GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning

Glycans are basic biomolecules and perform essential functions within living organisms. The rapid increase of functional glycan data provides a good opportunity for machine learning solutions to glycan understanding. However, there still lacks a standard machine learning benchmark for glycan function prediction. In this work, we fill this blank by building a comprehensive benchmark for Glycan Machine Learning (GlycanML). The GlycanML benchmark consists of diverse types of tasks including glycan taxonomy prediction, glycan immunogenicity prediction, glycosylation type prediction, and protein-glycan interaction prediction. Glycans can be represented by both sequences and graphs in GlycanML, which enables us to extensively evaluate sequence-based models and graph neural networks (GNNs) on benchmark tasks. Furthermore, by concurrently performing eight glycan taxonomy prediction tasks, we introduce the GlycanML-MTL testbed for multi-task learning (MTL) algorithms. Experimental results show the superiority of modeling glycans with multi-relational GNNs, and suitable MTL methods can further boost model performance. We provide all datasets and source codes at https://github.com/GlycanML/GlycanML and maintain a leaderboard at https://GlycanML.github.io/project

DoLLM: How Large Language Models Understanding Network Flow Data to Detect Carpet Bombing DDoS

It is an interesting question Can and How Large Language Models (LLMs) understand non-language network data, and help us detect unknown malicious flows. This paper takes Carpet Bombing as a case study and shows how to exploit LLMs' powerful capability in the networking area. Carpet Bombing is a new DDoS attack that has dramatically increased in recent years, significantly threatening network infrastructures. It targets multiple victim IPs within subnets, causing congestion on access links and disrupting network services for a vast number of users. Characterized by low-rates, multi-vectors, these attacks challenge traditional DDoS defenses. We propose DoLLM, a DDoS detection model utilizes open-source LLMs as backbone. By reorganizing non-contextual network flows into Flow-Sequences and projecting them into LLMs semantic space as token embeddings, DoLLM leverages LLMs' contextual understanding to extract flow representations in overall network context. The representations are used to improve the DDoS detection performance. We evaluate DoLLM with public datasets CIC-DDoS2019 and real NetFlow trace from Top-3 countrywide ISP. The tests have proven that DoLLM possesses strong detection capabilities. Its F1 score increased by up to 33.3% in zero-shot scenarios and by at least 20.6% in real ISP traces.

AAT: Adapting Audio Transformer for Various Acoustics Recognition Tasks

Recently, Transformers have been introduced into the field of acoustics recognition. They are pre-trained on large-scale datasets using methods such as supervised learning and semi-supervised learning, demonstrating robust generality--It fine-tunes easily to downstream tasks and shows more robust performance. However, the predominant fine-tuning method currently used is still full fine-tuning, which involves updating all parameters during training. This not only incurs significant memory usage and time costs but also compromises the model's generality. Other fine-tuning methods either struggle to address this issue or fail to achieve matching performance. Therefore, we conducted a comprehensive analysis of existing fine-tuning methods and proposed an efficient fine-tuning approach based on Adapter tuning, namely AAT. The core idea is to freeze the audio Transformer model and insert extra learnable Adapters, efficiently acquiring downstream task knowledge without compromising the model's original generality. Extensive experiments have shown that our method achieves performance comparable to or even superior to full fine-tuning while optimizing only 7.118% of the parameters. It also demonstrates superiority over other fine-tuning methods.

Integrated Traffic Simulation-Prediction System using Neural Networks with Application to the Los Angeles International Airport Road Network

Transportation networks are highly complex and the design of efficient traffic management systems is difficult due to lack of adequate measured data and accurate predictions of the traffic states. Traffic simulation models can capture the complex dynamics of transportation networks by using limited available traffic data and can help central traffic authorities in their decision-making, if appropriate input is fed into the simulator. In this paper, we design an integrated simulation-prediction system which estimates the Origin-Destination (OD) matrix of a road network using only flow rate information and predicts the behavior of the road network in different simulation scenarios. The proposed system includes an optimization-based OD matrix generation method, a Neural Network (NN) model trained to predict OD matrices via the pattern of traffic flow and a microscopic traffic simulator with a Dynamic Traffic Assignment (DTA) scheme to predict the behavior of the transportation system. We test the proposed system on the road network of the central terminal area (CTA) of the Los Angeles International Airport (LAX), which demonstrates that the integrated traffic simulation-prediction system can be used to simulate the effects of several real world scenarios such as lane closures, curbside parking and other changes. The model is an effective tool for learning the impact and possible benefits of changes in the network and for analyzing scenarios at a very low cost without disrupting the network.