In recent years, several reaction templates-based and template-free approaches have been reported for single-step retrosynthesis prediction. Even though many of these approaches perform well from traditional data-driven metrics standpoint, there is a disconnect between model architectures used and underlying chemistry principles governing retrosynthesis. Here, we propose a novel chemistry-aware retrosynthesis prediction framework that combines powerful data-driven models with chemistry knowledge. We report a tree-to-sequence transformer architecture based on hierarchical SMILES grammar trees as input containing underlying chemistry information that is otherwise ignored by models based on purely SMILES-based representations. The proposed framework, grammar-based molecular attention tree transformer (G-MATT), achieves significant performance improvements compared to baseline retrosynthesis models. G-MATT achieves a top-1 accuracy of 51% (top-10 accuracy of 79.1%), invalid rate of 1.5%, and bioactive similarity rate of 74.8%. Further analyses based on attention maps demonstrate G-MATT's ability to preserve chemistry knowledge without having to use extremely complex model architectures.
We investigate the feasibility of employing large language models (LLMs) for conducting the security audit of smart contracts, a traditionally time-consuming and costly process. Our research focuses on the optimization of prompt engineering for enhanced security analysis, and we evaluate the performance and accuracy of LLMs using a benchmark dataset comprising 52 Decentralized Finance (DeFi) smart contracts that have previously been compromised. Our findings reveal that, when applied to vulnerable contracts, both GPT-4 and Claude models correctly identify the vulnerability type in 40% of the cases. However, these models also demonstrate a high false positive rate, necessitating continued involvement from manual auditors. The LLMs tested outperform a random model by 20% in terms of F1-score. To ensure the integrity of our study, we conduct mutation testing on five newly developed and ostensibly secure smart contracts, into which we manually insert two and 15 vulnerabilities each. This testing yielded a remarkable best-case 78.7% true positive rate for the GPT-4-32k model. We tested both, asking the models to perform a binary classification on whether a contract is vulnerable, and a non-binary prompt. We also examined the influence of model temperature variations and context length on the LLM's performance. Despite the potential for many further enhancements, this work lays the groundwork for a more efficient and economical approach to smart contract security audits.
Deep learning (DL) is characterised by its dynamic nature, with new deep neural network (DNN) architectures and approaches emerging every few years, driving the field's advancement. At the same time, the ever-increasing use of mobile devices (MDs) has resulted in a surge of DNN-based mobile applications. Although traditional architectures, like CNNs and RNNs, have been successfully integrated into MDs, this is not the case for Transformers, a relatively new model family that has achieved new levels of accuracy across AI tasks, but poses significant computational challenges. In this work, we aim to make steps towards bridging this gap by examining the current state of Transformers' on-device execution. To this end, we construct a benchmark of representative models and thoroughly evaluate their performance across MDs with different computational capabilities. Our experimental results show that Transformers are not accelerator-friendly and indicate the need for software and hardware optimisations to achieve efficient deployment.
Motion prediction for automated vehicles in complex environments is a difficult task that is to be mastered when automated vehicles are to be used in arbitrary situations. Many factors influence the future motion of traffic participants starting with traffic rules and reaching from the interaction between each other to personal habits of human drivers. Therefore we present a novel approach for a graph-based prediction based on a heterogeneous holistic graph representation that combines temporal information, properties and relations between traffic participants as well as relations with static elements like the road network. The information are encoded through different types of nodes and edges that both are enriched with arbitrary features. We evaluated the approach on the INTERACTION and the Argoverse dataset and conducted an informative ablation study to demonstrate the benefit of different types of information for the motion prediction quality.
Denoising diffusion probabilistic models (DDPMs) have recently taken the field of generative modeling by storm, pioneering new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided protein design. Along this latter line of research, methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a DDPM framework. However, such methods are unable to learn important geometric and physical properties of 3D molecules during molecular graph generation, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which negatively impacts their ability to effectively scale to datasets of large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset as well as for the larger GEOM-Drugs dataset. Importantly, we demonstrate that the geometry-complete denoising process GCDM learns for 3D molecule generation allows the model to generate realistic and stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that GCDM's geometric features can effectively be repurposed to directly optimize the geometry and chemical composition of existing 3D molecules for specific molecular properties, demonstrating new, real-world versatility of molecular diffusion models. Our source code, data, and reproducibility instructions are freely available at //github.com/BioinfoMachineLearning/Bio-Diffusion.
With the increasing popularity of Internet of Things (IoT) devices, there is a growing need for energy-efficient Machine Learning (ML) models that can run on constrained edge nodes. Decision tree ensembles, such as Random Forests (RFs) and Gradient Boosting (GBTs), are particularly suited for this task, given their relatively low complexity compared to other alternatives. However, their inference time and energy costs are still significant for edge hardware. Given that said costs grow linearly with the ensemble size, this paper proposes the use of dynamic ensembles, that adjust the number of executed trees based both on a latency/energy target and on the complexity of the processed input, to trade-off computational cost and accuracy. We focus on deploying these algorithms on multi-core low-power IoT devices, designing a tool that automatically converts a Python ensemble into optimized C code, and exploring several optimizations that account for the available parallelism and memory hierarchy. We extensively benchmark both static and dynamic RFs and GBTs on three state-of-the-art IoT-relevant datasets, using an 8-core ultra-lowpower System-on-Chip (SoC), GAP8, as the target platform. Thanks to the proposed early-stopping mechanisms, we achieve an energy reduction of up to 37.9% with respect to static GBTs (8.82 uJ vs 14.20 uJ per inference) and 41.7% with respect to static RFs (2.86 uJ vs 4.90 uJ per inference), without losing accuracy compared to the static model.
Transformer is popular in recent 3D human pose estimation, which utilizes long-term modeling to lift 2D keypoints into the 3D space. However, current transformer-based methods do not fully exploit the prior knowledge of the human skeleton provided by the kinematic structure. In this paper, we propose a novel transformer-based model EvoPose to introduce the human body prior knowledge for 3D human pose estimation effectively. Specifically, a Structural Priors Representation (SPR) module represents human priors as structural features carrying rich body patterns, e.g. joint relationships. The structural features are interacted with 2D pose sequences and help the model to achieve more informative spatiotemporal features. Moreover, a Recursive Refinement (RR) module is applied to refine the 3D pose outputs by utilizing estimated results and further injects human priors simultaneously. Extensive experiments demonstrate the effectiveness of EvoPose which achieves a new state of the art on two most popular benchmarks, Human3.6M and MPI-INF-3DHP.
Adaptive sampling and planning in robotic environmental monitoring are challenging when the target environmental process varies over space and time. The underlying environmental dynamics require the planning module to integrate future environmental changes so that action decisions made earlier do not quickly become outdated. We propose a Monte Carlo tree search method which not only well balances the environment exploration and exploitation in space, but also catches up to the temporal environmental dynamics. This is achieved by incorporating multi-objective optimization and a look-ahead model-predictive rewarding mechanism. We show that by allowing the robot to leverage the simulated and predicted spatiotemporal environmental process, the proposed informative planning approach achieves a superior performance after comparing with other baseline methods in terms of the root mean square error of the environment model and the distance to the ground truth.
Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecule property by GNNs is the scarcity of labeled data. Though graph contrastive learning (GCL) methods have achieved extraordinary performance with insufficient labeled data, most focused on designing data augmentation schemes for general graphs. However, the fundamental property of a molecule could be altered with the augmentation method (like random perturbation) on molecular graphs. Whereas, the critical geometric information of molecules remains rarely explored under the current GNN and GCL architectures. To this end, we propose a novel graph contrastive learning method utilizing the geometry of the molecule across 2D and 3D views, which is named GeomGCL. Specifically, we first devise a dual-view geometric message passing network (GeomMPNN) to adaptively leverage the rich information of both 2D and 3D graphs of a molecule. The incorporation of geometric properties at different levels can greatly facilitate the molecular representation learning. Then a novel geometric graph contrastive scheme is designed to make both geometric views collaboratively supervise each other to improve the generalization ability of GeomMPNN. We evaluate GeomGCL on various downstream property prediction tasks via a finetune process. Experimental results on seven real-life molecular datasets demonstrate the effectiveness of our proposed GeomGCL against state-of-the-art baselines.
Humans perceive the world by concurrently processing and fusing high-dimensional inputs from multiple modalities such as vision and audio. Machine perception models, in stark contrast, are typically modality-specific and optimised for unimodal benchmarks, and hence late-stage fusion of final representations or predictions from each modality (`late-fusion') is still a dominant paradigm for multimodal video classification. Instead, we introduce a novel transformer based architecture that uses `fusion bottlenecks' for modality fusion at multiple layers. Compared to traditional pairwise self-attention, our model forces information between different modalities to pass through a small number of bottleneck latents, requiring the model to collate and condense the most relevant information in each modality and only share what is necessary. We find that such a strategy improves fusion performance, at the same time reducing computational cost. We conduct thorough ablation studies, and achieve state-of-the-art results on multiple audio-visual classification benchmarks including Audioset, Epic-Kitchens and VGGSound. All code and models will be released.
Relying entirely on an attention mechanism, the Transformer introduced by Vaswani et al. (2017) achieves state-of-the-art results for machine translation. In contrast to recurrent and convolutional neural networks, it does not explicitly model relative or absolute position information in its structure. Instead, it requires adding representations of absolute positions to its inputs. In this work we present an alternative approach, extending the self-attention mechanism to efficiently consider representations of the relative positions, or distances between sequence elements. On the WMT 2014 English-to-German and English-to-French translation tasks, this approach yields improvements of 1.3 BLEU and 0.3 BLEU over absolute position representations, respectively. Notably, we observe that combining relative and absolute position representations yields no further improvement in translation quality. We describe an efficient implementation of our method and cast it as an instance of relation-aware self-attention mechanisms that can generalize to arbitrary graph-labeled inputs.