This work was done when Mingyu was at MIT.

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

Furthermore, we explore the potential of language models in generating co-crystals. Finally, we present numerous previously unknown co-crystals predicted by GEM-CODE and discuss its potential in accelerating drug development.

This work was done when Mingyu was at MIT.

Composites are amongst the most important materials manufactured today, as evidenced by their use in countless applications. In order to establish the suitability of composites in specific applications, finite element (FE) modelling, a numerical method based on partial differential equations, is the industry standard for assessing their mechanical properties. However, FE modelling is exceptionally costly from a computational viewpoint, a limitation which has led to efforts towards applying AI models to this task. However, in these approaches: the chosen model architectures were rudimentary, feed-forward neural networks giving limited accuracy; the studies focused on predicting elastic mechanical properties, without considering material strength limits; and the models lacked transparency, hindering trustworthiness by users. In this paper, we show that convolutional neural networks (CNNs) equipped with methods from explainable AI (XAI) can be successfully deployed to solve this problem. Our approach uses customised CNNs trained on a dataset we generate using transverse tension tests in FE modelling to predict composites' mechanical properties, i.e., Y oung's modulus and yield strength. We show empirically that our approach achieves high accuracy, outperforming a baseline, ResNet-34, in estimating the mechanical properties. We then use SHAP and Integrated Gradients, two post-hoc XAI methods, to explain the predictions, showing that the CNNs use the critical geometrical features that influence the composites' behaviour, thus allowing engineers to verify that the models are trustworthy by representing the science of composites.

We introduce PROD (Palpative Reconstruction of Deformables), a novel method for reconstructing the shape and mechanical properties of deformable objects using elastostatic signed distance functions (SDFs). Unlike traditional approaches that rely on purely geometric or visual data, PROD integrates palpative interaction -- measured through force-controlled surface probing -- to estimate both the static and dynamic response of soft materials. We model the deformation of an object as an elastostatic process and derive a governing Poisson equation for estimating its SDF from a sparse set of pose and force measurements. By incorporating steady-state elastodynamic assumptions, we show that the undeformed SDF can be recovered from deformed observations with provable convergence. Our approach also enables the estimation of material stiffness by analyzing displacement responses to varying force inputs. We demonstrate the robustness of PROD in handling pose errors, non-normal force application, and curvature errors in simulated soft body interactions. These capabilities make PROD a powerful tool for reconstructing deformable objects in applications ranging from robotic manipulation to medical imaging and haptic feedback systems.

To enable robots to develop human-like fine manipulation, it is essential to understand how mechanical compliance, multi-modal sensing, and purposeful interaction jointly shape tactile perception. In this study, we use a dedicated modular e-Skin with tunable mechanical compliance and multi-modal sensing (normal, shear forces and vibrations) to systematically investigate how sensing embodiment and interaction strategies influence robotic perception of objects. Leveraging a curated set of soft wave objects with controlled viscoelastic and surface properties, we explore a rich set of palpation primitives-pressing, precession, sliding that vary indentation depth, frequency, and directionality. In addition, we propose the latent filter, an unsupervised, action-conditioned deep state-space model of the sophisticated interaction dynamics and infer causal mechanical properties into a structured latent space. This provides generalizable and in-depth interpretable representation of how embodiment and interaction determine and influence perception. Our investigation demonstrates that multi-modal sensing outperforms uni-modal sensing. It highlights a nuanced interaction between the environment and mechanical properties of e-Skin, which should be examined alongside the interaction by incorporating temporal dynamics.

The complex behavior of highly deformable mechanical metamaterials can substantially enhance the performance of soft robots. Metamaterials are rapidly emerging from electromagnetic, acoustic, or mechanical properties governed by structure rather than composition. Mechanical metamaterials, in particular, hav e been designed to show superior mechanical properties, such as ultrahigh stiffness and strength - to - weight ratio, or unusual properties, such as a negative Poisson's ratio and a negative coefficient of thermal expansion. Whereas earlier research focused on designing mechanical metamaterials with linear elastic responses, more recently, nonlinear large deformations and mechanical instabilities - typically associated with failure - have emerged as promising tools for new functionalities, including programmabl e shape transformations, tunable mechanical properties, and energy absorption (1). Ongoing advances in additive manufacturing technologies facilitate the fabrication of functional mechanical metamaterials with unprecedented complexity.

Metamaterials are artificial materials that are designed to meet unseen properties in nature, such as ultra-stiffness and negative materials indices. In mechanical metamaterial design, three key modalities are typically involved, i.e., 3D topology, density condition, and mechanical property. Real-world complex application scenarios place the demanding requirements on machine learning models to consider all three modalities together. However, a comprehensive literature review indicates that most existing works only consider two modalities, e.g., predicting mechanical properties given the 3D topology or generating 3D topology given the required properties. Therefore, there is still a significant gap for the state-of-the-art machine learning models capturing the whole. Hence, we propose a unified model named UNIMATE, which consists of a modality alignment module and a synergetic diffusion generation module. Experiments indicate that UNIMATE outperforms the other baseline models in topology generation task, property prediction task, and condition confirmation task by up to 80.2%, 5.1%, and 50.2%, respectively. We opensource our proposed UNIMATE model and corresponding results at https://github.com/wzhan24/UniMate.