ICML Topological Deep Learning Challenge 2024: Beyond the Graph Domain

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

AutoML-guided Fusion of Entity and LLM-based representations

Large semantic knowledge bases are grounded in factual knowledge. However, recent approaches to dense text representations (embeddings) do not efficiently exploit these resources. Dense and robust representations of documents are essential for effectively solving downstream classification and retrieval tasks. This work demonstrates that injecting embedded information from knowledge bases can augment the performance of contemporary Large Language Model (LLM)-based representations for the task of text classification. Further, by considering automated machine learning (AutoML) with the fused representation space, we demonstrate it is possible to improve classification accuracy even if we use low-dimensional projections of the original representation space obtained via efficient matrix factorization. This result shows that significantly faster classifiers can be achieved with minimal or no loss in predictive performance, as demonstrated using five strong LLM baselines on six diverse real-life datasets.

A Bag of Tricks for Scaling CPU-based Deep FFMs to more than 300m Predictions per Second

Field-aware Factorization Machines (FFMs) have emerged as a powerful model for click-through rate prediction, particularly excelling in capturing complex feature interactions. In this work, we present an in-depth analysis of our in-house, Rust-based Deep FFM implementation, and detail its deployment on a CPU-only, multi-data-center scale. We overview key optimizations devised for both training and inference, demonstrated by previously unpublished benchmark results in efficient model search and online training. Further, we detail an in-house weight quantization that resulted in more than an order of magnitude reduction in bandwidth footprint related to weight transfers across data-centres. We disclose the engine and associated techniques under an open-source license to contribute to the broader machine learning community. This paper showcases one of the first successful CPU-only deployments of Deep FFMs at such scale, marking a significant stride in practical, low-footprint click-through rate prediction methodologies.

AHAM: Adapt, Help, Ask, Model -- Harvesting LLMs for literature mining

In an era marked by a rapid increase in scientific publications, researchers grapple with the challenge of keeping pace with field-specific advances. We present the `AHAM' methodology and a metric that guides the domain-specific \textbf{adapt}ation of the BERTopic topic modeling framework to improve scientific text analysis. By utilizing the LLaMa2 generative language model, we generate topic definitions via one-shot learning by crafting prompts with the \textbf{help} of domain experts to guide the LLM for literature mining by \textbf{asking} it to model the topic names. For inter-topic similarity evaluation, we leverage metrics from language generation and translation processes to assess lexical and semantic similarity of the generated topics. Our system aims to reduce both the ratio of outlier topics to the total number of topics and the similarity between topic definitions. The methodology has been assessed on a newly gathered corpus of scientific papers on literature-based discovery. Through rigorous evaluation by domain experts, AHAM has been validated as effective in uncovering intriguing and novel insights within broad research areas. We explore the impact of domain adaptation of sentence-transformers for the task of topic \textbf{model}ing using two datasets, each specialized to specific scientific domains within arXiv and medarxiv. We evaluate the impact of data size, the niche of adaptation, and the importance of domain adaptation. Our results suggest a strong interaction between domain adaptation and topic modeling precision in terms of outliers and topic definitions.

Latent Graphs for Semi-Supervised Learning on Biomedical Tabular Data

In the domain of semi-supervised learning, the current approaches insufficiently exploit the potential of considering inter-instance relationships among (un)labeled data. In this work, we address this limitation by providing an approach for inferring latent graphs that capture the intrinsic data relationships. By leveraging graph-based representations, our approach facilitates the seamless propagation of information throughout the graph, effectively incorporating global and local knowledge. Through evaluations on biomedical tabular datasets, we compare the capabilities of our approach to other contemporary methods. Our work demonstrates the significance of inter-instance relationship discovery as practical means for constructing robust latent graphs to enhance semi-supervised learning techniques. The experiments show that the proposed methodology outperforms contemporary state-of-the-art methods for (semi-)supervised learning on three biomedical datasets.

Drifter: Efficient Online Feature Monitoring for Improved Data Integrity in Large-Scale Recommendation Systems

Real-world production systems often grapple with maintaining data quality in large-scale, dynamic streams. We introduce Drifter, an efficient and lightweight system for online feature monitoring and verification in recommendation use cases. Drifter addresses limitations of existing methods by delivering agile, responsive, and adaptable data quality monitoring, enabling real-time root cause analysis, drift detection and insights into problematic production events. Integrating state-of-the-art online feature ranking for sparse data and anomaly detection ideas, Drifter is highly scalable and resource-efficient, requiring only two threads and less than a gigabyte of RAM per production deployments that handle millions of instances per minute. Evaluation on real-world data sets demonstrates Drifter's effectiveness in alerting and mitigating data quality issues, substantially improving reliability and performance of real-time live recommender systems.

Measuring Catastrophic Forgetting in Cross-Lingual Transfer Paradigms: Exploring Tuning Strategies

The cross-lingual transfer is a promising technique to solve tasks in less-resourced languages. In this empirical study, we compare two fine-tuning approaches combined with zero-shot and full-shot learning approaches for large language models in a cross-lingual setting. As fine-tuning strategies, we compare parameter-efficient adapter methods with fine-tuning of all parameters. As cross-lingual transfer strategies, we compare the intermediate-training (\textit{IT}) that uses each language sequentially and cross-lingual validation (\textit{CLV}) that uses a target language already in the validation phase of fine-tuning. We assess the success of transfer and the extent of catastrophic forgetting in a source language due to cross-lingual transfer, i.e., how much previously acquired knowledge is lost when we learn new information in a different language. The results on two different classification problems, hate speech detection and product reviews, each containing datasets in several languages, show that the \textit{IT} cross-lingual strategy outperforms \textit{CLV} for the target language. Our findings indicate that, in the majority of cases, the \textit{CLV} strategy demonstrates superior retention of knowledge in the base language (English) compared to the \textit{IT} strategy, when evaluating catastrophic forgetting in multiple cross-lingual transfers.

OutRank: Speeding up AutoML-based Model Search for Large Sparse Data sets with Cardinality-aware Feature Ranking

The design of modern recommender systems relies on understanding which parts of the feature space are relevant for solving a given recommendation task. However, real-world data sets in this domain are often characterized by their large size, sparsity, and noise, making it challenging to identify meaningful signals. Feature ranking represents an efficient branch of algorithms that can help address these challenges by identifying the most informative features and facilitating the automated search for more compact and better-performing models (AutoML). We introduce OutRank, a system for versatile feature ranking and data quality-related anomaly detection. OutRank was built with categorical data in mind, utilizing a variant of mutual information that is normalized with regard to the noise produced by features of the same cardinality. We further extend the similarity measure by incorporating information on feature similarity and combined relevance. The proposed approach's feasibility is demonstrated by speeding up the state-of-the-art AutoML system on a synthetic data set with no performance loss. Furthermore, we considered a real-life click-through-rate prediction data set where it outperformed strong baselines such as random forest-based approaches. The proposed approach enables exploration of up to 300% larger feature spaces compared to AutoML-only approaches, enabling faster search for better models on off-the-shelf hardware.

DDeMON: Ontology-based function prediction by Deep Learning from Dynamic Multiplex Networks

Biological systems can be studied at multiple levels of information, including gene, protein, RNA and different interaction networks levels. The goal of this work is to explore how the fusion of systems' level information with temporal dynamics of gene expression can be used in combination with non-linear approximation power of deep neural networks to predict novel gene functions in a non-model organism potato \emph{Solanum tuberosum}. We propose DDeMON (Dynamic Deep learning from temporal Multiplex Ontology-annotated Networks), an approach for scalable, systems-level inference of function annotation using time-dependent multiscale biological information. The proposed method, which is capable of considering billions of potential links between the genes of interest, was applied on experimental gene expression data and the background knowledge network to reliably classify genes with unknown function into five different functional ontology categories, linked to the experimental data set. Predicted novel functions of genes were validated using extensive protein domain search approach.

Dynamic Surrogate Switching: Sample-Efficient Search for Factorization Machine Configurations in Online Recommendations

Hyperparameter optimization is the process of identifying the appropriate hyperparameter configuration of a given machine learning model with regard to a given learning task. For smaller data sets, an exhaustive search is possible; However, when the data size and model complexity increase, the number of configuration evaluations becomes the main computational bottleneck. A promising paradigm for tackling this type of problem is surrogate-based optimization. The main idea underlying this paradigm considers an incrementally updated model of the relation between the hyperparameter space and the output (target) space; the data for this model are obtained by evaluating the main learning engine, which is, for example, a factorization machine-based model. By learning to approximate the hyperparameter-target relation, the surrogate (machine learning) model can be used to score large amounts of hyperparameter configurations, exploring parts of the configuration space beyond the reach of direct machine learning engine evaluation. Commonly, a surrogate is selected prior to optimization initialization and remains the same during the search. We investigated whether dynamic switching of surrogates during the optimization itself is a sensible idea of practical relevance for selecting the most appropriate factorization machine-based models for large-scale online recommendation. We conducted benchmarks on data sets containing hundreds of millions of instances against established baselines such as Random Forest- and Gaussian process-based surrogates. The results indicate that surrogate switching can offer good performance while considering fewer learning engine evaluations.