sparsity of the search space operations. Quantitative analyses demonstrate that our search architectures outperform those used in the stateof-the-art sparse networks on the CIFAR-10 and ImageNet datasets. In terms of performance and hardware effectiveness, DASS increases the accuracy of the sparse version of MobileNet-v2 from 73.44% to 81.35% (+7.91% improvement) with 3.87x faster inference time.

We present a feasibility-seeking approach to neural network training. This mathematical optimization framework is distinct from conventional gradient-based loss minimization and uses projection operators and iterative projection algorithms. We reformulate training as a large-scale feasibility problem: finding network parameters and states that satisfy local constraints derived from its elementary operations. Training then involves projecting onto these constraints, a local operation that can be parallelized across the network. We introduce PJAX, a JAX-based software framework that enables this paradigm. PJAX composes projection operators for elementary operations, automatically deriving the solution operators for the feasibility problems (akin to autodiff for derivatives). It inherently supports GPU/TPU acceleration, provides a familiar NumPy-like API, and is extensible. We train diverse architectures (MLPs, CNNs, RNNs) on standard benchmarks using PJAX, demonstrating its functionality and generality. Our results show that this approach is as a compelling alternative to gradient-based training, with clear advantages in parallelism and the ability to handle non-differentiable operations.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

The complete connectome of the Drosophila larva brain offers a unique opportunity to investigate whether biologically evolved circuits can support artificial intelligence. We convert this wiring diagram into a Biological Processing Unit (BPU), a fixed recurrent network derived directly from synaptic connectivity. Despite its modest size 3,000 neurons and 65,000 weights between them), the unmodified BPU achieves 98% accuracy on MNIST and 58% on CIFAR-10, surpassing size-matched MLPs. Scaling the BPU via structured connectome expansions further improves CIFAR-10 performance, while modality-specific ablations reveal the uneven contributions of different sensory subsystems. On the ChessBench dataset, a lightweight GNN-BPU model trained on only 10,000 games achieves 60% move accuracy, nearly 10x better than any size transformer. Moreover, CNN-BPU models with ~2M parameters outperform parameter-matched Transformers, and with a depth-6 minimax search at inference, reach 91.7% accuracy, exceeding even a 9M-parameter Transformer baseline. These results demonstrate the potential of biofidelic neural architectures to support complex cognitive tasks and motivate scaling to larger and more intelligent connectomes in future work.

Architecture design and optimization are challenging problems in the field of artificial neural networks. Working in this context, we here present SPARCS (SPectral ARchiteCture Search), a novel architecture search protocol which exploits the spectral attributes of the inter-layer transfer matrices. SPARCS allows one to explore the space of possible architectures by spanning continuous and differentiable manifolds, thus enabling for gradient-based optimization algorithms to be eventually employed. With reference to simple benchmark models, we show that the newly proposed method yields a self-emerging architecture with a minimal degree of expressivity to handle the task under investigation and with a reduced parameter count as compared to other viable alternatives.

In deep learning, performance is strongly affected by the choice of architecture and hyperparameters. While there has been extensive work on automatic hyperparameter optimization for simple spaces, complex spaces such as the space of deep architectures remain largely unexplored. As a result, the choice of architecture is done manually by the human expert through a slow trial and error process guided mainly by intuition. In this paper we describe a framework for automatically designing and training deep models. We propose an extensible and modular language that allows the human expert to compactly represent complex search spaces over architectures and their hyperparameters. The resulting search spaces are tree-structured and therefore easy to traverse. Models can be automatically compiled to computational graphs once values for all hyperparameters have been chosen. We can leverage the structure of the search space to introduce different model search algorithms, such as random search, Monte Carlo tree search (MCTS), and sequential model-based optimization (SMBO). We present experiments comparing the different algorithms on CIFAR-10 and show that MCTS and SMBO outperform random search. In addition, these experiments show that our framework can be used effectively for model discovery, as it is possible to describe expressive search spaces and discover competitive models without much effort from the human expert. Code for our framework and experiments has been made publicly available.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

We introduce a new function-preserving transformation for efficient neural architecture search. This network transformation allows reusing previously trained networks and existing successful architectures that improves sample efficiency. We aim to address the limitation of current network transformation operations that can only perform layer-level architecture modifications, such as adding (pruning) filters or inserting (removing) a layer, which fails to change the topology of connection paths. Our proposed path-level transformation operations enable the meta-controller to modify the path topology of the given network while keeping the merits of reusing weights, and thus allow efficiently designing effective structures with complex path topologies like Inception models. We further propose a bidirectional tree-structured reinforcement learning meta-controller to explore a simple yet highly expressive tree-structured architecture space that can be viewed as a generalization of multi-branch architectures. We experimented on the image classification datasets with limited computational resources (about 200 GPU-hours), where we observed improved parameter efficiency and better test results (97.70% test accuracy on CIFAR-10 with 14.3M parameters and 74.6% top-1 accuracy on ImageNet in the mobile setting), demonstrating the effectiveness and transferability of our designed architectures.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

Predicting neural architecture performance is a challenging task and is crucial to neural architecture design and search. Existing approaches either rely on neural performance predictors which are limited to modeling architectures in a predefined design space involving specific sets of operators and connection rules, and cannot generalize to unseen architectures, or resort to zero-cost proxies which are not always accurate. In this paper, we propose GENNAPE, a Generalized Neural Architecture Performance Estimator, which is pretrained on open neural architecture benchmarks, and aims to generalize to completely unseen architectures through combined innovations in network representation, contrastive pretraining, and fuzzy clustering-based predictor ensemble. Specifically, GENNAPE represents a given neural network as a Computation Graph (CG) of atomic operations which can model an arbitrary architecture. It first learns a graph encoder via Contrastive Learning to encourage network separation by topological features, and then trains multiple predictor heads, which are soft-aggregated according to the fuzzy membership of a neural network. Experiments show that GENNAPE pretrained on NAS-Bench-101 can achieve superior transferability to 5 different public neural network benchmarks, including NAS-Bench-201, NAS-Bench-301, MobileNet and ResNet families under no or minimum fine-tuning. We further introduce 3 challenging newly labelled neural network benchmarks: HiAML, Inception and Two-Path, which can concentrate in narrow accuracy ranges. Extensive experiments show that GENNAPE can correctly discern high-performance architectures in these families. Finally, when paired with a search algorithm, GENNAPE can find architectures that improve accuracy while reducing FLOPs on three families.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Brain simulation builds dynamical models to mimic the structure and functions of the brain, while brain-inspired computing (BIC) develops intelligent systems by learning from the structure and functions of the brain. The two fields are intertwined and should share a common programming framework to facilitate each other's development. However, none of the existing software in the fields can achieve this goal, because traditional brain simulators lack differentiability for training, while existing deep learning (DL) frameworks fail to capture the biophysical realism and complexity of brain dynamics. In this paper, we introduce BrainPy, a differentiable brain simulator developed using JAX and XLA, with the aim of bridging the gap between brain simulation and BIC. BrainPy expands upon the functionalities of JAX, a powerful AI framework, by introducing complete capabilities for flexible, efficient, and scalable brain simulation. It offers a range of sparse and event-driven operators for efficient and scalable brain simulation, an abstraction for managing the intricacies of synaptic computations, a modular and flexible interface for constructing multi-scale brain models, and an object-oriented just-in-time compilation approach to handle the memory-intensive nature of brain dynamics. We showcase the efficiency and scalability of BrainPy on benchmark tasks, highlight its differentiable simulation for biologically plausible spiking models, and discuss its potential to support research at the intersection of brain simulation and BIC.

Toward combining inductive reasoning with perception abilities, we develop techniques for neurosymbolic program synthesis where perceptual input is first parsed by neural nets into a low-dimensional interpretable representation, which is then processed by a synthesized program. We explore several techniques for relaxing the problem and jointly learning all modules end-to-end with gradient descent: multitask learning; amortized inference; overparameterization; and a differentiable strategy for penalizing lengthy programs. Collectedly this toolbox improves the stability of gradient-guided program search, and suggests ways of learning both how to perceive input as discrete abstractions, and how to symbolically process those abstractions as programs.

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their rewards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search, which focuses on exploiting high-rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via backtracking and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme, which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: https://github.com/dbsxodud-11/ls_gfn.

Can we automatically design a Convolutional Network (ConvNet) with the highest image classification accuracy under the runtime constraint of a mobile device? Neural architecture search (NAS) has revolutionized the design of hardware-efficient ConvNets by automating this process. However, the NAS problem remains challenging due to the combinatorially large design space, causing a significant searching time (at least 200 GPU-hours). To alleviate this complexity, we propose Single-Path NAS, a novel differentiable NAS method for designing hardware-efficient ConvNets in less than 4 hours. Our contributions are as follows: 1. Single-path search space: Compared to previous differentiable NAS methods, Single-Path NAS uses one single-path over-parameterized ConvNet to encode all architectural decisions with shared convolutional kernel parameters, hence drastically decreasing the number of trainable parameters and the search cost down to few epochs. 2. Hardware-efficient ImageNet classification: Single-Path NAS achieves 74.96% top-1 accuracy on ImageNet with 79ms latency on a Pixel 1 phone, which is state-of-the-art accuracy compared to NAS methods with similar constraints (<80ms). 3. NAS efficiency: Single-Path NAS search cost is only 8 epochs (30 TPU-hours), which is up to 5,000x faster compared to prior work. 4. Reproducibility: Unlike all recent mobile-efficient NAS methods which only release pretrained models, we open-source our entire codebase at: https://github.com/dstamoulis/single-path-nas.

Training a high-quality deep neural network requires choosing suitable hyperparameters, which is a non-trivial and expensive process. Current works try to automatically optimize or design principles of hyperparameters, such that they can generalize to diverse unseen scenarios. However, most designs or optimization methods are agnostic to the choice of network structures, and thus largely ignore the impact of neural architectures on hyperparameters. In this work, we precisely characterize the dependence of initializations and maximal learning rates on the network architecture, which includes the network depth, width, convolutional kernel size, and connectivity patterns. By pursuing every parameter to be maximally updated with the same mean squared change in pre-activations, we can generalize our initialization and learning rates across MLPs (multi-layer perception) and CNNs (convolutional neural network) with sophisticated graph topologies. We verify our principles with comprehensive experiments. More importantly, our strategy further sheds light on advancing current benchmarks for architecture design. A fair comparison of AutoML algorithms requires accurate network rankings. However, we demonstrate that network rankings can be easily changed by better training networks in benchmarks with our architecture-aware learning rates and initialization.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.