pwc-archive/papers-with-abstracts huggingface dataset:
MCNC: Manifold Constrained Network Compression
Authors: Chayne Thrash, Ali Abbasi, Parsa Nooralinejad, Soroush Abbasi Koohpayegani, Reed Andreas, Hamed Pirsiavash, Soheil Kolouri
Date: 2024-06-27 00:00:00
Tasks: Model Compression, Quantization

The outstanding performance of large foundational models across diverse tasks-from computer vision to speech and natural language processing-has significantly increased their demand. However, storing and transmitting these models pose significant challenges due to their massive size (e.g., 350GB for GPT-3). Recent literature has focused on compressing the original weights or reducing the number of parameters required for fine-tuning these models. These compression methods typically involve constraining the parameter space, for example, through low-rank reparametrization (e.g., LoRA) or quantization (e.g., QLoRA) during model training. In this paper, we present MCNC as a novel model compression method that constrains the parameter space to low-dimensional pre-defined and frozen nonlinear manifolds, which effectively cover this space. Given the prevalence of good solutions in over-parameterized deep neural networks, we show that by constraining the parameter space to our proposed manifold, we can identify high-quality solutions while achieving unprecedented compression rates across a wide variety of tasks. Through extensive experiments in computer vision and natural language processing tasks, we demonstrate that our method, MCNC, significantly outperforms state-of-the-art baselines in terms of compression, accuracy, and/or model reconstruction time.
scTree: Discovering Cellular Hierarchies in the Presence of Batch Effects in scRNA-seq Data
Authors: Moritz Vandenhirtz, Florian Barkmann, Laura Manduchi, Julia E. Vogt, Valentina Boeva
Date: 2024-06-27 00:00:00
Tasks: Clustering

We propose a novel method, scTree, for single-cell Tree Variational Autoencoders, extending a hierarchical clustering approach to single-cell RNA sequencing data. scTree corrects for batch effects while simultaneously learning a tree-structured data representation. This VAE-based method allows for a more in-depth understanding of complex cellular landscapes independently of the biasing effects of batches. We show empirically on seven datasets that scTree discovers the underlying clusters of the data and the hierarchical relations between them, as well as outperforms established baseline methods across these datasets. Additionally, we analyze the learned hierarchy to understand its biological relevance, thus underpinning the importance of integrating batch correction directly into the clustering procedure.
Stochastic Concept Bottleneck Models
Authors: Moritz Vandenhirtz, Sonia Laguna, Ričards Marcinkevičs, Julia E. Vogt
Date: 2024-06-27 00:00:00

Concept Bottleneck Models (CBMs) have emerged as a promising interpretable method whose final prediction is based on intermediate, human-understandable concepts rather than the raw input. Through time-consuming manual interventions, a user can correct wrongly predicted concept values to enhance the model's downstream performance. We propose Stochastic Concept Bottleneck Models (SCBMs), a novel approach that models concept dependencies. In SCBMs, a single-concept intervention affects all correlated concepts, thereby improving intervention effectiveness. Unlike previous approaches that model the concept relations via an autoregressive structure, we introduce an explicit, distributional parameterization that allows SCBMs to retain the CBMs' efficient training and inference procedure. Additionally, we leverage the parameterization to derive an effective intervention strategy based on the confidence region. We show empirically on synthetic tabular and natural image datasets that our approach improves intervention effectiveness significantly. Notably, we showcase the versatility and usability of SCBMs by examining a setting with CLIP-inferred concepts, alleviating the need for manual concept annotations.
Leveraging Contrastive Learning for Enhanced Node Representations in Tokenized Graph Transformers
Authors: Jinsong Chen, Hanpeng Liu, John E. Hopcroft, Kun He
Date: 2024-06-27 00:00:00
Tasks: Contrastive Learning, Node Classification

While tokenized graph Transformers have demonstrated strong performance in node classification tasks, their reliance on a limited subset of nodes with high similarity scores for constructing token sequences overlooks valuable information from other nodes, hindering their ability to fully harness graph information for learning optimal node representations. To address this limitation, we propose a novel graph Transformer called GCFormer. Unlike previous approaches, GCFormer develops a hybrid token generator to create two types of token sequences, positive and negative, to capture diverse graph information. And a tailored Transformer-based backbone is adopted to learn meaningful node representations from these generated token sequences. Additionally, GCFormer introduces contrastive learning to extract valuable information from both positive and negative token sequences, enhancing the quality of learned node representations. Extensive experimental results across various datasets, including homophily and heterophily graphs, demonstrate the superiority of GCFormer in node classification, when compared to representative graph neural networks (GNNs) and graph Transformers.
Advection Augmented Convolutional Neural Networks
Authors: Niloufar Zakariaei, Siddharth Rout, Eldad Haber, Moshe Eliasof
Date: 2024-06-27 00:00:00
Tasks: Prediction, Video Prediction

Many problems in physical sciences are characterized by the prediction of space-time sequences. Such problems range from weather prediction to the analysis of disease propagation and video prediction. Modern techniques for the solution of these problems typically combine Convolution Neural Networks (CNN) architecture with a time prediction mechanism. However, oftentimes, such approaches underperform in the long-range propagation of information and lack explainability. In this work, we introduce a physically inspired architecture for the solution of such problems. Namely, we propose to augment CNNs with advection by designing a novel semi-Lagrangian push operator. We show that the proposed operator allows for the non-local transformation of information compared with standard convolutional kernels. We then complement it with Reaction and Diffusion neural components to form a network that mimics the Reaction-Advection-Diffusion equation, in high dimensions. We demonstrate the effectiveness of our network on a number of spatio-temporal datasets that show their merit.
NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification
Authors: Jinsong Chen, Siyu Jiang, Kun He
Date: 2024-06-27 00:00:00
Tasks: Node Classification, Representation Learning

Recently, the emerging graph Transformers have made significant advancements for node classification on graphs. In most graph Transformers, a crucial step involves transforming the input graph into token sequences as the model input, enabling Transformer to effectively learn the node representations. However, we observe that existing methods only express partial graph information of nodes through single-type token generation. Consequently, they require tailored strategies to encode additional graph-specific features into the Transformer to ensure the quality of node representation learning, limiting the model flexibility to handle diverse graphs. To this end, we propose a new graph Transformer called NTFormer to address this issue. NTFormer introduces a novel token generator called Node2Par, which constructs various token sequences using different token elements for each node. This flexibility allows Node2Par to generate valuable token sequences from different perspectives, ensuring comprehensive expression of rich graph features. Benefiting from the merits of Node2Par, NTFormer only leverages a Transformer-based backbone without graph-specific modifications to learn node representations, eliminating the need for graph-specific modifications. Extensive experiments conducted on various benchmark datasets containing homophily and heterophily graphs with different scales demonstrate the superiority of NTFormer over representative graph Transformers and graph neural networks for node classification.
Improving the Expressiveness of $K$-hop Message-Passing GNNs by Injecting Contextualized Substructure Information
Authors: Tianjun Yao, Yiongxu Wang, Kun Zhang, Shangsong Liang
Date: 2024-06-27 00:00:00

Graph neural networks (GNNs) have become the \textit{de facto} standard for representational learning in graphs, and have achieved state-of-the-art performance in many graph-related tasks; however, it has been shown that the expressive power of standard GNNs are equivalent maximally to 1-dimensional Weisfeiler-Lehman (1-WL) Test. Recently, there is a line of works aiming to enhance the expressive power of graph neural networks. One line of such works aim at developing $K$-hop message-passing GNNs where node representation is updated by aggregating information from not only direct neighbors but all neighbors within $K$-hop of the node. Another line of works leverages subgraph information to enhance the expressive power which is proven to be strictly more powerful than 1-WL test. In this work, we discuss the limitation of $K$-hop message-passing GNNs and propose \textit{substructure encoding function} to uplift the expressive power of any $K$-hop message-passing GNN. We further inject contextualized substructure information to enhance the expressiveness of $K$-hop message-passing GNNs. Our method is provably more powerful than previous works on $K$-hop graph neural networks and 1-WL subgraph GNNs, which is a specific type of subgraph based GNN models, and not less powerful than 3-WL. Empirically, our proposed method set new state-of-the-art performance or achieves comparable performance for a variety of datasets. Our code is available at \url{https://github.com/tianyao-aka/Expresive_K_hop_GNNs}.
Revealing Fine-Grained Values and Opinions in Large Language Models
Authors: Dustin Wright, Arnav Arora, Nadav Borenstein, Srishti Yadav, Serge Belongie, Isabelle Augenstein
Date: 2024-06-27 00:00:00

Uncovering latent values and opinions embedded in large language models (LLMs) can help identify biases and mitigate potential harm. Recently, this has been approached by prompting LLMs with survey questions and quantifying the stances in the outputs towards morally and politically charged statements. However, the stances generated by LLMs can vary greatly depending on how they are prompted, and there are many ways to argue for or against a given position. In this work, we propose to address this by analysing a large and robust dataset of 156k LLM responses to the 62 propositions of the Political Compass Test (PCT) generated by 6 LLMs using 420 prompt variations. We perform coarse-grained analysis of their generated stances and fine-grained analysis of the plain text justifications for those stances. For fine-grained analysis, we propose to identify tropes in the responses: semantically similar phrases that are recurrent and consistent across different prompts, revealing natural patterns in the text that a given LLM is prone to produce. We find that demographic features added to prompts significantly affect outcomes on the PCT, reflecting bias, as well as disparities between the results of tests when eliciting closed-form vs. open domain responses. Additionally, patterns in the plain text rationales via tropes show that similar justifications are repeatedly generated across models and prompts even with disparate stances.
Averaging log-likelihoods in direct alignment
Authors: Nathan Grinsztajn, Yannis Flet-Berliac, Mohammad Gheshlaghi Azar, Florian Strub, Bill Wu, Eugene Choi, Chris Cremer, Arash Ahmadian, Yash Chandak, Olivier Pietquin, Matthieu Geist
Date: 2024-06-27 00:00:00

To better align Large Language Models (LLMs) with human judgment, Reinforcement Learning from Human Feedback (RLHF) learns a reward model and then optimizes it using regularized RL. Recently, direct alignment methods were introduced to learn such a fine-tuned model directly from a preference dataset without computing a proxy reward function. These methods are built upon contrastive losses involving the log-likelihood of (dis)preferred completions according to the trained model. However, completions have various lengths, and the log-likelihood is not length-invariant. On the other side, the cross-entropy loss used in supervised training is length-invariant, as batches are typically averaged token-wise. To reconcile these approaches, we introduce a principled approach for making direct alignment length-invariant. Formally, we introduce a new averaging operator, to be composed with the optimality operator giving the best policy for the underlying RL problem. It translates into averaging the log-likelihood within the loss. We empirically study the effect of such averaging, observing a trade-off between the length of generations and their scores.
Contrastive Policy Gradient: Aligning LLMs on sequence-level scores in a supervised-friendly fashion
Authors: Yannis Flet-Berliac, Nathan Grinsztajn, Florian Strub, Bill Wu, Eugene Choi, Chris Cremer, Arash Ahmadian, Yash Chandak, Mohammad Gheshlaghi Azar, Olivier Pietquin, Matthieu Geist
Date: 2024-06-27 00:00:00
Tasks: Code Generation, Natural Language Inference, Reinforcement Learning (RL)

Reinforcement Learning (RL) has been used to finetune Large Language Models (LLMs) using a reward model trained from preference data, to better align with human judgment. The recently introduced direct alignment methods, which are often simpler, more stable, and computationally lighter, can more directly achieve this. However, these approaches cannot optimize arbitrary rewards, and the preference-based ones are not the only rewards of interest for LLMs (eg., unit tests for code generation or textual entailment for summarization, among others). RL-finetuning is usually done with a variation of policy gradient, which calls for on-policy or near-on-policy samples, requiring costly generations. We introduce Contrastive Policy Gradient, or CoPG, a simple and mathematically principled new RL algorithm that can estimate the optimal policy even from off-policy data. It can be seen as an off-policy policy gradient approach that does not rely on important sampling techniques and highlights the importance of using (the right) state baseline. We show this approach to generalize the direct alignment method IPO (identity preference optimization) and classic policy gradient. We experiment with the proposed CoPG on a toy bandit problem to illustrate its properties, as well as for finetuning LLMs on a summarization task, using a learned reward function considered as ground truth for the purpose of the experiments.
Heterogeneous Causal Metapath Graph Neural Network for Gene-Microbe-Disease Association Prediction
Authors: Kexin Zhang, Feng Huang, Luotao Liu, Zhankun Xiong, Hongyu Zhang, Yuan Quan, Wen Zhang
Date: 2024-06-27 00:00:00
Tasks: Graph Neural Network, Representation Learning

The recent focus on microbes in human medicine highlights their potential role in the genetic framework of diseases. To decode the complex interactions among genes, microbes, and diseases, computational predictions of gene-microbe-disease (GMD) associations are crucial. Existing methods primarily address gene-disease and microbe-disease associations, but the more intricate triple-wise GMD associations remain less explored. In this paper, we propose a Heterogeneous Causal Metapath Graph Neural Network (HCMGNN) to predict GMD associations. HCMGNN constructs a heterogeneous graph linking genes, microbes, and diseases through their pairwise associations, and utilizes six predefined causal metapaths to extract directed causal subgraphs, which facilitate the multi-view analysis of causal relations among three entity types. Within each subgraph, we employ a causal semantic sharing message passing network for node representation learning, coupled with an attentive fusion method to integrate these representations for predicting GMD associations. Our extensive experiments show that HCMGNN effectively predicts GMD associations and addresses association sparsity issue by enhancing the graph's semantics and structure.
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis
Authors: Shikun Feng, Jiaxin Zheng, Yinjun Jia, Yanwen Huang, Fengfeng Zhou, Wei-Ying Ma, Yanyan Lan
Date: 2024-06-13 00:00:00
Tasks: Drug Discovery, Molecular Property Prediction, molecular representation, Property Prediction, Representation Learning

Molecular representation learning is pivotal for various molecular property prediction tasks related to drug discovery. Robust and accurate benchmarks are essential for refining and validating current methods. Existing molecular property benchmarks derived from wet experiments, however, face limitations such as data volume constraints, unbalanced label distribution, and noisy labels. To address these issues, we construct a large-scale and precise molecular representation dataset of approximately 140,000 small molecules, meticulously designed to capture an extensive array of chemical, physical, and biological properties, derived through a robust computational ligand-target binding analysis pipeline. We conduct extensive experiments on various deep learning models, demonstrating that our dataset offers significant physicochemical interpretability to guide model development and design. Notably, the dataset's properties are linked to binding affinity metrics, providing additional insights into model performance in drug-target interaction tasks. We believe this dataset will serve as a more accurate and reliable benchmark for molecular representation learning, thereby expediting progress in the field of artificial intelligence-driven drug discovery.
Advancing operational PM2.5 forecasting with dual deep neural networks (D-DNet)
Authors: Shengjuan Cai, Fangxin Fang, Vincent-Henri Peuch, Mihai Alexe, Ionel Michael Navon, Yanghua Wang
Date: 2024-06-27 00:00:00
Tasks: Management

PM2.5 forecasting is crucial for public health, air quality management, and policy development. Traditional physics-based models are computationally demanding and slow to adapt to real-time conditions. Deep learning models show potential in efficiency but still suffer from accuracy loss over time due to error accumulation. To address these challenges, we propose a dual deep neural network (D-DNet) prediction and data assimilation system that efficiently integrates real-time observations, ensuring reliable operational forecasting. D-DNet excels in global operational forecasting for PM2.5 and AOD550, maintaining consistent accuracy throughout the entire year of 2019. It demonstrates notably higher efficiency than the Copernicus Atmosphere Monitoring Service (CAMS) 4D-Var operational forecasting system while maintaining comparable accuracy. This efficiency benefits ensemble forecasting, uncertainty analysis, and large-scale tasks.
Resolving Discrepancies in Compute-Optimal Scaling of Language Models
Authors: Tomer Porian, Mitchell Wortsman, Jenia Jitsev, Ludwig Schmidt, Yair Carmon
Date: 2024-06-27 00:00:00

Kaplan et al. and Hoffmann et al. developed influential scaling laws for the optimal model size as a function of the compute budget, but these laws yield substantially different predictions. We explain the discrepancy by reproducing the Kaplan scaling law on two datasets (OpenWebText2 and RefinedWeb) and identifying three factors causing the difference: last layer computational cost, warmup duration, and scale-dependent optimizer tuning. With these factors corrected, we obtain excellent agreement with the Hoffmann et al. (i.e., "Chinchilla") scaling law. Counter to a hypothesis of Hoffmann et al., we find that careful learning rate decay is not essential for the validity of their scaling law. As a secondary result, we derive scaling laws for the optimal learning rate and batch size, finding that tuning the AdamW $\beta_2$ parameter is essential at lower batch sizes.
A Teacher Is Worth A Million Instructions
Authors: Nikhil Kothari, Ravindra Nayak, Shreyas Shetty, Amey Patil, Nikesh Garera
Date: 2024-06-27 00:00:00
Tasks: Mixture-of-Experts

Large Language Models(LLMs) have shown exceptional abilities, yet training these models can be quite challenging. There is a strong dependence on the quality of data and finding the best instruction tuning set. Further, the inherent limitations in training methods create substantial difficulties to train relatively smaller models with 7B and 13B parameters. In our research, we suggest an improved training method for these models by utilising knowledge from larger models, such as a mixture of experts (8x7B) architectures. The scale of these larger models allows them to capture a wide range of variations from data alone, making them effective teachers for smaller models. Moreover, we implement a novel post-training domain alignment phase that employs domain-specific expert models to boost domain-specific knowledge during training while preserving the model's ability to generalise. Fine-tuning Mistral 7B and 2x7B with our method surpasses the performance of state-of-the-art language models with more than 7B and 13B parameters: achieving up to $7.9$ in MT-Bench and $93.04\%$ on AlpacaEval.
Adaptive Stochastic Weight Averaging
Authors: Caglar Demir, Arnab Sharma, Axel-Cyrille Ngonga Ngomo
Date: 2024-06-27 00:00:00
Tasks: image-classification, Image Classification, Knowledge Graphs

Ensemble models often improve generalization performances in challenging tasks. Yet, traditional techniques based on prediction averaging incur three well-known disadvantages: the computational overhead of training multiple models, increased latency, and memory requirements at test time. To address these issues, the Stochastic Weight Averaging (SWA) technique maintains a running average of model parameters from a specific epoch onward. Despite its potential benefits, maintaining a running average of parameters can hinder generalization, as an underlying running model begins to overfit. Conversely, an inadequately chosen starting point can render SWA more susceptible to underfitting compared to an underlying running model. In this work, we propose Adaptive Stochastic Weight Averaging (ASWA) technique that updates a running average of model parameters, only when generalization performance is improved on the validation dataset. Hence, ASWA can be seen as a combination of SWA with the early stopping technique, where the former accepts all updates on a parameter ensemble model and the latter rejects any update on an underlying running model. We conducted extensive experiments ranging from image classification to multi-hop reasoning over knowledge graphs. Our experiments over 11 benchmark datasets with 7 baseline models suggest that ASWA leads to a statistically better generalization across models and datasets
Dancing in the Shadows: Harnessing Ambiguity for Fairer Classifiers
Authors: Ainhize Barrainkua, Paula Gordaliza, Jose A. Lozano, Novi Quadrianto
Date: 2024-06-27 00:00:00
Tasks: Attribute, Fairness

This paper introduces a novel approach to bolster algorithmic fairness in scenarios where sensitive information is only partially known. In particular, we propose to leverage instances with uncertain identity with regards to the sensitive attribute to train a conventional machine learning classifier. The enhanced fairness observed in the final predictions of this classifier highlights the promising potential of prioritizing ambiguity (i.e., non-normativity) as a means to improve fairness guarantees in real-world classification tasks.