Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks

Graph Neural Networks (GNNs) have gained considerable traction for their capability to effectively process topological data, yet their interpretability remains a critical concern. Current interpretation methods are dominated by post-hoc explanations to provide a transparent and intuitive understanding of GNNs. However, they have limited performance in interpreting complicated subgraphs and can't utilize the explanation to advance GNN predictions. On the other hand, transparent GNN models are proposed to capture critical subgraphs. While such methods could improve GNN predictions, they usually don't perform well on explanations. Thus, it is desired for a new strategy to better couple GNN explanation and prediction. In this study, we have developed a novel interpretable causal GNN framework that incorporates retrieval-based causal learning with Graph Information Bottleneck (GIB) theory. The framework could semi-parametrically retrieve crucial subgraphs detected by GIB and compress the explanatory subgraphs via a causal module. The framework was demonstrated to consistently outperform state-of-the-art methods, and to achieve 32.71\% higher precision on real-world explanation scenarios with diverse explanation types. More importantly, the learned explanations were shown able to also improve GNN prediction performance.

Node-based Knowledge Graph Contrastive Learning for Medical Relationship Prediction

The embedding of Biomedical Knowledge Graphs (BKGs) generates robust representations, valuable for a variety of artificial intelligence applications, including predicting drug combinations and reasoning disease-drug relationships. Meanwhile, contrastive learning (CL) is widely employed to enhance the distinctiveness of these representations. However, constructing suitable contrastive pairs for CL, especially within Knowledge Graphs (KGs), has been challenging. In this paper, we proposed a novel node-based contrastive learning method for knowledge graph embedding, NC-KGE. NC-KGE enhances knowledge extraction in embeddings and speeds up training convergence by constructing appropriate contrastive node pairs on KGs. This scheme can be easily integrated with other knowledge graph embedding (KGE) methods. For downstream task such as biochemical relationship prediction, we have incorporated a relation-aware attention mechanism into NC-KGE, focusing on the semantic relationships and node interactions. Extensive experiments show that NC-KGE performs competitively with state-of-the-art models on public datasets like FB15k-237 and WN18RR. Particularly in biomedical relationship prediction tasks, NC-KGE outperforms all baselines on datasets such as PharmKG8k-28, DRKG17k-21, and BioKG72k-14, especially in predicting drug combination relationships. We release our code at https://github.com/zhi520/NC-KGE.

Efficient Low-rank Backpropagation for Vision Transformer Adaptation

The increasing scale of vision transformers (ViT) has made the efficient fine-tuning of these large models for specific needs a significant challenge in various applications. This issue originates from the computationally demanding matrix multiplications required during the backpropagation process through linear layers in ViT. In this paper, we tackle this problem by proposing a new Low-rank BackPropagation via Walsh-Hadamard Transformation (LBP-WHT) method. Intuitively, LBP-WHT projects the gradient into a low-rank space and carries out backpropagation. This approach substantially reduces the computation needed for adapting ViT, as matrix multiplication in the low-rank space is far less resource-intensive. We conduct extensive experiments with different models (ViT, hybrid convolution-ViT model) on multiple datasets to demonstrate the effectiveness of our method. For instance, when adapting an EfficientFormer-L1 model on CIFAR100, our LBP-WHT achieves 10.4% higher accuracy than the state-of-the-art baseline, while requiring 9 MFLOPs less computation. As the first work to accelerate ViT adaptation with low-rank backpropagation, our LBP-WHT method is complementary to many prior efforts and can be combined with them for better performance.

TIPS: Topologically Important Path Sampling for Anytime Neural Networks

Anytime neural networks (AnytimeNNs) are a promising solution to adaptively adjust the model complexity at runtime under various hardware resource constraints. However, the manually-designed AnytimeNNs are biased by designers' prior experience and thus provide sub-optimal solutions. To address the limitations of existing hand-crafted approaches, we first model the training process of AnytimeNNs as a discrete-time Markov chain (DTMC) and use it to identify the paths that contribute the most to the training of AnytimeNNs. Based on this new DTMC-based analysis, we further propose TIPS, a framework to automatically design AnytimeNNs under various hardware constraints. Our experimental results show that TIPS can improve the convergence rate and test accuracy of AnytimeNNs. Compared to the existing AnytimeNNs approaches, TIPS improves the accuracy by 2%-6.6% on multiple datasets and achieves SOTA accuracy-FLOPs tradeoffs.

Retrieval-based Knowledge Augmented Vision Language Pre-training

With recent progress in large-scale vision and language representation learning, Vision Language Pretraining (VLP) models have achieved promising improvements on various multi-modal downstream tasks. Albeit powerful, these pre-training models still do not take advantage of world knowledge, which is implicit in multi-modal data but comprises abundant and complementary information. In this work, we propose a REtrieval-based knowledge Augmented Vision Language Pre-training model (REAVL), which retrieves world knowledge from knowledge graphs (KGs) and incorporates them in vision-language pre-training. REAVL has two core components: a knowledge retriever that retrieves knowledge given multi-modal data, and a knowledge-augmented model that fuses multi-modal data and knowledge. By novelly unifying four knowledge-aware self-supervised tasks, REAVL promotes the mutual integration of multi-modal data and knowledge by fusing explicit knowledge with vision-language pairs for masked multi-modal data modeling and KG relational reasoning. Empirical experiments show that REAVL achieves new state-of-the-art performance uniformly on knowledge-based vision-language understanding and multimodal entity linking tasks, and competitive results on general vision-language tasks while only using 0.2% pre-training data of the best models.

ZiCo: Zero-shot NAS via Inverse Coefficient of Variation on Gradients

Neural Architecture Search (NAS) is widely used to automatically design the neural network with the best performance among a large number of candidate architectures. To reduce the search time, zero-shot NAS aims at designing training-free proxies that can predict the test performance of a given architecture. However, as shown recently, none of the zero-shot proxies proposed to date can actually work consistently better than a naive proxy, namely, the number of network parameters (#Params). To improve this state of affairs, as the main theoretical contribution, we first reveal how some specific gradient properties across different samples impact the convergence rate and generalization capacity of neural networks. Based on this theoretical analysis, we propose a new zero-shot proxy, ZiCo, the first proxy that works consistently better than #Params. We demonstrate that ZiCo works better than State-Of-The-Art (SOTA) proxies on several popular NAS-Benchmarks (NASBench101, NATSBench-SSS/TSS, TransNASBench-101) for multiple applications (e.g., image classification/reconstruction and pixel-level prediction). Finally, we demonstrate that the optimal architectures found via ZiCo are as competitive as the ones found by one-shot and multi-shot NAS methods, but with much less search time. For example, ZiCo-based NAS can find optimal architectures with 78.1%, 79.4%, and 80.4% test accuracy under inference budgets of 450M, 600M, and 1000M FLOPs on ImageNet within 0.4 GPU days.

Efficient On-device Training via Gradient Filtering

Despite its importance for federated learning, continuous learning and many other applications, on-device training remains an open problem for EdgeAI. The problem stems from the large number of operations (e.g., floating point multiplications and additions) and memory consumption required during training by the back-propagation algorithm. Consequently, in this paper, we propose a new gradient filtering approach which enables on-device DNN model training. More precisely, our approach creates a special structure with fewer unique elements in the gradient map, thus significantly reducing the computational complexity and memory consumption of back propagation during training. Extensive experiments on image classification and semantic segmentation with multiple DNN models (e.g., MobileNet, DeepLabV3, UPerNet) and devices (e.g., Raspberry Pi and Jetson Nano) demonstrate the effectiveness and wide applicability of our approach. For example, compared to SOTA, we achieve up to 19$\times$ speedup and 77.1% memory savings on ImageNet classification with only 0.1% accuracy loss. Finally, our method is easy to implement and deploy; over 20$\times$ speedup and 90% energy savings have been observed compared to highly optimized baselines in MKLDNN and CUDNN on NVIDIA Jetson Nano. Consequently, our approach opens up a new direction of research with a huge potential for on-device training.

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc. In addition, existing methods either heavily rely on high-quality domain features or are intrinsically transductive, which limits the capacity of models to generalize to drugs/genes that lack external information or are unseen during the training process. To address these problems, we propose a novel Communicative Subgraph representation learning for Multi-relational Inductive drug-Gene interactions prediction (CoSMIG), where the predictions of drug-gene relations are made through subgraph patterns, and thus are naturally inductive for unseen drugs/genes without retraining or utilizing external domain features. Moreover, the model strengthened the relations on the drug-gene graph through a communicative message passing mechanism. To evaluate our method, we compiled two new benchmark datasets from DrugBank and DGIdb. The comprehensive experiments on the two datasets showed that our method outperformed state-of-the-art baselines in the transductive scenarios and achieved superior performance in the inductive ones. Further experimental analysis including LINCS experimental validation and literature verification also demonstrated the value of our model.

SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning

Graph Neural Networks (GNNs) have demonstrated a great potential in a variety of graph-based applications, such as recommender systems, drug discovery, and object recognition. Nevertheless, resource-efficient GNN learning is a rarely explored topic despite its many benefits for edge computing and Internet of Things (IoT) applications. To improve this state of affairs, this work proposes efficient subgraph-level training via resource-aware graph partitioning (SUGAR). SUGAR first partitions the initial graph into a set of disjoint subgraphs and then performs local training at the subgraph-level. We provide a theoretical analysis and conduct extensive experiments on five graph benchmarks to verify its efficacy in practice. Our results show that SUGAR can achieve up to 33 times runtime speedup and 3.8 times memory reduction on large-scale graphs. We believe SUGAR opens a new research direction towards developing GNN methods that are resource-efficient, hence suitable for IoT deployment.