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Dec 9

Cephalo: Multi-Modal Vision-Language Models for Bio-Inspired Materials Analysis and Design

We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding and interaction within human-AI and multi-agent AI frameworks. A key innovation of Cephalo is its advanced dataset generation method, which employs a sophisticated algorithm to accurately detect and separate images and their corresponding textual descriptions from PDF documents, such as scientific papers. The method includes a careful refinement of image-text pairs through integrated vision and language processing, ensuring high-quality, contextually relevant, and well reasoned training data. Cephalo is trained on integrated image and text data extracted from thousands of scientific papers and science-focused Wikipedia pages demonstrates can interpret complex visual scenes, generate precise language descriptions, and answer queries about images effectively. The combination of a vision encoder with an autoregressive transformer supports complex natural language understanding in an integrated model, which can be coupled with other generative methods to create an image-to-text-to-image or image-to-text-to-3D pipeline. To explore the development of larger models from smaller ones, we merge sets of layers that originate from different pre-trained source models. This hybrid approach allows us to leverage the domain-specific expertise and general conversational capabilities to harness the strengths of multiple models. We examine the models in diverse use cases that incorporate biological materials, fracture and engineering analysis, protein biophysics, and bio-inspired design based on insect behavior. Generative applications include bio-inspired designs, including pollen-inspired architected materials, as well as the synthesis of bio-inspired material microstructures from a photograph of a solar eclipse.

  • 1 authors
·
May 29, 2024

BioinspiredLLM: Conversational Large Language Model for the Mechanics of Biological and Bio-inspired Materials

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

  • 2 authors
·
Sep 15, 2023

MeLM, a generative pretrained language modeling framework that solves forward and inverse mechanics problems

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

  • 1 authors
·
Jun 30, 2023

Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

  • 3 authors
·
Apr 11, 2023

X-LoRA: Mixture of Low-Rank Adapter Experts, a Flexible Framework for Large Language Models with Applications in Protein Mechanics and Design

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, we propose a gating strategy that uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations of adaptations are established to solve specific tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

  • 2 authors
·
Feb 11, 2024

Impact of Static Disorder and Dephasing on Quantum Transport in LH1-RC Models

We numerically study excitation transfer in an artificial LH1-RC complex -- an N-site donor ring coupled to a central acceptor -- driven by a narrowband optical mode and evolved under a Lindblad master equation with loss and dephasing. In the absence of disorder, the light-driven system exhibits a tall, narrow on-resonance efficiency peak (near unity for our parameters); dephasing lowers and narrows this peak without shifting its position. Off resonance, the efficiency shows environmentally assisted transport with a clear non-monotonic dependence on dephasing and a finite optimum. Under static disorder, two regimes emerge: photon-ring coupling and diagonal energetic disorder mix the drive into dark ring modes, activate dissipative channels, and depress efficiency over a detuning window, whereas intra-ring coupling disorder has a much smaller impact in the tested range; increasing the intra-ring coupling g moves dark-mode crossings away from the operating detuning and restores near-peak performance. In the ordered, symmetric, single-excitation, narrowband limit we analytically derive closed-form transfer efficiencies by projecting onto the k{=}0 bright mode and solving the photon--bright mode--acceptor trimer via a Laplace/linear-algebra (determinant) formula; these expressions include a probability-conservation identity eta + sum_k L_k = 1 that benchmarks the simulations and quantitatively predicts the resonant line shape and its dephasing-induced narrowing. A minimal ring toy model further reproduces coherent trapping and its relief by moderate dephasing (ENAQT). These analytics are exact in the ordered limit and serve as mechanistic guides outside this limit, yielding practical design rules for robust, bio-inspired light-harvesting devices.

  • 4 authors
·
Sep 23

Fine-tuning large language models for domain adaptation: Exploration of training strategies, scaling, model merging and synergistic capabilities

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

  • 3 authors
·
Sep 5, 2024

Linguistic and Structural Basis of Engineering Design Knowledge

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

  • 2 authors
·
Dec 11, 2023

Neural Circuit Architectural Priors for Embodied Control

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

  • 3 authors
·
Jan 13, 2022

Bio-inspired computational memory model of the Hippocampus: an approach to a neuromorphic spike-based Content-Addressable Memory

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

  • 5 authors
·
Oct 9, 2023

Evolution Gym: A Large-Scale Benchmark for Evolving Soft Robots

Both the design and control of a robot play equally important roles in its task performance. However, while optimal control is well studied in the machine learning and robotics community, less attention is placed on finding the optimal robot design. This is mainly because co-optimizing design and control in robotics is characterized as a challenging problem, and more importantly, a comprehensive evaluation benchmark for co-optimization does not exist. In this paper, we propose Evolution Gym, the first large-scale benchmark for co-optimizing the design and control of soft robots. In our benchmark, each robot is composed of different types of voxels (e.g., soft, rigid, actuators), resulting in a modular and expressive robot design space. Our benchmark environments span a wide range of tasks, including locomotion on various types of terrains and manipulation. Furthermore, we develop several robot co-evolution algorithms by combining state-of-the-art design optimization methods and deep reinforcement learning techniques. Evaluating the algorithms on our benchmark platform, we observe robots exhibiting increasingly complex behaviors as evolution progresses, with the best evolved designs solving many of our proposed tasks. Additionally, even though robot designs are evolved autonomously from scratch without prior knowledge, they often grow to resemble existing natural creatures while outperforming hand-designed robots. Nevertheless, all tested algorithms fail to find robots that succeed in our hardest environments. This suggests that more advanced algorithms are required to explore the high-dimensional design space and evolve increasingly intelligent robots -- an area of research in which we hope Evolution Gym will accelerate progress. Our website with code, environments, documentation, and tutorials is available at http://evogym.csail.mit.edu.

  • 5 authors
·
Jan 24, 2022

COLE: A Hierarchical Generation Framework for Multi-Layered and Editable Graphic Design

Graphic design, which has been evolving since the 15th century, plays a crucial role in advertising. The creation of high-quality designs demands design-oriented planning, reasoning, and layer-wise generation. Unlike the recent CanvaGPT, which integrates GPT-4 with existing design templates to build a custom GPT, this paper introduces the COLE system - a hierarchical generation framework designed to comprehensively address these challenges. This COLE system can transform a vague intention prompt into a high-quality multi-layered graphic design, while also supporting flexible editing based on user input. Examples of such input might include directives like ``design a poster for Hisaishi's concert.'' The key insight is to dissect the complex task of text-to-design generation into a hierarchy of simpler sub-tasks, each addressed by specialized models working collaboratively. The results from these models are then consolidated to produce a cohesive final output. Our hierarchical task decomposition can streamline the complex process and significantly enhance generation reliability. Our COLE system comprises multiple fine-tuned Large Language Models (LLMs), Large Multimodal Models (LMMs), and Diffusion Models (DMs), each specifically tailored for design-aware layer-wise captioning, layout planning, reasoning, and the task of generating images and text. Furthermore, we construct the DESIGNINTENTION benchmark to demonstrate the superiority of our COLE system over existing methods in generating high-quality graphic designs from user intent. Last, we present a Canva-like multi-layered image editing tool to support flexible editing of the generated multi-layered graphic design images. We perceive our COLE system as an important step towards addressing more complex and multi-layered graphic design generation tasks in the future.

  • 13 authors
·
Nov 28, 2023

Large Language and Text-to-3D Models for Engineering Design Optimization

The current advances in generative AI for learning large neural network models with the capability to produce essays, images, music and even 3D assets from text prompts create opportunities for a manifold of disciplines. In the present paper, we study the potential of deep text-to-3D models in the engineering domain, with focus on the chances and challenges when integrating and interacting with 3D assets in computational simulation-based design optimization. In contrast to traditional design optimization of 3D geometries that often searches for the optimum designs using numerical representations, such as B-Spline surface or deformation parameters in vehicle aerodynamic optimization, natural language challenges the optimization framework by requiring a different interpretation of variation operators while at the same time may ease and motivate the human user interaction. Here, we propose and realize a fully automated evolutionary design optimization framework using Shap-E, a recently published text-to-3D asset network by OpenAI, in the context of aerodynamic vehicle optimization. For representing text prompts in the evolutionary optimization, we evaluate (a) a bag-of-words approach based on prompt templates and Wordnet samples, and (b) a tokenisation approach based on prompt templates and the byte pair encoding method from GPT4. Our main findings from the optimizations indicate that, first, it is important to ensure that the designs generated from prompts are within the object class of application, i.e. diverse and novel designs need to be realistic, and, second, that more research is required to develop methods where the strength of text prompt variations and the resulting variations of the 3D designs share causal relations to some degree to improve the optimization.

  • 3 authors
·
Jul 3, 2023

SoftZoo: A Soft Robot Co-design Benchmark For Locomotion In Diverse Environments

While significant research progress has been made in robot learning for control, unique challenges arise when simultaneously co-optimizing morphology. Existing work has typically been tailored for particular environments or representations. In order to more fully understand inherent design and performance tradeoffs and accelerate the development of new breeds of soft robots, a comprehensive virtual platform with well-established tasks, environments, and evaluation metrics is needed. In this work, we introduce SoftZoo, a soft robot co-design platform for locomotion in diverse environments. SoftZoo supports an extensive, naturally-inspired material set, including the ability to simulate environments such as flat ground, desert, wetland, clay, ice, snow, shallow water, and ocean. Further, it provides a variety of tasks relevant for soft robotics, including fast locomotion, agile turning, and path following, as well as differentiable design representations for morphology and control. Combined, these elements form a feature-rich platform for analysis and development of soft robot co-design algorithms. We benchmark prevalent representations and co-design algorithms, and shed light on 1) the interplay between environment, morphology, and behavior; 2) the importance of design space representations; 3) the ambiguity in muscle formation and controller synthesis; and 4) the value of differentiable physics. We envision that SoftZoo will serve as a standard platform and template an approach toward the development of novel representations and algorithms for co-designing soft robots' behavioral and morphological intelligence.

  • 8 authors
·
Mar 16, 2023

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

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.

  • 10 authors
·
Oct 17, 2024

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

  • 5 authors
·
May 31, 2019

Neural Brain: A Neuroscience-inspired Framework for Embodied Agents

The rapid evolution of artificial intelligence (AI) has shifted from static, data-driven models to dynamic systems capable of perceiving and interacting with real-world environments. Despite advancements in pattern recognition and symbolic reasoning, current AI systems, such as large language models, remain disembodied, unable to physically engage with the world. This limitation has driven the rise of embodied AI, where autonomous agents, such as humanoid robots, must navigate and manipulate unstructured environments with human-like adaptability. At the core of this challenge lies the concept of Neural Brain, a central intelligence system designed to drive embodied agents with human-like adaptability. A Neural Brain must seamlessly integrate multimodal sensing and perception with cognitive capabilities. Achieving this also requires an adaptive memory system and energy-efficient hardware-software co-design, enabling real-time action in dynamic environments. This paper introduces a unified framework for the Neural Brain of embodied agents, addressing two fundamental challenges: (1) defining the core components of Neural Brain and (2) bridging the gap between static AI models and the dynamic adaptability required for real-world deployment. To this end, we propose a biologically inspired architecture that integrates multimodal active sensing, perception-cognition-action function, neuroplasticity-based memory storage and updating, and neuromorphic hardware/software optimization. Furthermore, we also review the latest research on embodied agents across these four aspects and analyze the gap between current AI systems and human intelligence. By synthesizing insights from neuroscience, we outline a roadmap towards the development of generalizable, autonomous agents capable of human-level intelligence in real-world scenarios.

LifeGPT: Topology-Agnostic Generative Pretrained Transformer Model for Cellular Automata

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

  • 2 authors
·
Sep 3, 2024

Intelligent Design 4.0: Paradigm Evolution Toward the Agentic AI Era

Research and practice in Intelligent Design (ID) have significantly enhanced engineering innovation, efficiency, quality, and productivity over recent decades, fundamentally reshaping how engineering designers think, behave, and interact with design processes. The recent emergence of Foundation Models (FMs), particularly Large Language Models (LLMs), has demonstrated general knowledge-based reasoning capabilities, and open new paths and avenues for further transformation in engineering design. In this context, this paper introduces Intelligent Design 4.0 (ID 4.0) as an emerging paradigm empowered by agentic AI systems. We review the historical evolution of ID across four distinct stages: rule-based expert systems, task-specific machine learning models, large-scale foundation AI models, and the recent emerging paradigm of multi-agent collaboration. We propose a conceptual framework for ID 4.0 and discuss its potential to support end-to-end automation of engineering design processes through coordinated, autonomous multi-agent-based systems. Furthermore, we discuss future perspectives to enhance and fully realize ID 4.0's potential, including more complex design scenarios, more practical design implementations, novel agent coordination mechanisms, and autonomous design goal-setting with better human value alignment. In sum, these insights lay a foundation for advancing Intelligent Design toward greater adaptivity, autonomy, and effectiveness in addressing increasingly complex design challenges.

  • 5 authors
·
Jun 11

SciAgents: Automating scientific discovery through multi-agent intelligent graph reasoning

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

  • 2 authors
·
Sep 9, 2024

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding

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}.

  • 10 authors
·
Aug 15, 2024

BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Robust Model-Based Optimization for Challenging Fitness Landscapes

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

  • 6 authors
·
May 22, 2023

IDEA-Bench: How Far are Generative Models from Professional Designing?

Real-world design tasks - such as picture book creation, film storyboard development using character sets, photo retouching, visual effects, and font transfer - are highly diverse and complex, requiring deep interpretation and extraction of various elements from instructions, descriptions, and reference images. The resulting images often implicitly capture key features from references or user inputs, making it challenging to develop models that can effectively address such varied tasks. While existing visual generative models can produce high-quality images based on prompts, they face significant limitations in professional design scenarios that involve varied forms and multiple inputs and outputs, even when enhanced with adapters like ControlNets and LoRAs. To address this, we introduce IDEA-Bench, a comprehensive benchmark encompassing 100 real-world design tasks, including rendering, visual effects, storyboarding, picture books, fonts, style-based, and identity-preserving generation, with 275 test cases to thoroughly evaluate a model's general-purpose generation capabilities. Notably, even the best-performing model only achieves 22.48 on IDEA-Bench, while the best general-purpose model only achieves 6.81. We provide a detailed analysis of these results, highlighting the inherent challenges and providing actionable directions for improvement. Additionally, we provide a subset of 18 representative tasks equipped with multimodal large language model (MLLM)-based auto-evaluation techniques to facilitate rapid model development and comparison. We releases the benchmark data, evaluation toolkits, and an online leaderboard at https://github.com/ali-vilab/IDEA-Bench, aiming to drive the advancement of generative models toward more versatile and applicable intelligent design systems.

  • 10 authors
·
Dec 16, 2024

CGB-DM: Content and Graphic Balance Layout Generation with Transformer-based Diffusion Model

Layout generation is the foundation task of intelligent design, which requires the integration of visual aesthetics and harmonious expression of content delivery. However, existing methods still face challenges in generating precise and visually appealing layouts, including blocking, overlap, or spatial misalignment between layouts, which are closely related to the spatial structure of graphic layouts. We find that these methods overly focus on content information and lack constraints on layout spatial structure, resulting in an imbalance of learning content-aware and graphic-aware features. To tackle this issue, we propose Content and Graphic Balance Layout Generation with Transformer-based Diffusion Model (CGB-DM). Specifically, we first design a regulator that balances the predicted content and graphic weight, overcoming the tendency of paying more attention to the content on canvas. Secondly, we introduce a graphic constraint of saliency bounding box to further enhance the alignment of geometric features between layout representations and images. In addition, we adapt a transformer-based diffusion model as the backbone, whose powerful generation capability ensures the quality in layout generation. Extensive experimental results indicate that our method has achieved state-of-the-art performance in both quantitative and qualitative evaluations. Our model framework can also be expanded to other graphic design fields.

  • 5 authors
·
Jul 21, 2024 2

DEsignBench: Exploring and Benchmarking DALL-E 3 for Imagining Visual Design

We introduce DEsignBench, a text-to-image (T2I) generation benchmark tailored for visual design scenarios. Recent T2I models like DALL-E 3 and others, have demonstrated remarkable capabilities in generating photorealistic images that align closely with textual inputs. While the allure of creating visually captivating images is undeniable, our emphasis extends beyond mere aesthetic pleasure. We aim to investigate the potential of using these powerful models in authentic design contexts. In pursuit of this goal, we develop DEsignBench, which incorporates test samples designed to assess T2I models on both "design technical capability" and "design application scenario." Each of these two dimensions is supported by a diverse set of specific design categories. We explore DALL-E 3 together with other leading T2I models on DEsignBench, resulting in a comprehensive visual gallery for side-by-side comparisons. For DEsignBench benchmarking, we perform human evaluations on generated images in DEsignBench gallery, against the criteria of image-text alignment, visual aesthetic, and design creativity. Our evaluation also considers other specialized design capabilities, including text rendering, layout composition, color harmony, 3D design, and medium style. In addition to human evaluations, we introduce the first automatic image generation evaluator powered by GPT-4V. This evaluator provides ratings that align well with human judgments, while being easily replicable and cost-efficient. A high-resolution version is available at https://github.com/design-bench/design-bench.github.io/raw/main/designbench.pdf?download=

  • 5 authors
·
Oct 23, 2023 2

BioMARS: A Multi-Agent Robotic System for Autonomous Biological Experiments

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

  • 10 authors
·
Jul 2

Accelerating Scientific Discovery with Generative Knowledge Extraction, Graph-Based Representation, and Multimodal Intelligent Graph Reasoning

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

  • 1 authors
·
Mar 18, 2024

BIOCLIP: A Vision Foundation Model for the Tree of Life

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

imageomics HDR Imageomics Institute
·
Nov 30, 2023

BioAnalyst: A Foundation Model for Biodiversity

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

  • 7 authors
·
Jul 11

DreamCreature: Crafting Photorealistic Virtual Creatures from Imagination

Recent text-to-image (T2I) generative models allow for high-quality synthesis following either text instructions or visual examples. Despite their capabilities, these models face limitations in creating new, detailed creatures within specific categories (e.g., virtual dog or bird species), which are valuable in digital asset creation and biodiversity analysis. To bridge this gap, we introduce a novel task, Virtual Creatures Generation: Given a set of unlabeled images of the target concepts (e.g., 200 bird species), we aim to train a T2I model capable of creating new, hybrid concepts within diverse backgrounds and contexts. We propose a new method called DreamCreature, which identifies and extracts the underlying sub-concepts (e.g., body parts of a specific species) in an unsupervised manner. The T2I thus adapts to generate novel concepts (e.g., new bird species) with faithful structures and photorealistic appearance by seamlessly and flexibly composing learned sub-concepts. To enhance sub-concept fidelity and disentanglement, we extend the textual inversion technique by incorporating an additional projector and tailored attention loss regularization. Extensive experiments on two fine-grained image benchmarks demonstrate the superiority of DreamCreature over prior methods in both qualitative and quantitative evaluation. Ultimately, the learned sub-concepts facilitate diverse creative applications, including innovative consumer product designs and nuanced property modifications.

  • 4 authors
·
Nov 26, 2023

Exploring the Evolution of Physics Cognition in Video Generation: A Survey

Recent advancements in video generation have witnessed significant progress, especially with the rapid advancement of diffusion models. Despite this, their deficiencies in physical cognition have gradually received widespread attention - generated content often violates the fundamental laws of physics, falling into the dilemma of ''visual realism but physical absurdity". Researchers began to increasingly recognize the importance of physical fidelity in video generation and attempted to integrate heuristic physical cognition such as motion representations and physical knowledge into generative systems to simulate real-world dynamic scenarios. Considering the lack of a systematic overview in this field, this survey aims to provide a comprehensive summary of architecture designs and their applications to fill this gap. Specifically, we discuss and organize the evolutionary process of physical cognition in video generation from a cognitive science perspective, while proposing a three-tier taxonomy: 1) basic schema perception for generation, 2) passive cognition of physical knowledge for generation, and 3) active cognition for world simulation, encompassing state-of-the-art methods, classical paradigms, and benchmarks. Subsequently, we emphasize the inherent key challenges in this domain and delineate potential pathways for future research, contributing to advancing the frontiers of discussion in both academia and industry. Through structured review and interdisciplinary analysis, this survey aims to provide directional guidance for developing interpretable, controllable, and physically consistent video generation paradigms, thereby propelling generative models from the stage of ''visual mimicry'' towards a new phase of ''human-like physical comprehension''.

  • 11 authors
·
Mar 27 2

Bidirectional Learning for Offline Model-based Biological Sequence Design

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.}

  • 4 authors
·
Jan 7, 2023

ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

  • 2 authors
·
Jan 27, 2024

CreatiDesign: A Unified Multi-Conditional Diffusion Transformer for Creative Graphic Design

Graphic design plays a vital role in visual communication across advertising, marketing, and multimedia entertainment. Prior work has explored automated graphic design generation using diffusion models, aiming to streamline creative workflows and democratize design capabilities. However, complex graphic design scenarios require accurately adhering to design intent specified by multiple heterogeneous user-provided elements (\eg images, layouts, and texts), which pose multi-condition control challenges for existing methods. Specifically, previous single-condition control models demonstrate effectiveness only within their specialized domains but fail to generalize to other conditions, while existing multi-condition methods often lack fine-grained control over each sub-condition and compromise overall compositional harmony. To address these limitations, we introduce CreatiDesign, a systematic solution for automated graphic design covering both model architecture and dataset construction. First, we design a unified multi-condition driven architecture that enables flexible and precise integration of heterogeneous design elements with minimal architectural modifications to the base diffusion model. Furthermore, to ensure that each condition precisely controls its designated image region and to avoid interference between conditions, we propose a multimodal attention mask mechanism. Additionally, we develop a fully automated pipeline for constructing graphic design datasets, and introduce a new dataset with 400K samples featuring multi-condition annotations, along with a comprehensive benchmark. Experimental results show that CreatiDesign outperforms existing models by a clear margin in faithfully adhering to user intent.

  • 9 authors
·
May 25

Dressing the Imagination: A Dataset for AI-Powered Translation of Text into Fashion Outfits and A Novel KAN Adapter for Enhanced Feature Adaptation

Specialized datasets that capture the fashion industry's rich language and styling elements can boost progress in AI-driven fashion design. We present FLORA, (Fashion Language Outfit Representation for Apparel Generation), the first comprehensive dataset containing 4,330 curated pairs of fashion outfits and corresponding textual descriptions. Each description utilizes industry-specific terminology and jargon commonly used by professional fashion designers, providing precise and detailed insights into the outfits. Hence, the dataset captures the delicate features and subtle stylistic elements necessary to create high-fidelity fashion designs. We demonstrate that fine-tuning generative models on the FLORA dataset significantly enhances their capability to generate accurate and stylistically rich images from textual descriptions of fashion sketches. FLORA will catalyze the creation of advanced AI models capable of comprehending and producing subtle, stylistically rich fashion designs. It will also help fashion designers and end-users to bring their ideas to life. As a second orthogonal contribution, we introduce NeRA (Nonlinear low-rank Expressive Representation Adapter), a novel adapter architecture based on Kolmogorov-Arnold Networks (KAN). Unlike traditional PEFT techniques such as LoRA, LoKR, DoRA, and LoHA that use MLP adapters, NeRA uses learnable spline-based nonlinear transformations, enabling superior modeling of complex semantic relationships, achieving strong fidelity, faster convergence and semantic alignment. Extensive experiments on our proposed FLORA and LAION-5B datasets validate the superiority of NeRA over existing adapters. We will open-source both the FLORA dataset and our implementation code.

  • 5 authors
·
Nov 21, 2024

FlyLoRA: Boosting Task Decoupling and Parameter Efficiency via Implicit Rank-Wise Mixture-of-Experts

Low-Rank Adaptation (LoRA) is a widely used parameter-efficient fine-tuning method for foundation models, but it suffers from parameter interference, resulting in suboptimal performance. Although Mixture-of-Experts (MoE)-based LoRA variants show promise in mitigating intra-task correlations in single-task instruction tuning, they introduce additional router parameters and remain ineffective in multi-task model merging where inter-task interference arises. Inspired by the fly olfactory circuit, we propose FlyLoRA, an implicit MoE-based LoRA variant that introduces: (1) rank-wise expert activation in the up-projection matrix, and (2) an implicit router that unifies expert routing and down-projection, where a frozen sparse random projection matrix replaces the traditional dense trainable version. This design resolves the trade-off between intra-task decorrelation and computational efficiency by eliminating the need for an explicit router, while inherently mitigating inter-task interference due to the orthogonality property of random matrices. Extensive experiments across four domains -- general knowledge understanding, scientific question answering, mathematical reasoning, and code generation -- demonstrate consistent performance improvements over existing methods. Beyond empirical gains, FlyLoRA highlights how biological structures can inspire innovations in AI technologies. Code is available at https://github.com/gfyddha/FlyLoRA.

  • 5 authors
·
Oct 9

Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

  • 2 authors
·
Jan 29, 2023

PosterLLaVa: Constructing a Unified Multi-modal Layout Generator with LLM

Layout generation is the keystone in achieving automated graphic design, requiring arranging the position and size of various multi-modal design elements in a visually pleasing and constraint-following manner. Previous approaches are either inefficient for large-scale applications or lack flexibility for varying design requirements. Our research introduces a unified framework for automated graphic layout generation, leveraging the multi-modal large language model (MLLM) to accommodate diverse design tasks. In contrast, our data-driven method employs structured text (JSON format) and visual instruction tuning to generate layouts under specific visual and textual constraints, including user-defined natural language specifications. We conducted extensive experiments and achieved state-of-the-art (SOTA) performance on public multi-modal layout generation benchmarks, demonstrating the effectiveness of our method. Moreover, recognizing existing datasets' limitations in capturing the complexity of real-world graphic designs, we propose two new datasets for much more challenging tasks (user-constrained generation and complicated poster), further validating our model's utility in real-life settings. Marking by its superior accessibility and adaptability, this approach further automates large-scale graphic design tasks. The code and datasets will be publicly available on https://github.com/posterllava/PosterLLaVA.

  • 6 authors
·
Jun 4, 2024 2

Efficient Architecture Search by Network Transformation

Techniques for automatically designing deep neural network architectures such as reinforcement learning based approaches have recently shown promising results. However, their success is based on vast computational resources (e.g. hundreds of GPUs), making them difficult to be widely used. A noticeable limitation is that they still design and train each network from scratch during the exploration of the architecture space, which is highly inefficient. In this paper, we propose a new framework toward efficient architecture search by exploring the architecture space based on the current network and reusing its weights. We employ a reinforcement learning agent as the meta-controller, whose action is to grow the network depth or layer width with function-preserving transformations. As such, the previously validated networks can be reused for further exploration, thus saves a large amount of computational cost. We apply our method to explore the architecture space of the plain convolutional neural networks (no skip-connections, branching etc.) on image benchmark datasets (CIFAR-10, SVHN) with restricted computational resources (5 GPUs). Our method can design highly competitive networks that outperform existing networks using the same design scheme. On CIFAR-10, our model without skip-connections achieves 4.23\% test error rate, exceeding a vast majority of modern architectures and approaching DenseNet. Furthermore, by applying our method to explore the DenseNet architecture space, we are able to achieve more accurate networks with fewer parameters.

  • 5 authors
·
Jul 16, 2017

PosterLayout: A New Benchmark and Approach for Content-aware Visual-Textual Presentation Layout

Content-aware visual-textual presentation layout aims at arranging spatial space on the given canvas for pre-defined elements, including text, logo, and underlay, which is a key to automatic template-free creative graphic design. In practical applications, e.g., poster designs, the canvas is originally non-empty, and both inter-element relationships as well as inter-layer relationships should be concerned when generating a proper layout. A few recent works deal with them simultaneously, but they still suffer from poor graphic performance, such as a lack of layout variety or spatial non-alignment. Since content-aware visual-textual presentation layout is a novel task, we first construct a new dataset named PosterLayout, which consists of 9,974 poster-layout pairs and 905 images, i.e., non-empty canvases. It is more challenging and useful for greater layout variety, domain diversity, and content diversity. Then, we propose design sequence formation (DSF) that reorganizes elements in layouts to imitate the design processes of human designers, and a novel CNN-LSTM-based conditional generative adversarial network (GAN) is presented to generate proper layouts. Specifically, the discriminator is design-sequence-aware and will supervise the "design" process of the generator. Experimental results verify the usefulness of the new benchmark and the effectiveness of the proposed approach, which achieves the best performance by generating suitable layouts for diverse canvases.

  • 5 authors
·
Mar 28, 2023

Towards an AI co-scientist

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

sharpDARTS: Faster and More Accurate Differentiable Architecture Search

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.

  • 3 authors
·
Mar 23, 2019

MultiRef: Controllable Image Generation with Multiple Visual References

Visual designers naturally draw inspiration from multiple visual references, combining diverse elements and aesthetic principles to create artwork. However, current image generative frameworks predominantly rely on single-source inputs -- either text prompts or individual reference images. In this paper, we focus on the task of controllable image generation using multiple visual references. We introduce MultiRef-bench, a rigorous evaluation framework comprising 990 synthetic and 1,000 real-world samples that require incorporating visual content from multiple reference images. The synthetic samples are synthetically generated through our data engine RefBlend, with 10 reference types and 33 reference combinations. Based on RefBlend, we further construct a dataset MultiRef containing 38k high-quality images to facilitate further research. Our experiments across three interleaved image-text models (i.e., OmniGen, ACE, and Show-o) and six agentic frameworks (e.g., ChatDiT and LLM + SD) reveal that even state-of-the-art systems struggle with multi-reference conditioning, with the best model OmniGen achieving only 66.6% in synthetic samples and 79.0% in real-world cases on average compared to the golden answer. These findings provide valuable directions for developing more flexible and human-like creative tools that can effectively integrate multiple sources of visual inspiration. The dataset is publicly available at: https://multiref.github.io/.

A Critical Assessment of Modern Generative Models' Ability to Replicate Artistic Styles

In recent years, advancements in generative artificial intelligence have led to the development of sophisticated tools capable of mimicking diverse artistic styles, opening new possibilities for digital creativity and artistic expression. This paper presents a critical assessment of the style replication capabilities of contemporary generative models, evaluating their strengths and limitations across multiple dimensions. We examine how effectively these models reproduce traditional artistic styles while maintaining structural integrity and compositional balance in the generated images. The analysis is based on a new large dataset of AI-generated works imitating artistic styles of the past, holding potential for a wide range of applications: the "AI-pastiche" dataset. The study is supported by extensive user surveys, collecting diverse opinions on the dataset and investigation both technical and aesthetic challenges, including the ability to generate outputs that are realistic and visually convincing, the versatility of models in handling a wide range of artistic styles, and the extent to which they adhere to the content and stylistic specifications outlined in prompts. This paper aims to provide a comprehensive overview of the current state of generative tools in style replication, offering insights into their technical and artistic limitations, potential advancements in model design and training methodologies, and emerging opportunities for enhancing digital artistry, human-AI collaboration, and the broader creative landscape.

  • 5 authors
·
Feb 21

Aligning Optimization Trajectories with Diffusion Models for Constrained Design Generation

Generative models have had a profound impact on vision and language, paving the way for a new era of multimodal generative applications. While these successes have inspired researchers to explore using generative models in science and engineering to accelerate the design process and reduce the reliance on iterative optimization, challenges remain. Specifically, engineering optimization methods based on physics still outperform generative models when dealing with constrained environments where data is scarce and precision is paramount. To address these challenges, we introduce Diffusion Optimization Models (DOM) and Trajectory Alignment (TA), a learning framework that demonstrates the efficacy of aligning the sampling trajectory of diffusion models with the optimization trajectory derived from traditional physics-based methods. This alignment ensures that the sampling process remains grounded in the underlying physical principles. Our method allows for generating feasible and high-performance designs in as few as two steps without the need for expensive preprocessing, external surrogate models, or additional labeled data. We apply our framework to structural topology optimization, a fundamental problem in mechanical design, evaluating its performance on in- and out-of-distribution configurations. Our results demonstrate that TA outperforms state-of-the-art deep generative models on in-distribution configurations and halves the inference computational cost. When coupled with a few steps of optimization, it also improves manufacturability for out-of-distribution conditions. By significantly improving performance and inference efficiency, DOM enables us to generate high-quality designs in just a few steps and guide them toward regions of high performance and manufacturability, paving the way for the widespread application of generative models in large-scale data-driven design.

  • 4 authors
·
May 29, 2023

Drawing2CAD: Sequence-to-Sequence Learning for CAD Generation from Vector Drawings

Computer-Aided Design (CAD) generative modeling is driving significant innovations across industrial applications. Recent works have shown remarkable progress in creating solid models from various inputs such as point clouds, meshes, and text descriptions. However, these methods fundamentally diverge from traditional industrial workflows that begin with 2D engineering drawings. The automatic generation of parametric CAD models from these 2D vector drawings remains underexplored despite being a critical step in engineering design. To address this gap, our key insight is to reframe CAD generation as a sequence-to-sequence learning problem where vector drawing primitives directly inform the generation of parametric CAD operations, preserving geometric precision and design intent throughout the transformation process. We propose Drawing2CAD, a framework with three key technical components: a network-friendly vector primitive representation that preserves precise geometric information, a dual-decoder transformer architecture that decouples command type and parameter generation while maintaining precise correspondence, and a soft target distribution loss function accommodating inherent flexibility in CAD parameters. To train and evaluate Drawing2CAD, we create CAD-VGDrawing, a dataset of paired engineering drawings and parametric CAD models, and conduct thorough experiments to demonstrate the effectiveness of our method. Code and dataset are available at https://github.com/lllssc/Drawing2CAD.

  • 6 authors
·
Aug 26 3

ComposeAnyone: Controllable Layout-to-Human Generation with Decoupled Multimodal Conditions

Building on the success of diffusion models, significant advancements have been made in multimodal image generation tasks. Among these, human image generation has emerged as a promising technique, offering the potential to revolutionize the fashion design process. However, existing methods often focus solely on text-to-image or image reference-based human generation, which fails to satisfy the increasingly sophisticated demands. To address the limitations of flexibility and precision in human generation, we introduce ComposeAnyone, a controllable layout-to-human generation method with decoupled multimodal conditions. Specifically, our method allows decoupled control of any part in hand-drawn human layouts using text or reference images, seamlessly integrating them during the generation process. The hand-drawn layout, which utilizes color-blocked geometric shapes such as ellipses and rectangles, can be easily drawn, offering a more flexible and accessible way to define spatial layouts. Additionally, we introduce the ComposeHuman dataset, which provides decoupled text and reference image annotations for different components of each human image, enabling broader applications in human image generation tasks. Extensive experiments on multiple datasets demonstrate that ComposeAnyone generates human images with better alignment to given layouts, text descriptions, and reference images, showcasing its multi-task capability and controllability.

  • 9 authors
·
Jan 21

BikeBench: A Bicycle Design Benchmark for Generative Models with Objectives and Constraints

We introduce BikeBench, an engineering design benchmark for evaluating generative models on problems with multiple real-world objectives and constraints. As generative AI's reach continues to grow, evaluating its capability to understand physical laws, human guidelines, and hard constraints grows increasingly important. Engineering product design lies at the intersection of these difficult tasks, providing new challenges for AI capabilities. BikeBench evaluates AI models' capabilities to generate bicycle designs that not only resemble the dataset, but meet specific performance objectives and constraints. To do so, BikeBench quantifies a variety of human-centered and multiphysics performance characteristics, such as aerodynamics, ergonomics, structural mechanics, human-rated usability, and similarity to subjective text or image prompts. Supporting the benchmark are several datasets of simulation results, a dataset of 10,000 human-rated bicycle assessments, and a synthetically generated dataset of 1.6M designs, each with a parametric, CAD/XML, SVG, and PNG representation. BikeBench is uniquely configured to evaluate tabular generative models, large language models (LLMs), design optimization, and hybrid algorithms side-by-side. Our experiments indicate that LLMs and tabular generative models fall short of hybrid GenAI+optimization algorithms in design quality, constraint satisfaction, and similarity scores, suggesting significant room for improvement. We hope that BikeBench, a first-of-its-kind benchmark, will help catalyze progress in generative AI for constrained multi-objective engineering design problems. We provide code, data, an interactive leaderboard, and other resources at https://github.com/Lyleregenwetter/BikeBench.

  • 5 authors
·
May 25

Automated Design of Agentic Systems

Researchers are investing substantial effort in developing powerful general-purpose agents, wherein Foundation Models are used as modules within agentic systems (e.g. Chain-of-Thought, Self-Reflection, Toolformer). However, the history of machine learning teaches us that hand-designed solutions are eventually replaced by learned solutions. We formulate a new research area, Automated Design of Agentic Systems (ADAS), which aims to automatically create powerful agentic system designs, including inventing novel building blocks and/or combining them in new ways. We further demonstrate that there is an unexplored yet promising approach within ADAS where agents can be defined in code and new agents can be automatically discovered by a meta agent programming ever better ones in code. Given that programming languages are Turing Complete, this approach theoretically enables the learning of any possible agentic system: including novel prompts, tool use, control flows, and combinations thereof. We present a simple yet effective algorithm named Meta Agent Search to demonstrate this idea, where a meta agent iteratively programs interesting new agents based on an ever-growing archive of previous discoveries. Through extensive experiments across multiple domains including coding, science, and math, we show that our algorithm can progressively invent agents with novel designs that greatly outperform state-of-the-art hand-designed agents. Importantly, we consistently observe the surprising result that agents invented by Meta Agent Search maintain superior performance even when transferred across domains and models, demonstrating their robustness and generality. Provided we develop it safely, our work illustrates the potential of an exciting new research direction toward automatically designing ever-more powerful agentic systems to benefit humanity.

  • 3 authors
·
Aug 15, 2024 3

ArchGym: An Open-Source Gymnasium for Machine Learning Assisted Architecture Design

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

  • 11 authors
·
Jun 15, 2023

Layout-Corrector: Alleviating Layout Sticking Phenomenon in Discrete Diffusion Model

Layout generation is a task to synthesize a harmonious layout with elements characterized by attributes such as category, position, and size. Human designers experiment with the placement and modification of elements to create aesthetic layouts, however, we observed that current discrete diffusion models (DDMs) struggle to correct inharmonious layouts after they have been generated. In this paper, we first provide novel insights into layout sticking phenomenon in DDMs and then propose a simple yet effective layout-assessment module Layout-Corrector, which works in conjunction with existing DDMs to address the layout sticking problem. We present a learning-based module capable of identifying inharmonious elements within layouts, considering overall layout harmony characterized by complex composition. During the generation process, Layout-Corrector evaluates the correctness of each token in the generated layout, reinitializing those with low scores to the ungenerated state. The DDM then uses the high-scored tokens as clues to regenerate the harmonized tokens. Layout-Corrector, tested on common benchmarks, consistently boosts layout-generation performance when in conjunction with various state-of-the-art DDMs. Furthermore, our extensive analysis demonstrates that the Layout-Corrector (1) successfully identifies erroneous tokens, (2) facilitates control over the fidelity-diversity trade-off, and (3) significantly mitigates the performance drop associated with fast sampling.

  • 4 authors
·
Sep 25, 2024

BANG: Dividing 3D Assets via Generative Exploded Dynamics

3D creation has always been a unique human strength, driven by our ability to deconstruct and reassemble objects using our eyes, mind and hand. However, current 3D design tools struggle to replicate this natural process, requiring considerable artistic expertise and manual labor. This paper introduces BANG, a novel generative approach that bridges 3D generation and reasoning, allowing for intuitive and flexible part-level decomposition of 3D objects. At the heart of BANG is "Generative Exploded Dynamics", which creates a smooth sequence of exploded states for an input geometry, progressively separating parts while preserving their geometric and semantic coherence. BANG utilizes a pre-trained large-scale latent diffusion model, fine-tuned for exploded dynamics with a lightweight exploded view adapter, allowing precise control over the decomposition process. It also incorporates a temporal attention module to ensure smooth transitions and consistency across time. BANG enhances control with spatial prompts, such as bounding boxes and surface regions, enabling users to specify which parts to decompose and how. This interaction can be extended with multimodal models like GPT-4, enabling 2D-to-3D manipulations for more intuitive and creative workflows. The capabilities of BANG extend to generating detailed part-level geometry, associating parts with functional descriptions, and facilitating component-aware 3D creation and manufacturing workflows. Additionally, BANG offers applications in 3D printing, where separable parts are generated for easy printing and reassembly. In essence, BANG enables seamless transformation from imaginative concepts to detailed 3D assets, offering a new perspective on creation that resonates with human intuition.

  • 7 authors
·
Jul 29 3

Counter-Current Learning: A Biologically Plausible Dual Network Approach for Deep Learning

Despite its widespread use in neural networks, error backpropagation has faced criticism for its lack of biological plausibility, suffering from issues such as the backward locking problem and the weight transport problem. These limitations have motivated researchers to explore more biologically plausible learning algorithms that could potentially shed light on how biological neural systems adapt and learn. Inspired by the counter-current exchange mechanisms observed in biological systems, we propose counter-current learning (CCL), a biologically plausible framework for credit assignment in neural networks. This framework employs a feedforward network to process input data and a feedback network to process targets, with each network enhancing the other through anti-parallel signal propagation. By leveraging the more informative signals from the bottom layer of the feedback network to guide the updates of the top layer of the feedforward network and vice versa, CCL enables the simultaneous transformation of source inputs to target outputs and the dynamic mutual influence of these transformations. Experimental results on MNIST, FashionMNIST, CIFAR10, and CIFAR100 datasets using multi-layer perceptrons and convolutional neural networks demonstrate that CCL achieves comparable performance to other biologically plausible algorithms while offering a more biologically realistic learning mechanism. Furthermore, we showcase the applicability of our approach to an autoencoder task, underscoring its potential for unsupervised representation learning. Our work presents a direction for biologically inspired and plausible learning algorithms, offering an alternative mechanism of learning and adaptation in neural networks.

  • 2 authors
·
Sep 29, 2024

Classical Sorting Algorithms as a Model of Morphogenesis: self-sorting arrays reveal unexpected competencies in a minimal model of basal intelligence

The emerging field of Diverse Intelligence seeks to identify, formalize, and understand commonalities in behavioral competencies across a wide range of implementations. Especially interesting are simple systems that provide unexpected examples of memory, decision-making, or problem-solving in substrates that at first glance do not appear to be complex enough to implement such capabilities. We seek to develop tools to help understand the minimal requirements for such capabilities, and to learn to recognize and predict basal forms of intelligence in unconventional substrates. Here, we apply novel analyses to the behavior of classical sorting algorithms, short pieces of code which have been studied for many decades. To study these sorting algorithms as a model of biological morphogenesis and its competencies, we break two formerly-ubiquitous assumptions: top-down control (instead, showing how each element within a array of numbers can exert minimal agency and implement sorting policies from the bottom up), and fully reliable hardware (instead, allowing some of the elements to be "damaged" and fail to execute the algorithm). We quantitatively characterize sorting activity as the traversal of a problem space, showing that arrays of autonomous elements sort themselves more reliably and robustly than traditional implementations in the presence of errors. Moreover, we find the ability to temporarily reduce progress in order to navigate around a defect, and unexpected clustering behavior among the elements in chimeric arrays whose elements follow one of two different algorithms. The discovery of emergent problem-solving capacities in simple, familiar algorithms contributes a new perspective to the field of Diverse Intelligence, showing how basal forms of intelligence can emerge in simple systems without being explicitly encoded in their underlying mechanics.

  • 3 authors
·
Dec 15, 2023

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

  • 7 authors
·
Jan 25, 2023

NAS-Bench-201: Extending the Scope of Reproducible Neural Architecture Search

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.

  • 2 authors
·
Jan 2, 2020