arXiv subjects

Gaël Varoquaux

Publications and source records attributed to Gaël Varoquaux.

At least 55 records · Page 3Linked to original sources

arXiv2024

Learning High-Quality and General-Purpose Phrase Representations

Phrase representations play an important role in data science and natural language processing, benefiting various tasks like Entity Alignment, Record Linkage, Fuzzy Joins, and Paraphrase Classification. The current state-of-the-art method involves fine-tuning pre-trained language models for phrasal embeddings using contrastive learning. However, we have identified areas for improvement. First, these pre-trained models tend to be unnecessarily complex and require to be pre-trained on a corpus with context sentences. Second, leveraging the phrase type and morphology gives phrase representations that are both more precise and more flexible. We propose an improved framework to learn phrase representations in a context-free fashion. The framework employs phrase type classification as an auxiliary task and incorporates character-level information more effectively into the phrase representation. Furthermore, we design three granularities of data augmentation to increase the diversity of training samples. Our experiments across a wide range of tasks show that our approach generates superior phrase embeddings compared to previous methods while requiring a smaller model size. [PEARL-small]: https://huggingface.co/Lihuchen/pearl_small; [PEARL-base]: https://huggingface.co/Lihuchen/pearl_base; [Code and Dataset]: https://github.com/tigerchen52/PEARL

cs.CL↗

arXiv2023

Vectorizing string entries for data processing on tables: when are larger language models better?

There are increasingly efficient data processing pipelines that work on vectors of numbers, for instance most machine learning models, or vector databases for fast similarity search. These require converting the data to numbers. While this conversion is easy for simple numerical and categorical entries, databases are strife with text entries, such as names or descriptions. In the age of large language models, what's the best strategies to vectorize tables entries, baring in mind that larger models entail more operational complexity? We study the benefits of language models in 14 analytical tasks on tables while varying the training size, as well as for a fuzzy join benchmark. We introduce a simple characterization of a column that reveals two settings: 1) a dirty categories setting, where strings share much similarities across entries, and conversely 2) a diverse entries setting. For dirty categories, pretrained language models bring little-to-no benefit compared to simpler string models. For diverse entries, we show that larger language models improve data processing. For these we investigate the complexity-performance tradeoffs and show that they reflect those of classic text embedding: larger models tend to perform better, but it is useful to fine tune them for embedding purposes.

stat.ML↗

arXiv2023

Common Limitations of Image Processing Metrics: A Picture Story

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

eess.IV↗

arXiv2023

The Locality and Symmetry of Positional Encodings

Positional Encodings (PEs) are used to inject word-order information into transformer-based language models. While they can significantly enhance the quality of sentence representations, their specific contribution to language models is not fully understood, especially given recent findings that various positional encodings are insensitive to word order. In this work, we conduct a systematic study of positional encodings in \textbf{Bidirectional Masked Language Models} (BERT-style) , which complements existing work in three aspects: (1) We uncover the core function of PEs by identifying two common properties, Locality and Symmetry; (2) We show that the two properties are closely correlated with the performances of downstream tasks; (3) We quantify the weakness of current PEs by introducing two new probing tasks, on which current PEs perform poorly. We believe that these results are the basis for developing better PEs for transformer-based language models. The code is available at \faGithub~ \url{https://github.com/tigerchen52/locality\_symmetry}

cs.CL↗

arXiv2023

How to select predictive models for causal inference?

As predictive models -- e.g., from machine learning -- give likely outcomes, they may be used to reason on the effect of an intervention, a causal-inference task. The increasing complexity of health data has opened the door to a plethora of models, but also the Pandora box of model selection: which of these models yield the most valid causal estimates? Here we highlight that classic machine-learning model selection does not select the best outcome models for causal inference. Indeed, causal model selection should control both outcome errors for each individual, treated or not treated, whereas only one outcome is observed. Theoretically, simple risks used in machine learning do not control causal effects when treated and non-treated population differ too much. More elaborate risks build proxies of the causal error using ``nuisance'' re-weighting to compute it on the observed data. But does computing these nuisance adds noise to model selection? Drawing from an extensive empirical study, we outline a good causal model-selection procedure: using the so-called $R\text{-risk}$; using flexible estimators to compute the nuisance models on the train set; and splitting out 10\% of the data to compute risks.

stat.ML↗

arXiv2023

Beyond calibration: estimating the grouping loss of modern neural networks

The ability to ensure that a classifier gives reliable confidence scores is essential to ensure informed decision-making. To this end, recent work has focused on miscalibration, i.e., the over or under confidence of model scores. Yet calibration is not enough: even a perfectly calibrated classifier with the best possible accuracy can have confidence scores that are far from the true posterior probabilities. This is due to the grouping loss, created by samples with the same confidence scores but different true posterior probabilities. Proper scoring rule theory shows that given the calibration loss, the missing piece to characterize individual errors is the grouping loss. While there are many estimators of the calibration loss, none exists for the grouping loss in standard settings. Here, we propose an estimator to approximate the grouping loss. We show that modern neural network architectures in vision and NLP exhibit grouping loss, notably in distribution shifts settings, which highlights the importance of pre-production validation.

cs.LG↗

arXiv2023

GLADIS: A General and Large Acronym Disambiguation Benchmark

Acronym Disambiguation (AD) is crucial for natural language understanding on various sources, including biomedical reports, scientific papers, and search engine queries. However, existing acronym disambiguation benchmarks and tools are limited to specific domains, and the size of prior benchmarks is rather small. To accelerate the research on acronym disambiguation, we construct a new benchmark named GLADIS with three components: (1) a much larger acronym dictionary with 1.5M acronyms and 6.4M long forms; (2) a pre-training corpus with 160 million sentences; (3) three datasets that cover the general, scientific, and biomedical domains. We then pre-train a language model, \emph{AcroBERT}, on our constructed corpus for general acronym disambiguation, and show the challenges and values of our new benchmark.

cs.CL↗

arXiv2023

Causal inference methods for combining randomized trials and observational studies: a review

With increasing data availability, causal effects can be evaluated across different data sets, both randomized controlled trials (RCTs) and observational studies. RCTs isolate the effect of the treatment from that of unwanted (confounding) co-occurring effects but they may suffer from unrepresentativeness, and thus lack external validity. On the other hand, large observational samples are often more representative of the target population but can conflate confounding effects with the treatment of interest. In this paper, we review the growing literature on methods for causal inference on combined RCTs and observational studies, striving for the best of both worlds. We first discuss identification and estimation methods that improve generalizability of RCTs using the representativeness of observational data. Classical estimators include weighting, difference between conditional outcome models, and doubly robust estimators. We then discuss methods that combine RCTs and observational data to either ensure uncounfoundedness of the observational analysis or to improve (conditional) average treatment effect estimation. We also connect and contrast works developed in both the potential outcomes literature and the structural causal model literature. Finally, we compare the main methods using a simulation study and real world data to analyze the effect of tranexamic acid on the mortality rate in major trauma patients. A review of available codes and new implementations is also provided.

stat.ME↗

arXiv2023

Causal effect on a target population: a sensitivity analysis to handle missing covariates

Randomized Controlled Trials (RCTs) are often considered the gold standard for estimating causal effect, but they may lack external validity when the population eligible to the RCT is substantially different from the target population. Having at hand a sample of the target population of interest allows us to generalize the causal effect. Identifying the treatment effect in the target population requires covariates to capture all treatment effect modifiers that are shifted between the two sets. Standard estimators then use either weighting (IPSW), outcome modeling (G-formula), or combine the two in doubly robust approaches (AIPSW). However such covariates are often not available in both sets. In this paper, after proving L1-consistency of these three estimators, we compute the expected bias induced by a missing covariate, assuming a Gaussian distribution, a continuous outcome, and a semi-parametric model. Under this setting, we perform a sensitivity analysis for each missing covariate pattern and compute the sign of the expected bias. We also show that there is no gain in linearly imputing a partially-unobserved covariate. Finally we study the substitution of a missing covariate by a proxy. We illustrate all these results on simulations, as well as semi-synthetic benchmarks using data from the Tennessee Student/Teacher Achievement Ratio (STAR), and a real-world example from critical care medicine.

stat.ME↗

arXiv2022

Why do tree-based models still outperform deep learning on tabular data?

While deep learning has enabled tremendous progress on text and image datasets, its superiority on tabular data is not clear. We contribute extensive benchmarks of standard and novel deep learning methods as well as tree-based models such as XGBoost and Random Forests, across a large number of datasets and hyperparameter combinations. We define a standard set of 45 datasets from varied domains with clear characteristics of tabular data and a benchmarking methodology accounting for both fitting models and finding good hyperparameters. Results show that tree-based models remain state-of-the-art on medium-sized data ($\sim$10K samples) even without accounting for their superior speed. To understand this gap, we conduct an empirical investigation into the differing inductive biases of tree-based models and Neural Networks (NNs). This leads to a series of challenges which should guide researchers aiming to build tabular-specific NNs: 1. be robust to uninformative features, 2. preserve the orientation of the data, and 3. be able to easily learn irregular functions. To stimulate research on tabular architectures, we contribute a standard benchmark and raw data for baselines: every point of a 20 000 compute hours hyperparameter search for each learner.

cs.LG↗

arXiv2022

How I failed machine learning in medical imaging -- shortcomings and recommendations

Medical imaging is an important research field with many opportunities for improving patients' health. However, there are a number of challenges that are slowing down the progress of the field as a whole, such optimizing for publication. In this paper we reviewed several problems related to choosing datasets, methods, evaluation metrics, and publication strategies. With a review of literature and our own analysis, we show that at every step, potential biases can creep in. On a positive note, we also see that initiatives to counteract these problems are already being started. Finally we provide a broad range of recommendations on how to further these address problems in the future. For reproducibility, data and code for our analyses are available on \url{https://github.com/GaelVaroquaux/ml_med_imaging_failures}

eess.IV↗

arXiv2022

Imputing Out-of-Vocabulary Embeddings with LOVE Makes Language Models Robust with Little Cost

State-of-the-art NLP systems represent inputs with word embeddings, but these are brittle when faced with Out-of-Vocabulary (OOV) words. To address this issue, we follow the principle of mimick-like models to generate vectors for unseen words, by learning the behavior of pre-trained embeddings using only the surface form of words. We present a simple contrastive learning framework, LOVE, which extends the word representation of an existing pre-trained language model (such as BERT), and makes it robust to OOV with few additional parameters. Extensive evaluations demonstrate that our lightweight model achieves similar or even better performances than prior competitors, both on original datasets and on corrupted variants. Moreover, it can be used in a plug-and-play fashion with FastText and BERT, where it significantly improves their robustness.

cs.CL↗

arXiv2022

Benchmarking missing-values approaches for predictive models on health databases

BACKGROUND: As databases grow larger, it becomes harder to fully control their collection, and they frequently come with missing values: incomplete observations. These large databases are well suited to train machine-learning models, for instance for forecasting or to extract biomarkers in biomedical settings. Such predictive approaches can use discriminative -- rather than generative -- modeling, and thus open the door to new missing-values strategies. Yet existing empirical evaluations of strategies to handle missing values have focused on inferential statistics. RESULTS: Here we conduct a systematic benchmark of missing-values strategies in predictive models with a focus on large health databases: four electronic health record datasets, a population brain imaging one, a health survey and two intensive care ones. Using gradient-boosted trees, we compare native support for missing values with simple and state-of-the-art imputation prior to learning. We investigate prediction accuracy and computational time. For prediction after imputation, we find that adding an indicator to express which values have been imputed is important, suggesting that the data are missing not at random. Elaborate missing values imputation can improve prediction compared to simple strategies but requires longer computational time on large data. Learning trees that model missing values-with missing incorporated attribute-leads to robust, fast, and well-performing predictive modeling. CONCLUSIONS: Native support for missing values in supervised machine learning predicts better than state-of-the-art imputation with much less computational cost. When using imputation, it is important to add indicator columns expressing which values have been imputed.

cs.LG↗

arXiv2021

What's a good imputation to predict with missing values?

How to learn a good predictor on data with missing values? Most efforts focus on first imputing as well as possible and second learning on the completed data to predict the outcome. Yet, this widespread practice has no theoretical grounding. Here we show that for almost all imputation functions, an impute-then-regress procedure with a powerful learner is Bayes optimal. This result holds for all missing-values mechanisms, in contrast with the classic statistical results that require missing-at-random settings to use imputation in probabilistic modeling. Moreover, it implies that perfect conditional imputation is not needed for good prediction asymptotically. In fact, we show that on perfectly imputed data the best regression function will generally be discontinuous, which makes it hard to learn. Crafting instead the imputation so as to leave the regression function unchanged simply shifts the problem to learning discontinuous imputations. Rather, we suggest that it is easier to learn imputation and regression jointly. We propose such a procedure, adapting NeuMiss, a neural network capturing the conditional links across observed and unobserved variables whatever the missing-value pattern. Experiments confirm that joint imputation and regression through NeuMiss is better than various two step procedures in our experiments with finite number of samples.

stat.ML↗

arXiv2021

Label scarcity in biomedicine: Data-rich latent factor discovery enhances phenotype prediction

High-quality data accumulation is now becoming ubiquitous in the health domain. There is increasing opportunity to exploit rich data from normal subjects to improve supervised estimators in specific diseases with notorious data scarcity. We demonstrate that low-dimensional embedding spaces can be derived from the UK Biobank population dataset and used to enhance data-scarce prediction of health indicators, lifestyle and demographic characteristics. Phenotype predictions facilitated by Variational Autoencoder manifolds typically scaled better with increasing unlabeled data than dimensionality reduction by PCA or Isomap. Performances gains from semisupervison approaches will probably become an important ingredient for various medical data science applications.

cs.LG↗

arXiv2021

Preventing dataset shift from breaking machine-learning biomarkers

Machine learning brings the hope of finding new biomarkers extracted from cohorts with rich biomedical measurements. A good biomarker is one that gives reliable detection of the corresponding condition. However, biomarkers are often extracted from a cohort that differs from the target population. Such a mismatch, known as a dataset shift, can undermine the application of the biomarker to new individuals. Dataset shifts are frequent in biomedical research, e.g. because of recruitment biases. When a dataset shift occurs, standard machine-learning techniques do not suffice to extract and validate biomarkers. This article provides an overview of when and how dataset shifts breaks machine-learning extracted biomarkers, as well as detection and correction strategies.

cs.LG↗

arXiv2021

A Lightweight Neural Model for Biomedical Entity Linking

Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names, including synonyms, morphological variations, and names with different word orderings. Recently, BERT-based methods have advanced the state-of-the-art by allowing for rich representations of word sequences. However, they often have hundreds of millions of parameters and require heavy computing resources, which limits their applications in resource-limited scenarios. Here, we propose a lightweight neural method for biomedical entity linking, which needs just a fraction of the parameters of a BERT model and much less computing resources. Our method uses a simple alignment layer with attention mechanisms to capture the variations between mention and entity names. Yet, we show that our model is competitive with previous work on standard evaluation benchmarks.

cs.CL↗

arXiv2021

Extracting representations of cognition across neuroimaging studies improves brain decoding

Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more statistical power; yet the current brain-imaging analytic framework cannot be used at scale as it requires casting all cognitive tasks in a unified theoretical framework. We introduce a new methodology to analyze brain responses across tasks without a joint model of the psychological processes. The method boosts statistical power in small studies with specific cognitive focus by analyzing them jointly with large studies that probe less focal mental processes. Our approach improves decoding performance for 80% of 35 widely-different functional-imaging studies. It finds commonalities across tasks in a data-driven way, via common brain representations that predict mental processes. These are brain networks tuned to psychological manipulations. They outline interpretable and plausible brain structures. The extracted networks have been made available; they can be readily reused in new neuro-imaging studies. We provide a multi-study decoding tool to adapt to new data.

stat.ML↗