Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models

Large language models (LLMs) are widely applied in various natural language processing tasks such as question answering and machine translation. However, due to the lack of labeled data and the difficulty of manual annotation for biochemical properties, the performance for molecule generation tasks is still limited, especially for tasks involving multi-properties constraints. In this work, we present a two-step framework PEIT (Property Enhanced Instruction Tuning) to improve LLMs for molecular-related tasks. In the first step, we use textual descriptions, SMILES, and biochemical properties as multimodal inputs to pre-train a model called PEIT-GEN, by aligning multi-modal representations to synthesize instruction data. In the second step, we fine-tune existing open-source LLMs with the synthesized data, the resulting PEIT-LLM can handle molecule captioning, text-based molecule generation, molecular property prediction, and our newly proposed multi-constraint molecule generation tasks. Experimental results show that our pre-trained PEIT-GEN outperforms MolT5 and BioT5 in molecule captioning, demonstrating modalities align well between textual descriptions, structures, and biochemical properties. Furthermore, PEIT-LLM shows promising improvements in multi-task molecule generation, proving the scalability of the PEIT framework for various molecular tasks. We release the code, constructed instruction data, and model checkpoints in https://github.com/chenlong164/PEIT.

S$^2$DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion

Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent studies have shown promising results in inferring such entities through knowledge subgraph reasoning, they suffer from (i) the semantic inconsistencies of similar relations, and (ii) noisy interactions inherent in KGs due to the presence of unconvincing knowledge for emerging entities. To address these challenges, we propose a Semantic Structure-aware Denoising Network (S$^2$DN) for inductive KGC. Our goal is to learn adaptable general semantics and reliable structures to distill consistent semantic knowledge while preserving reliable interactions within KGs. Specifically, we introduce a semantic smoothing module over the enclosing subgraphs to retain the universal semantic knowledge of relations. We incorporate a structure refining module to filter out unreliable interactions and offer additional knowledge, retaining robust structure surrounding target links. Extensive experiments conducted on three benchmark KGs demonstrate that S$^2$DN surpasses the performance of state-of-the-art models. These results demonstrate the effectiveness of S$^2$DN in preserving semantic consistency and enhancing the robustness of filtering out unreliable interactions in contaminated KGs.

Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development

Large Language Models (LLMs) have recently demonstrated remarkable performance in general tasks across various fields. However, their effectiveness within specific domains such as drug development remains challenges. To solve these challenges, we introduce \textbf{Y-Mol}, forming a well-established LLM paradigm for the flow of drug development. Y-Mol is a multiscale biomedical knowledge-guided LLM designed to accomplish tasks across lead compound discovery, pre-clinic, and clinic prediction. By integrating millions of multiscale biomedical knowledge and using LLaMA2 as the base LLM, Y-Mol augments the reasoning capability in the biomedical domain by learning from a corpus of publications, knowledge graphs, and expert-designed synthetic data. The capability is further enriched with three types of drug-oriented instructions: description-based prompts from processed publications, semantic-based prompts for extracting associations from knowledge graphs, and template-based prompts for understanding expert knowledge from biomedical tools. Besides, Y-Mol offers a set of LLM paradigms that can autonomously execute the downstream tasks across the entire process of drug development, including virtual screening, drug design, pharmacological properties prediction, and drug-related interaction prediction. Our extensive evaluations of various biomedical sources demonstrate that Y-Mol significantly outperforms general-purpose LLMs in discovering lead compounds, predicting molecular properties, and identifying drug interaction events.

Optimization-based Task and Motion Planning under Signal Temporal Logic Specifications using Logic Network Flow

This paper proposes an optimization-based task and motion planning framework, named ``Logic Network Flow", to integrate signal temporal logic (STL) specifications into efficient mixed-binary linear programmings. In this framework, temporal predicates are encoded as polyhedron constraints on each edge of the network flow, instead of as constraints between the nodes as in the traditional Logic Tree formulation. Synthesized with Dynamic Network Flows, Logic Network Flows render a tighter convex relaxation compared to Logic Trees derived from these STL specifications. Our formulation is evaluated on several multi-robot motion planning case studies. Empirical results demonstrate that our formulation outperforms Logic Tree formulation in terms of computation time for several planning problems. As the problem size scales up, our method still discovers better lower and upper bounds by exploring fewer number of nodes during the branch-and-bound process, although this comes at the cost of increased computational load for each node when exploring branches.

Evaluating Data-driven Performances of Mixed Integer Bilinear Formulations for Book Placement Planning

Mixed integer bilinear programs (MIBLPs) offer tools to resolve robotics motion planning problems with orthogonal rotation matrices or static moment balance, but require long solving times. Recent work utilizing data-driven methods has shown potential to overcome this issue allowing for applications on larger scale problems. To solve mixed-integer bilinear programs online with data-driven methods, several re-formulations exist including mathematical programming with complementary constraints (MPCC), and mixed-integer programming (MIP). In this work, we compare the data-driven performances of various MIBLP reformulations using a book placement problem that has discrete configuration switches and bilinear constraints. The success rate, cost, and solving time are compared along with non-data-driven methods. Our results demonstrate the advantage of using data-driven methods to accelerate the solving speed of MIBLPs, and provide references for users to choose the suitable re-formulation.

Accelerate Hybrid Model Predictive Control using Generalized Benders Decomposition

Hybrid model predictive control with both continuous and discrete variables is widely applicable to robotics tasks. Due to the combinatorial complexity, the solving speed of hybrid MPC can be insufficient for real-time applications. In this paper, we propose to accelerate hybrid MPC using Generalized Benders Decomposition (GBD). GBD enumerates cuts online and stores inside a finite buffer to provide warm-starts for the new problem instances. Leveraging on the sparsity of feasibility cuts, a fast algorithm is designed for Benders master problems. We also propose to construct initial optimality cuts from heuristic solutions allowing GBD to plan for longer time horizons. The proposed algorithm successfully controls a cart-pole system with randomly moving soft-contact walls reaching speeds 2-3 times faster than Gurobi, oftentimes exceeding 1000Hz. It also guides a free-flying robot through a maze with a time horizon of 50 re-planning at 20Hz. The code is available at https://github.com/XuanLin/Benders-MPC.

Fast and Continual Learning for Hybrid Control Policies using Generalized Benders Decomposition

Hybrid model predictive control with both continuous and discrete variables is widely applicable to robotic control tasks, especially those involving contact with the environment. Due to the combinatorial complexity, the solving speed of hybrid MPC can be insufficient for real-time applications. In this paper, we proposed a hybrid MPC solver based on Generalized Benders Decomposition (GBD). The algorithm enumerates and stores cutting planes online inside a finite buffer. After a short cold-start phase, the stored cuts provide warm-starts for the new problem instances to enhance the solving speed. Despite the disturbance and randomly changing environment, the solving speed maintains. Leveraging on the sparsity of feasibility cuts, we also propose a fast algorithm for Benders master problems. Our solver is validated through controlling a cart-pole system with randomly moving soft contact walls, and a free-flying robot navigating around obstacles. The results show that with significantly less data than previous works, the solver reaches competitive speeds to the off-the-shelf solver Gurobi despite the Python overhead.

Learning to Denoise Unreliable Interactions for Link Prediction on Biomedical Knowledge Graph

Link prediction in biomedical knowledge graphs (KGs) aims at predicting unknown interactions between entities, including drug-target interaction (DTI) and drug-drug interaction (DDI), which is critical for drug discovery and therapeutics. Previous methods prefer to utilize the rich semantic relations and topological structure of the KG to predict missing links, yielding promising outcomes. However, all these works only focus on improving the predictive performance without considering the inevitable noise and unreliable interactions existing in the KGs, which limits the development of KG-based computational methods. To address these limitations, we propose a Denoised Link Prediction framework, called DenoisedLP. DenoisedLP obtains reliable interactions based on the local subgraph by denoising noisy links in a learnable way, providing a universal module for mining underlying task-relevant relations. To collaborate with the smoothed semantic information, DenoisedLP introduces the semantic subgraph by blurring conflict relations around the predicted link. By maximizing the mutual information between the reliable structure and smoothed semantic relations, DenoisedLP emphasizes the informative interactions for predicting relation-specific links. Experimental results on real-world datasets demonstrate that DenoisedLP outperforms state-of-the-art methods on DTI and DDI prediction tasks, and verify the effectiveness and robustness of denoising unreliable interactions on the contaminated KGs.

SCALER: Versatile Multi-Limbed Robot for Free-Climbing in Extreme Terrains

This paper presents SCALER, a versatile free-climbing multi-limbed robot that is designed to achieve tightly coupled simultaneous locomotion and dexterous grasping. Although existing quadruped-limbed robots have shown impressive dexterous skills such as object manipulation, it is essential to balance power-intensive locomotion and dexterous grasping capabilities. We design a torso linkage and a parallel-serial limb to meet such conflicting skills that pose unique challenges in the hardware designs. SCALER employs underactuated two-fingered GOAT grippers that can mechanically adapt and offer 7 modes of grasping, enabling SCALER to traverse extreme terrains with multi-modal grasping strategies. We study the whole-body approach, where SCALER uses its body and limbs to generate additional forces for stable grasping with environments, further enhancing versatility. Furthermore, we improve the GOAT gripper actuation speed to realize more dynamic climbing in a closed-loop control fashion. With these proposed technologies, SCALER can traverse vertical, overhang, upside-down, slippery terrains, and bouldering walls with non-convex-shaped climbing holds under the Earth's gravity.

Generalized Benders Decomposition with Continual Learning for Hybrid Model Predictive Control in Dynamic Environment

Hybrid model predictive control (MPC) with both continuous and discrete variables is widely applicable to robotic control tasks, especially those involving contact with the environment. Due to the combinatorial complexity, the solving speed of hybrid MPC can be insufficient for real-time applications. In this paper, we proposed a hybrid MPC solver based on Generalized Benders Decomposition (GBD) with continual learning. The algorithm accumulates cutting planes from the invariant dual space of the subproblems. After a short cold-start phase, the accumulated cuts provide warm-starts for the new problem instances to increase the solving speed. Despite the randomly changing environment that the control is unprepared for, the solving speed maintains. We verified our solver on controlling a cart-pole system with randomly moving soft contact walls and show that the solving speed is 2-3 times faster than the off-the-shelf solver Gurobi.