Combinatorial optimization problems are typically tackled by the branch-and-bound paradigm. We propose a new graph convolutional neural network model for learning branch-and-bound variable selection policies, which leverages the natural variable-constraint bipartite graph representation of mixed-integer linear programs. We train our model via imitation learning from the strong branching expert rule, and demonstrate on a series of hard problems that our approach produces policies that improve upon state-of-the-art machine-learning methods for branching and generalize to instances significantly larger than seen during training. Moreover, we improve for the first time over expert-designed branching rules implemented in a state-of-the-art solver on large problems.

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models (PLMs). Others use Graph Neural Networks (GNNs) for 3D protein structures. This study explores less computationally intensive alternatives. We introduce a novel framework for downstream PPI prediction through link prediction. Methods We introduce a two-stage graph representation learning framework, ProtGram-DirectGCN. First, we developed ProtGram. This approach models a protein's primary structure as a hierarchy of globally inferred n-gram graphs. In these graphs, residue transition probabilities define edge weights. Each edge connects a pair of residues in a directed graph. The probabilities are aggregated from a large corpus of sequences. Second, we propose DirectGCN, a custom directed graph convolutional neural network. This model features a unique convolutional layer. It processes information through separate path-specific transformations: incoming, outgoing, and undirected. A shared transformation is also applied. These paths are combined via a learnable gating mechanism. We apply DirectGCN to ProtGram graphs to learn residue-level embeddings. These embeddings are pooled via attention to generate protein-level embeddings for prediction. Results We first established the efficacy of DirectGCN on standard node classification benchmarks. Its performance matches established methods on general datasets. The model excels at complex, directed graphs with dense, heterophilic structures. When applied to PPI prediction, the full ProtGram-DirectGCN framework delivers robust predictive power. This strong performance holds even with limited training data.

Neural Information Processing Systems http://nips.cc/

Insomnia affects a vast population of the world and can have a wide range of causes. Existing treatments for insomnia have been linked with many side effects like headaches, dizziness, etc. As such, there is a clear need for improved insomnia treatment. Brain modelling has helped with assessing the effects of brain pathology on brain network dynamics and with supporting clinical decisions in the treatment of Alzheimer's disease, epilepsy, etc. However, such models have not been developed for insomnia. Therefore, this project attempts to understand the characteristics of the brain of individuals experiencing insomnia using continuous long-duration EEG data. Brain networks are derived based on functional connectivity and spatial distance between EEG channels. The power spectral density of the channels is then computed for the major brain wave frequency bands. A graph convolutional neural network (GCNN) model is then trained to capture the functional characteristics associated with insomnia and configured for the classification task to judge performance. Results indicated a 50-second non-overlapping sliding window was the most suitable choice for EEG segmentation. This approach achieved a classification accuracy of 70% at window level and 68% at subject level. Additionally, the omission of EEG channels C4-P4, F4-C4 and C4-A1 caused higher degradation in model performance than the removal of other channels. These channel electrodes are positioned near brain regions known to exhibit atypical levels of functional connectivity in individuals with insomnia, which can explain such results.

Update following rebuttal: thanks for taking the time to run additional experiments and reporting back! I am generally supportive of the paper and as such have increased my score to 7. I hope the updates about related work will be incorporated if the paper is accepted, as well as additional experiments you found added value. Summary: This paper proposes an imitation learning approach for learning a branching strategy for integer programming. Key to this approach is the use of a graph neural network representation of the integer programs, together with feature engineering. This work differs from other recent learning-to-branch approaches in that the learning task, using imitation, might be simpler than previous ranking or regression formulations, and that the graph neural network can capture structural information of the instance beyond the simple handcrafted features of previous work.

The reviewers have converged to support the paper but there are still some issues with the fairness of the experimental evaluation. I would like to strongly encourage the authors to update the paper according to the suggestions.

Graph convolutional neural networks (GCNs) have shown tremendous promise in addressing data-intensive challenges in recent years. In particular, some attempts have been made to improve predictions of Susceptible-Infected-Recovered (SIR) models by incorporating human mobility between metapopulations and using graph approaches to estimate corresponding hyperparameters. Recently, researchers have found that a hybrid GCN-SIR approach outperformed existing methodologies when used on the data collected on a precinct level in Japan. In our work, we extend this approach to data collected from the continental US, adjusting for the differing mobility patterns and varying policy responses. We also develop the strategy for real-time continuous estimation of the reproduction number and study the accuracy of model predictions for the overall population as well as individual states. Strengths and limitations of the GCN-SIR approach are discussed as a potential candidate for modeling disease dynamics.

Electronic commerce, or e-commerce, is the buying and selling of goods and services, or the transmitting of funds or data online. E-commerce platforms come in many kinds, with global players such as Amazon, Airbnb, Alibaba, eBay and platforms targeting specific geographic regions. Information retrieval has a natural role to play in e-commerce, especially in connecting people to goods and services. Information discovery in e-commerce concerns different types of search (e.g., exploratory search vs. lookup tasks), recommender systems, and natural language processing in e-commerce portals. The rise in popularity of e-commerce sites has made research on information discovery in e-commerce an increasingly active research area. This is witnessed by an increase in publications and dedicated workshops in this space. Methods for information discovery in e-commerce largely focus on improving the effectiveness of e-commerce search and recommender systems, on enriching and using knowledge graphs to support e-commerce, and on developing innovative question answering and bot-based solutions that help to connect people to goods and services. In this survey, an overview is given of the fundamental infrastructure, algorithms, and technical solutions for information discovery in e-commerce. The topics covered include user behavior and profiling, search, recommendation, and language technology in e-commerce.

Combinatorial optimization problems are typically tackled by the branch-and-bound paradigm. We propose a new graph convolutional neural network model for learning branch-and-bound variable selection policies, which leverages the natural variable-constraint bipartite graph representation of mixed-integer linear programs. We train our model via imitation learning from the strong branching expert rule, and demonstrate on a series of hard problems that our approach produces policies that improve upon state-of-the-art machine-learning methods for branching and generalize to instances significantly larger than seen during training. Moreover, we improve for the first time over expert-designed branching rules implemented in a state-of-the-art solver on large problems.

As global temperatures continue to rise, the need for effective and systematic evaluation of climate intervention strategies becomes increasingly important. Stratospheric Aerosol Injection (SAI) is one such strategy and like all brings significant risks [4, 17] necessitating careful planning and evaluation of the positive and negative impacts. The Performance Assessment (PA) framework, a methodology originally designed for nuclear waste management [13], can be applied to the assessment of climate intervention strategies. The Performance Assessment for Climate Intervention (PACI) framework[19] adapts the PA methodology to evaluate SAI by establishing a set of performance goals, identifying relevant system features, events, and processes (FEPs), and assessing the system's performance, including uncertainties, against these goals. The PACI framework aims to provide a structured and quantifiable approach to evaluate the risks and benefits of SAI in comparison to other climate pathways.