Designing proteins de novo with tailored structural, physicochemical, and functional properties remains a grand challenge in biotechnology, medicine, and materials science, due to the vastness of sequence space and the complex coupling between sequence, structure, and function. Current state-of-the-art generative methods, such as protein language models (PLMs) and diffusion-based architectures, often require extensive fine-tuning, task-specific data, or model reconfiguration to support objective-directed design, thereby limiting their flexibility and scalability. To overcome these limitations, we present a decentralized, agent-based framework inspired by swarm intelligence for de novo protein design. In this approach, multiple large language model (LLM) agents operate in parallel, each assigned to a specific residue position. These agents iteratively propose context-aware mutations by integrating design objectives, local neighborhood interactions, and memory and feedback from previous iterations. This position-wise, decentralized coordination enables emergent design of diverse, well-defined sequences without reliance on motif scaffolds or multiple sequence alignments, validated with experiments on proteins with alpha helix and coil structures. Through analyses of residue conservation, structure-based metrics, and sequence convergence and embeddings, we demonstrate that the framework exhibits emergent behaviors and effective navigation of the protein fitness landscape. Our method achieves efficient, objective-directed designs within a few GPU-hours and operates entirely without fine-tuning or specialized training, offering a generalizable and adaptable solution for protein design. Beyond proteins, the approach lays the groundwork for collective LLM-driven design across biomolecular systems and other scientific discovery tasks.

This research explores the application of Deep Reinforcement Learning (DRL) to optimize the design of a nuclear fusion reactor. DRL can efficiently address the challenging issues attributed to multiple physics and engineering constraints for steady-state operation. The fusion reactor design computation and the optimization code applicable to parallelization with DRL are developed. The proposed framework enables finding the optimal reactor design that satisfies the operational requirements while reducing building costs. Multi-objective design optimization for a fusion reactor is now simplified by DRL, indicating the high potential of the proposed framework for advancing the efficient and sustainable design of future reactors.

Manipulating the dispersive characteristics of vibrational waves is beneficial for many applications, e.g., high-precision instruments. architected hierarchical phononic materials have sparked promise tunability of elastodynamic waves and vibrations over multiple frequency ranges. In this article, hierarchical unit-cells are obtained, where features at each length scale result in a band gap within a targeted frequency range. Our novel approach, the ``hierarchical unit-cell template method,'' is an interpretable machine-learning approach that uncovers global unit-cell shape/topology patterns corresponding to predefined band-gap objectives. A scale-separation effect is observed where the coarse-scale band-gap objective is mostly unaffected by the fine-scale features despite the closeness of their length scales, thus enabling an efficient hierarchical algorithm. Moreover, the hierarchical patterns revealed are not predefined or self-similar hierarchies as common in current hierarchical phononic materials. Thus, our approach offers a flexible and efficient method for the exploration of new regions in the hierarchical design space, extracting minimal effective patterns for inverse design in applications targeting multiple frequency ranges.

Clinical randomized controlled trials (RCTs) collect hundreds of measurements spanning various metric types (e.g., laboratory tests, cognitive/motor assessments, etc.) across 100s-1000s of subjects to evaluate the effect of a treatment, but do so at the cost of significant trial expense. To reduce the number of measurements, trial protocols can be revised to remove metrics extraneous to the study's objective, but doing so requires additional human labor and limits the set of hypotheses that can be studied with the collected data. In contrast, a planned missing design (PMD) can reduce the amount of data collected without removing any metric by imputing the unsampled data. Standard PMDs randomly sample data to leverage statistical properties of imputation algorithms, but are ad hoc, hence suboptimal. Methods that learn PMDs produce more sample-efficient PMDs, but are not suitable for RCTs because they require ample prior data (150+ subjects) to model the data distribution. Therefore, we introduce a framework called Measurement EfficienT Randomized Controlled Trials using Transformers with Input MasKing (METRIK), which, for the first time, calculates a PMD specific to the RCT from a modest amount of prior data (e.g., 60 subjects). Specifically, METRIK models the PMD as a learnable input masking layer that is optimized with a state-of-the-art imputer based on the Transformer architecture. METRIK implements a novel sampling and selection algorithm to generate a PMD that satisfies the trial designer's objective, i.e., whether to maximize sampling efficiency or imputation performance for a given sampling budget. Evaluated across five real-world clinical RCT datasets, METRIK increases the sampling efficiency of and imputation performance under the generated PMD by leveraging correlations over time and across metrics, thereby removing the need to manually remove metrics from the RCT.

Inverse design, where we seek to design input variables in order to optimize an underlying objective function, is an important problem that arises across fields such as mechanical engineering to aerospace engineering. Inverse design is typically formulated as an optimization problem, with recent works leveraging optimization across learned dynamics models. However, as models are optimized they tend to fall into adversarial modes, preventing effective sampling. We illustrate that by instead optimizing over the learned energy function captured by the diffusion model, we can avoid such adversarial examples and significantly improve design performance. We further illustrate how such a design system is compositional, enabling us to combine multiple different diffusion models representing subcomponents of our desired system to design systems with every specified component. In an N-body interaction task and a challenging 2D multi-airfoil design task, we demonstrate that by composing the learned diffusion model at test time, our method allows us to design initial states and boundary shapes that are more complex than those in the training data. Our method outperforms state-of-the-art neural inverse design method by an average of 41.5% in prediction MAE and 14.3% in design objective for the N-body dataset and discovers formation flying to minimize drag in the multi-airfoil design task. Project website and code can be found at https://github.com/AI4Science-WestlakeU/cindm.

Metaheuristics are prominent gradient-free optimizers for solving hard problems that do not meet the rigorous mathematical assumptions of analytical solvers. The canonical manual optimizer design could be laborious, untraceable and error-prone, let alone human experts are not always available. This arises increasing interest and demand in automating the optimizer design process. In response, this paper proposes AutoOptLib, the first platform for accessible automated design of metaheuristic optimizers. AutoOptLib leverages computing resources to conceive, build up, and verify the design choices of the optimizers. It requires much less labor resources and expertise than manual design, democratizing satisfactory metaheuristic optimizers to a much broader range of researchers and practitioners. Furthermore, by fully exploring the design choices with computing resources, AutoOptLib has the potential to surpass human experience, subsequently gaining enhanced performance compared with human problem-solving. To realize the automated design, AutoOptLib provides 1) a rich library of metaheuristic components for continuous, discrete, and permutation problems; 2) a flexible algorithm representation for evolving diverse algorithm structures; 3) different design objectives and techniques for different optimization scenarios; and 4) a graphic user interface for accessibility and practicability. AutoOptLib is fully written in Matlab/Octave; its source code and documentation are available at https://github.com/qz89/AutoOpt and https://AutoOpt.readthedocs.io/, respectively.

We consider linear-quadratic Gaussian (LQG) games in which players have quadratic payoffs that depend on the players' actions and an unknown payoff-relevant state, and signals on the state that follow a Gaussian distribution conditional on the state realization. An information designer decides the fidelity of information revealed to the players in order to maximize the social welfare of the players or reduce the disagreement among players' actions. Leveraging the semi-definiteness of the information design problem, we derive analytical solutions for these objectives under specific LQG games. We show that full information disclosure maximizes social welfare when there is a common payoff-relevant state, when there is strategic substitutability in the actions of players, or when the signals are public. Numerical results show that as strategic substitution increases, the value of the information disclosure increases. When the objective is to induce conformity among players' actions, hiding information is optimal. Lastly, we consider the information design objective that is a weighted combination of social welfare and cohesiveness of players' actions. We obtain an interval for the weights where full information disclosure is optimal under public signals for games with strategic substitutability. Numerical solutions show that the actual interval where full information disclosure is optimal gets close to the analytical interval obtained as substitution increases.

The 3D shape of a robot's end-effector plays a critical role in determining it's functionality and overall performance. Many industrial applications rely on task-specific gripper designs to ensure the system's robustness and accuracy. However, the process of manual hardware design is both costly and time-consuming, and the quality of the resulting design is dependent on the engineer's experience and domain expertise, which can easily be out-dated or inaccurate. The goal of this work is to use machine learning algorithms to automate the design of task-specific gripper fingers. We propose Fit2Form, a 3D generative design framework that generates pairs of finger shapes to maximize design objectives (i.e., grasp success, stability, and robustness) for target grasp objects. We model the design objectives by training a Fitness network to predict their values for pairs of gripper fingers and their corresponding grasp objects. This Fitness network then provides supervision to a 3D Generative network that produces a pair of 3D finger geometries for the target grasp object. Our experiments demonstrate that the proposed 3D generative design framework generates parallel jaw gripper finger shapes that achieve more stable and robust grasps compared to other general-purpose and task-specific gripper design algorithms. Video can be found at https://youtu.be/utKHP3qb1bg.