Hashing for Protein Structure Similarity Search

Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional alignment-based PSSS methods, which directly calculate alignment on the protein structures, are highly time-consuming with high memory cost. Recently, alignment-free methods, which represent protein structures as fixed-length real-valued vectors, are proposed for PSSS. Although these methods have lower time and memory cost than alignment-based methods, their time and memory cost is still too high for large-scale PSSS, and their accuracy is unsatisfactory. In this paper, we propose a novel method, called $\underline{\text{p}}$r$\underline{\text{o}}$tein $\underline{\text{s}}$tructure $\underline{\text{h}}$ashing (POSH), for PSSS. POSH learns a binary vector representation for each protein structure, which can dramatically reduce the time and memory cost for PSSS compared with real-valued vector representation based methods. Furthermore, in POSH we also propose expressive hand-crafted features and a structure encoder to well model both node and edge interactions in proteins. Experimental results on real datasets show that POSH can outperform other methods to achieve state-of-the-art accuracy. Furthermore, POSH achieves a memory saving of more than six times and speed improvement of more than four times, compared with other methods.

Hashing based Contrastive Learning for Virtual Screening

Virtual screening (VS) is a critical step in computer-aided drug discovery, aiming to identify molecules that bind to a specific target receptor like protein. Traditional VS methods, such as docking, are often too time-consuming for screening large-scale molecular databases. Recent advances in deep learning have demonstrated that learning vector representations for both proteins and molecules using contrastive learning can outperform traditional docking methods. However, given that target databases often contain billions of molecules, real-valued vector representations adopted by existing methods can still incur significant memory and time costs in VS. To address this problem, in this paper we propose a hashing-based contrastive learning method, called DrugHash, for VS. DrugHash treats VS as a retrieval task that uses efficient binary hash codes for retrieval. In particular, DrugHash designs a simple yet effective hashing strategy to enable end-to-end learning of binary hash codes for both protein and molecule modalities, which can dramatically reduce the memory and time costs with higher accuracy compared with existing methods. Experimental results show that DrugHash can outperform existing methods to achieve state-of-the-art accuracy, with a memory saving of 32$\times$ and a speed improvement of 3.5$\times$.

Ordered Momentum for Asynchronous SGD

Distributed learning is indispensable for training large-scale deep models. Asynchronous SGD~(ASGD) and its variants are commonly used distributed learning methods in many scenarios where the computing capabilities of workers in the cluster are heterogeneous. Momentum has been acknowledged for its benefits in both optimization and generalization in deep model training. However, existing works have found that naively incorporating momentum into ASGD can impede the convergence. In this paper, we propose a novel method, called ordered momentum (OrMo), for ASGD. In OrMo, momentum is incorporated into ASGD by organizing the gradients in order based on their iteration indexes. We theoretically prove the convergence of OrMo for non-convex problems. To the best of our knowledge, this is the first work to establish the convergence analysis of ASGD with momentum without relying on the bounded delay assumption. Empirical results demonstrate that OrMo can achieve better convergence performance compared with ASGD and other asynchronous methods with momentum.

Buffered Asynchronous Secure Aggregation for Cross-Device Federated Learning

Asynchronous federated learning (AFL) is an effective method to address the challenge of device heterogeneity in cross-device federated learning. However, AFL is usually incompatible with existing secure aggregation protocols used to protect user privacy in federated learning because most existing secure aggregation protocols are based on synchronous aggregation. To address this problem, we propose a novel secure aggregation protocol named buffered asynchronous secure aggregation (BASA) in this paper. Compared with existing protocols, BASA is fully compatible with AFL and provides secure aggregation under the condition that each user only needs one round of communication with the server without relying on any synchronous interaction among users. Based on BASA, we propose the first AFL method which achieves secure aggregation without extra requirements on hardware. We empirically demonstrate that BASA outperforms existing secure aggregation protocols for cross-device federated learning in terms of training efficiency and scalability.

LCQ: Low-Rank Codebook based Quantization for Large Language Models

Large language models~(LLMs) have recently demonstrated promising performance in many tasks. However, the high storage and computational cost of LLMs has become a challenge for deploying LLMs. Weight quantization has been widely used for model compression, which can reduce both storage and computational cost. Most existing weight quantization methods for LLMs use a rank-one codebook for quantization, which results in substantial accuracy loss when the compression ratio is high. In this paper, we propose a novel weight quantization method, called low-rank codebook based quantization~(LCQ), for LLMs. LCQ adopts a low-rank codebook, the rank of which can be larger than one, for quantization. Experiments show that LCQ can achieve better accuracy than existing methods with a negligibly extra storage cost.

NumLLM: Numeric-Sensitive Large Language Model for Chinese Finance

Recently, many works have proposed various financial large language models (FinLLMs) by pre-training from scratch or fine-tuning open-sourced LLMs on financial corpora. However, existing FinLLMs exhibit unsatisfactory performance in understanding financial text when numeric variables are involved in questions. In this paper, we propose a novel LLM, called numeric-sensitive large language model (NumLLM), for Chinese finance. We first construct a financial corpus from financial textbooks which is essential for improving numeric capability of LLMs during fine-tuning. After that, we train two individual low-rank adaptation (LoRA) modules by fine-tuning on our constructed financial corpus. One module is for adapting general-purpose LLMs to financial domain, and the other module is for enhancing the ability of NumLLM to understand financial text with numeric variables. Lastly, we merge the two LoRA modules into the foundation model to obtain NumLLM for inference. Experiments on financial question-answering benchmark show that NumLLM can boost the performance of the foundation model and can achieve the best overall performance compared to all baselines, on both numeric and non-numeric questions.

InfLoRA: Interference-Free Low-Rank Adaptation for Continual Learning

Continual learning requires the model to learn multiple tasks sequentially. In continual learning, the model should possess the ability to maintain its performance on old tasks (stability) and the ability to adapt to new tasks continuously (plasticity). Recently, parameter-efficient fine-tuning (PEFT), which involves freezing a pre-trained model and injecting a small number of learnable parameters to adapt to downstream tasks, has gained increasing popularity in continual learning. Although existing continual learning methods based on PEFT have demonstrated superior performance compared to those not based on PEFT, most of them do not consider how to eliminate the interference of the new task on the old tasks, which inhibits the model from making a good trade-off between stability and plasticity. In this work, we propose a new PEFT method, called interference-free low-rank adaptation (InfLoRA), for continual learning. InfLoRA injects a small number of parameters to reparameterize the pre-trained weights and shows that fine-tuning these injected parameters is equivalent to fine-tuning the pre-trained weights within a subspace. Furthermore, InfLoRA designs this subspace to eliminate the interference of the new task on the old tasks, making a good trade-off between stability and plasticity. Experimental results show that InfLoRA outperforms existing state-of-the-art continual learning methods on multiple datasets.

UniAP: Unifying Inter- and Intra-Layer Automatic Parallelism by Mixed Integer Quadratic Programming

Deep learning models have demonstrated impressive performance in various domains. However, the prolonged training time of these models remains a critical problem. Manually designed parallel training strategies could enhance efficiency but require considerable time and deliver little flexibility. Hence, automatic parallelism is proposed to automate the parallel strategy searching process. Even so, existing approaches suffer from sub-optimal strategy space because they treat automatic parallelism as two independent stages, namely inter- and intra-layer parallelism. To address this issue, we propose UniAP, which utilizes mixed integer quadratic programming to unify inter- and intra-layer automatic parallelism. To the best of our knowledge, UniAP is the first work to unify these two categories to search for a globally optimal strategy. The experimental results show that UniAP outperforms state-of-the-art methods by up to 1.70$\times$ in throughput and reduces strategy searching time by up to 16$\times$ across four Transformer-like models.

On the Optimal Batch Size for Byzantine-Robust Distributed Learning

Byzantine-robust distributed learning (BRDL), in which computing devices are likely to behave abnormally due to accidental failures or malicious attacks, has recently become a hot research topic. However, even in the independent and identically distributed (i.i.d.) case, existing BRDL methods will suffer from a significant drop on model accuracy due to the large variance of stochastic gradients. Increasing batch sizes is a simple yet effective way to reduce the variance. However, when the total number of gradient computation is fixed, a too-large batch size will lead to a too-small iteration number (update number), which may also degrade the model accuracy. In view of this challenge, we mainly study the optimal batch size when the total number of gradient computation is fixed in this work. In particular, we theoretically and empirically show that when the total number of gradient computation is fixed, the optimal batch size in BRDL increases with the fraction of Byzantine workers. Therefore, compared to the case without attacks, the batch size should be set larger when under Byzantine attacks. However, for existing BRDL methods, large batch sizes will lead to a drop on model accuracy, even if there is no Byzantine attack. To deal with this problem, we propose a novel BRDL method, called Byzantine-robust stochastic gradient descent with normalized momentum (ByzSGDnm), which can alleviate the drop on model accuracy in large-batch cases. Moreover, we theoretically prove the convergence of ByzSGDnm for general non-convex cases under Byzantine attacks. Empirical results show that ByzSGDnm has a comparable performance to existing BRDL methods under bit-flipping failure, but can outperform existing BRDL methods under deliberately crafted attacks.

GNNFormer: A Graph-based Framework for Cytopathology Report Generation

Cytopathology report generation is a necessary step for the standardized examination of pathology images. However, manually writing detailed reports brings heavy workloads for pathologists. To improve efficiency, some existing works have studied automatic generation of cytopathology reports, mainly by applying image caption generation frameworks with visual encoders originally proposed for natural images. A common weakness of these works is that they do not explicitly model the structural information among cells, which is a key feature of pathology images and provides significant information for making diagnoses. In this paper, we propose a novel graph-based framework called GNNFormer, which seamlessly integrates graph neural network (GNN) and Transformer into the same framework, for cytopathology report generation. To the best of our knowledge, GNNFormer is the first report generation method that explicitly models the structural information among cells in pathology images. It also effectively fuses structural information among cells, fine-grained morphology features of cells and background features to generate high-quality reports. Experimental results on the NMI-WSI dataset show that GNNFormer can outperform other state-of-the-art baselines.