arXiv subjects

Thomas Demeester

Publications and source records attributed to Thomas Demeester.

At least 37 records · Page 2Linked to original sources

arXiv2025

Prior Knowledge Injection into Deep Learning Models Predicting Gene Expression from Whole Slide Images

Cancer diagnosis and prognosis primarily depend on clinical parameters such as age and tumor grade, and are increasingly complemented by molecular data, such as gene expression, from tumor sequencing. However, sequencing is costly and delays oncology workflows. Recent advances in Deep Learning allow to predict molecular information from morphological features within Whole Slide Images (WSIs), offering a cost-effective proxy of the molecular markers. While promising, current methods lack the robustness to fully replace direct sequencing. Here we aim to improve existing methods by introducing a model-agnostic framework that allows to inject prior knowledge on gene-gene interactions into Deep Learning architectures, thereby increasing accuracy and robustness. We design the framework to be generic and flexibly adaptable to a wide range of architectures. In a case study on breast cancer, our strategy leads to an average increase of 983 significant genes (out of 25,761) across all 18 experiments, with 14 generalizing to an increase on an independent dataset. Our findings reveal a high potential for injection of prior knowledge to increase gene expression prediction performance from WSIs across a wide range of architectures.

cs.CV↗

arXiv2025

Debiasing Synthetic Data Generated by Deep Generative Models

While synthetic data hold great promise for privacy protection, their statistical analysis poses significant challenges that necessitate innovative solutions. The use of deep generative models (DGMs) for synthetic data generation is known to induce considerable bias and imprecision into synthetic data analyses, compromising their inferential utility as opposed to original data analyses. This bias and uncertainty can be substantial enough to impede statistical convergence rates, even in seemingly straightforward analyses like mean calculation. The standard errors of such estimators then exhibit slower shrinkage with sample size than the typical 1 over root-$n$ rate. This complicates fundamental calculations like p-values and confidence intervals, with no straightforward remedy currently available. In response to these challenges, we propose a new strategy that targets synthetic data created by DGMs for specific data analyses. Drawing insights from debiased and targeted machine learning, our approach accounts for biases, enhances convergence rates, and facilitates the calculation of estimators with easily approximated large sample variances. We exemplify our proposal through a simulation study on toy data and two case studies on real-world data, highlighting the importance of tailoring DGMs for targeted data analysis. This debiasing strategy contributes to advancing the reliability and applicability of synthetic data in statistical inference.

stat.ML↗

arXiv2024

ChocoLlama: Lessons Learned From Teaching Llamas Dutch

While Large Language Models (LLMs) have shown remarkable capabilities in natural language understanding and generation, their performance often lags in lower-resource, non-English languages due to biases in the training data. In this work, we explore strategies for adapting the primarily English LLMs (Llama-2 and Llama-3) to Dutch, a language spoken by 30 million people worldwide yet often underrepresented in LLM development. We collect 104GB of Dutch text ($32$B tokens) from various sources to first apply continued pretraining using low-rank adaptation (LoRA), complemented with Dutch posttraining strategies provided by prior work. For Llama-2, we consider using (i) the tokenizer of the original model, and (ii) training a new, Dutch-specific tokenizer combined with embedding reinitialization. We evaluate our adapted models, ChocoLlama-2, both on standard benchmarks and a novel Dutch benchmark, ChocoLlama-Bench. Our results demonstrate that LoRA can effectively scale for language adaptation, and that tokenizer modification with careful weight reinitialization can improve performance. Notably, Llama-3 was released during the course of this project and, upon evaluation, demonstrated superior Dutch capabilities compared to our Dutch-adapted versions of Llama-2. We hence apply the same adaptation technique to Llama-3, using its original tokenizer. While our adaptation methods enhanced Llama-2's Dutch capabilities, we found limited gains when applying the same techniques to Llama-3. This suggests that for ever improving, multilingual foundation models, language adaptation techniques may benefit more from focusing on language-specific posttraining rather than on continued pretraining. We hope this work contributes to the broader understanding of adapting LLMs to lower-resource languages, and to the development of Dutch LLMs in particular.

cs.CL↗

arXiv2024

From Text to Treatment Effects: A Meta-Learning Approach to Handling Text-Based Confounding

One of the central goals of causal machine learning is the accurate estimation of heterogeneous treatment effects from observational data. In recent years, meta-learning has emerged as a flexible, model-agnostic paradigm for estimating conditional average treatment effects (CATE) using any supervised model. This paper examines the performance of meta-learners when the confounding variables are expressed in text. Through synthetic data experiments, we show that learners using pre-trained text representations of confounders, in addition to tabular background variables, achieve improved CATE estimates compared to those relying solely on the tabular variables, particularly when sufficient data is available. However, due to the entangled nature of the text embeddings, these models do not fully match the performance of meta-learners with perfect confounder knowledge. These findings highlight both the potential and the limitations of pre-trained text representations for causal inference and open up interesting avenues for future research.

cs.AI↗

arXiv2024

SkillMatch: Evaluating Self-supervised Learning of Skill Relatedness

Accurately modeling the relationships between skills is a crucial part of human resources processes such as recruitment and employee development. Yet, no benchmarks exist to evaluate such methods directly. We construct and release SkillMatch, a benchmark for the task of skill relatedness, based on expert knowledge mining from millions of job ads. Additionally, we propose a scalable self-supervised learning technique to adapt a Sentence-BERT model based on skill co-occurrence in job ads. This new method greatly surpasses traditional models for skill relatedness as measured on SkillMatch. By releasing SkillMatch publicly, we aim to contribute a foundation for research towards increased accuracy and transparency of skill-based recommendation systems.

cs.CL↗

arXiv2024

On the Biased Assessment of Expert Finding Systems

In large organisations, identifying experts on a given topic is crucial in leveraging the internal knowledge spread across teams and departments. So-called enterprise expert retrieval systems automatically discover and structure employees' expertise based on the vast amount of heterogeneous data available about them and the work they perform. Evaluating these systems requires comprehensive ground truth expert annotations, which are hard to obtain. Therefore, the annotation process typically relies on automated recommendations of knowledge areas to validate. This case study provides an analysis of how these recommendations can impact the evaluation of expert finding systems. We demonstrate on a popular benchmark that system-validated annotations lead to overestimated performance of traditional term-based retrieval models and even invalidate comparisons with more recent neural methods. We also augment knowledge areas with synonyms to uncover a strong bias towards literal mentions of their constituent words. Finally, we propose constraints to the annotation process to prevent these biased evaluations, and show that this still allows annotation suggestions of high utility. These findings should inform benchmark creation or selection for expert finding, to guarantee meaningful comparison of methods.

cs.IR↗

arXiv2024

Anchored Preference Optimization and Contrastive Revisions: Addressing Underspecification in Alignment

Large Language Models (LLMs) are often aligned using contrastive alignment objectives and preference pair datasets. The interaction between model, paired data, and objective makes alignment a complicated procedure, sometimes producing subpar results. We study this and find that (i) preference data gives a better learning signal when the underlying responses are contrastive, and (ii) alignment objectives lead to better performance when they specify more control over the model during training. Based on these insights, we introduce Contrastive Learning from AI Revisions (CLAIR), a data-creation method which leads to more contrastive preference pairs, and Anchored Preference Optimization (APO), a controllable and more stable alignment objective. We align Llama-3-8B-Instruct using various comparable datasets and alignment objectives and measure MixEval-Hard scores, which correlate highly with human judgments. The CLAIR preferences lead to the strongest performance out of all datasets, and APO consistently outperforms less controllable objectives. Our best model, trained on 32K CLAIR preferences with APO, improves Llama-3-8B-Instruct by 7.65%, closing the gap with GPT4-turbo by 45%. Our code is available at https://github.com/ContextualAI/CLAIR_and_APO.

cs.LG↗

arXiv2024

Accelerating Hopfield Network Dynamics: Beyond Synchronous Updates and Forward Euler

The Hopfield network serves as a fundamental energy-based model in machine learning, capturing memory retrieval dynamics through an ordinary differential equation (ODE). The model's output, the equilibrium point of the ODE, is traditionally computed via synchronous updates using the forward Euler method. This paper aims to overcome some of the disadvantages of this approach. We propose a conceptual shift, viewing Hopfield networks as instances of Deep Equilibrium Models (DEQs). The DEQ framework not only allows for the use of specialized solvers, but also leads to new insights on an empirical inference technique that we will refer to as 'even-odd splitting'. Our theoretical analysis of the method uncovers a parallelizable asynchronous update scheme, which should converge roughly twice as fast as the conventional synchronous updates. Empirical evaluations validate these findings, showcasing the advantages of both the DEQ framework and even-odd splitting in digitally simulating energy minimization in Hopfield networks. The code is available at https://github.com/cgoemaere/hopdeq

cs.LG↗

arXiv2024

Trans-Tokenization and Cross-lingual Vocabulary Transfers: Language Adaptation of LLMs for Low-Resource NLP

The development of monolingual language models for low and mid-resource languages continues to be hindered by the difficulty in sourcing high-quality training data. In this study, we present a novel cross-lingual vocabulary transfer strategy, trans-tokenization, designed to tackle this challenge and enable more efficient language adaptation. Our approach focuses on adapting a high-resource monolingual LLM to an unseen target language by initializing the token embeddings of the target language using a weighted average of semantically similar token embeddings from the source language. For this, we leverage a translation resource covering both the source and target languages. We validate our method with the Tweeties, a series of trans-tokenized LLMs, and demonstrate their competitive performance on various downstream tasks across a small but diverse set of languages. Additionally, we introduce Hydra LLMs, models with multiple swappable language modeling heads and embedding tables, which further extend the capabilities of our trans-tokenization strategy. By designing a Hydra LLM based on the multilingual model TowerInstruct, we developed a state-of-the-art machine translation model for Tatar, in a zero-shot manner, completely bypassing the need for high-quality parallel data. This breakthrough is particularly significant for low-resource languages like Tatar, where high-quality parallel data is hard to come by. By lowering the data and time requirements for training high-quality models, our trans-tokenization strategy allows for the development of LLMs for a wider range of languages, especially those with limited resources. We hope that our work will inspire further research and collaboration in the field of cross-lingual vocabulary transfer and contribute to the empowerment of languages on a global scale.

cs.CL↗

arXiv2024

The Real Deal Behind the Artificial Appeal: Inferential Utility of Tabular Synthetic Data

Recent advances in generative models facilitate the creation of synthetic data to be made available for research in privacy-sensitive contexts. However, the analysis of synthetic data raises a unique set of methodological challenges. In this work, we highlight the importance of inferential utility and provide empirical evidence against naive inference from synthetic data, whereby synthetic data are treated as if they were actually observed. Before publishing synthetic data, it is essential to develop statistical inference tools for such data. By means of a simulation study, we show that the rate of false-positive findings (type 1 error) will be unacceptably high, even when the estimates are unbiased. Despite the use of a previously proposed correction factor, this problem persists for deep generative models, in part due to slower convergence of estimators and resulting underestimation of the true standard error. We further demonstrate our findings through a case study.

cs.LG↗

arXiv2024

Clinical Reasoning over Tabular Data and Text with Bayesian Networks

Bayesian networks are well-suited for clinical reasoning on tabular data, but are less compatible with natural language data, for which neural networks provide a successful framework. This paper compares and discusses strategies to augment Bayesian networks with neural text representations, both in a generative and discriminative manner. This is illustrated with simulation results for a primary care use case (diagnosis of pneumonia) and discussed in a broader clinical context.

cs.AI↗

arXiv2024

From Numbers to Words: Multi-Modal Bankruptcy Prediction Using the ECL Dataset

In this paper, we present ECL, a novel multi-modal dataset containing the textual and numerical data from corporate 10K filings and associated binary bankruptcy labels. Furthermore, we develop and critically evaluate several classical and neural bankruptcy prediction models using this dataset. Our findings suggest that the information contained in each data modality is complementary for bankruptcy prediction. We also see that the binary bankruptcy prediction target does not enable our models to distinguish next year bankruptcy from an unhealthy financial situation resulting in bankruptcy in later years. Finally, we explore the use of LLMs in the context of our task. We show how GPT-based models can be used to extract meaningful summaries from the textual data but zero-shot bankruptcy prediction results are poor. All resources required to access and update the dataset or replicate our experiments are available on github.com/henriarnoUG/ECL.

cs.CE↗

arXiv2024

In-Context Learning for Extreme Multi-Label Classification

Multi-label classification problems with thousands of classes are hard to solve with in-context learning alone, as language models (LMs) might lack prior knowledge about the precise classes or how to assign them, and it is generally infeasible to demonstrate every class in a prompt. We propose a general program, $\texttt{Infer--Retrieve--Rank}$, that defines multi-step interactions between LMs and retrievers to efficiently tackle such problems. We implement this program using the $\texttt{DSPy}$ programming model, which specifies in-context systems in a declarative manner, and use $\texttt{DSPy}$ optimizers to tune it towards specific datasets by bootstrapping only tens of few-shot examples. Our primary extreme classification program, optimized separately for each task, attains state-of-the-art results across three benchmarks (HOUSE, TECH, TECHWOLF). We apply the same program to a benchmark with vastly different characteristics and attain competitive performance as well (BioDEX). Unlike prior work, our proposed solution requires no finetuning, is easily applicable to new tasks, alleviates prompt engineering, and requires only tens of labeled examples. Our code is public at https://github.com/KarelDO/xmc.dspy.

cs.CL↗

arXiv2023

Exploring the Temperature-Dependent Phase Transition in Modern Hopfield Networks

The recent discovery of a connection between Transformers and Modern Hopfield Networks (MHNs) has reignited the study of neural networks from a physical energy-based perspective. This paper focuses on the pivotal effect of the inverse temperature hyperparameter $β$ on the distribution of energy minima of the MHN. To achieve this, the distribution of energy minima is tracked in a simplified MHN in which equidistant normalised patterns are stored. This network demonstrates a phase transition at a critical temperature $β_{\text{c}}$, from a single global attractor towards highly pattern specific minima as $β$ is increased. Importantly, the dynamics are not solely governed by the hyperparameter $β$ but are instead determined by an effective inverse temperature $β_{\text{eff}}$ which also depends on the distribution and size of the stored patterns. Recognizing the role of hyperparameters in the MHN could, in the future, aid researchers in the domain of Transformers to optimise their initial choices, potentially reducing the necessity for time and energy expensive hyperparameter fine-tuning.

cs.LG↗

arXiv2023

BioLORD-2023: Semantic Textual Representations Fusing LLM and Clinical Knowledge Graph Insights

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

cs.CL↗

arXiv2023

Training a Hopfield Variational Autoencoder with Equilibrium Propagation

On dedicated analog hardware, equilibrium propagation is an energy-efficient alternative to backpropagation. In spite of its theoretical guarantees, its application in the AI domain remains limited to the discriminative setting. Meanwhile, despite its high computational demands, generative AI is on the rise. In this paper, we demonstrate the application of Equilibrium Propagation in training a variational autoencoder (VAE) for generative modeling. Leveraging the symmetric nature of Hopfield networks, we propose using a single model to serve as both the encoder and decoder which could effectively halve the required chip size for VAE implementations, paving the way for more efficient analog hardware configurations.

cs.LG↗

arXiv2023

Flexible Model Interpretability through Natural Language Model Editing

Model interpretability and model editing are crucial goals in the age of large language models. Interestingly, there exists a link between these two goals: if a method is able to systematically edit model behavior with regard to a human concept of interest, this editor method can help make internal representations more interpretable by pointing towards relevant representations and systematically manipulating them.

cs.CL↗

arXiv2023

Zero-Shot Cross-Lingual Sentiment Classification under Distribution Shift: an Exploratory Study

The brittleness of finetuned language model performance on out-of-distribution (OOD) test samples in unseen domains has been well-studied for English, yet is unexplored for multi-lingual models. Therefore, we study generalization to OOD test data specifically in zero-shot cross-lingual transfer settings, analyzing performance impacts of both language and domain shifts between train and test data. We further assess the effectiveness of counterfactually augmented data (CAD) in improving OOD generalization for the cross-lingual setting, since CAD has been shown to benefit in a monolingual English setting. Finally, we propose two new approaches for OOD generalization that avoid the costly annotation process associated with CAD, by exploiting the power of recent large language models (LLMs). We experiment with 3 multilingual models, LaBSE, mBERT, and XLM-R trained on English IMDb movie reviews, and evaluate on OOD test sets in 13 languages: Amazon product reviews, Tweets, and Restaurant reviews. Results echo the OOD performance decline observed in the monolingual English setting. Further, (i) counterfactuals from the original high-resource language do improve OOD generalization in the low-resource language, and (ii) our newly proposed cost-effective approaches reach similar or up to +3.1% better accuracy than CAD for Amazon and Restaurant reviews.

cs.CL↗