arXiv subjects

Francisco Vargas

Publications and source records attributed to Francisco Vargas.

32 records · Page 2Linked to original sources

arXiv2024

Improving Antibody Design with Force-Guided Sampling in Diffusion Models

Antibodies, crucial for immune defense, primarily rely on complementarity-determining regions (CDRs) to bind and neutralize antigens, such as viruses. The design of these CDRs determines the antibody's affinity and specificity towards its target. Generative models, particularly denoising diffusion probabilistic models (DDPMs), have shown potential to advance the structure-based design of CDR regions. However, only a limited dataset of bound antibody-antigen structures is available, and generalization to out-of-distribution interfaces remains a challenge. Physics based force-fields, which approximate atomic interactions, offer a coarse but universal source of information to better mold designs to target interfaces. Integrating this foundational information into diffusion models is, therefore, highly desirable. Here, we propose a novel approach to enhance the sampling process of diffusion models by integrating force field energy-based feedback. Our model, DiffForce, employs forces to guide the diffusion sampling process, effectively blending the two distributions. Through extensive experiments, we demonstrate that our method guides the model to sample CDRs with lower energy, enhancing both the structure and sequence of the generated antibodies.

q-bio.QM↗

arXiv2024

To smooth a cloud or to pin it down: Guarantees and Insights on Score Matching in Denoising Diffusion Models

Denoising diffusion models are a class of generative models which have recently achieved state-of-the-art results across many domains. Gradual noise is added to the data using a diffusion process, which transforms the data distribution into a Gaussian. Samples from the generative model are then obtained by simulating an approximation of the time reversal of this diffusion initialized by Gaussian samples. Recent research has explored adapting diffusion models for sampling and inference tasks. In this paper, we leverage known connections to stochastic control akin to the Föllmer drift to extend established neural network approximation results for the Föllmer drift to denoising diffusion models and samplers.

stat.ML↗

arXiv2024

Beyond ELBOs: A Large-Scale Evaluation of Variational Methods for Sampling

Monte Carlo methods, Variational Inference, and their combinations play a pivotal role in sampling from intractable probability distributions. However, current studies lack a unified evaluation framework, relying on disparate performance measures and limited method comparisons across diverse tasks, complicating the assessment of progress and hindering the decision-making of practitioners. In response to these challenges, our work introduces a benchmark that evaluates sampling methods using a standardized task suite and a broad range of performance criteria. Moreover, we study existing metrics for quantifying mode collapse and introduce novel metrics for this purpose. Our findings provide insights into strengths and weaknesses of existing sampling methods, serving as a valuable reference for future developments. The code is publicly available here.

cs.LG↗

arXiv2024

Exploring the Linear Subspace Hypothesis in Gender Bias Mitigation

Bolukbasi et al. (2016) presents one of the first gender bias mitigation techniques for word representations. Their method takes pre-trained word representations as input and attempts to isolate a linear subspace that captures most of the gender bias in the representations. As judged by an analogical evaluation task, their method virtually eliminates gender bias in the representations. However, an implicit and untested assumption of their method is that the bias subspace is actually linear. In this work, we generalize their method to a kernelized, nonlinear version. We take inspiration from kernel principal component analysis and derive a nonlinear bias isolation technique. We discuss and overcome some of the practical drawbacks of our method for non-linear gender bias mitigation in word representations and analyze empirically whether the bias subspace is actually linear. Our analysis shows that gender bias is in fact well captured by a linear subspace, justifying the assumption of Bolukbasi et al. (2016).

cs.LG↗

arXiv2024

A framework for conditional diffusion modelling with applications in motif scaffolding for protein design

Many protein design applications, such as binder or enzyme design, require scaffolding a structural motif with high precision. Generative modelling paradigms based on denoising diffusion processes emerged as a leading candidate to address this motif scaffolding problem and have shown early experimental success in some cases. In the diffusion paradigm, motif scaffolding is treated as a conditional generation task, and several conditional generation protocols were proposed or imported from the Computer Vision literature. However, most of these protocols are motivated heuristically, e.g. via analogies to Langevin dynamics, and lack a unifying framework, obscuring connections between the different approaches. In this work, we unify conditional training and conditional sampling procedures under one common framework based on the mathematically well-understood Doob's h-transform. This new perspective allows us to draw connections between existing methods and propose a new variation on existing conditional training protocols. We illustrate the effectiveness of this new protocol in both, image outpainting and motif scaffolding and find that it outperforms standard methods.

cs.LG↗

arXiv2023

Denoising Diffusion Samplers

Denoising diffusion models are a popular class of generative models providing state-of-the-art results in many domains. One adds gradually noise to data using a diffusion to transform the data distribution into a Gaussian distribution. Samples from the generative model are then obtained by simulating an approximation of the time-reversal of this diffusion initialized by Gaussian samples. Practically, the intractable score terms appearing in the time-reversed process are approximated using score matching techniques. We explore here a similar idea to sample approximately from unnormalized probability density functions and estimate their normalizing constants. We consider a process where the target density diffuses towards a Gaussian. Denoising Diffusion Samplers (DDS) are obtained by approximating the corresponding time-reversal. While score matching is not applicable in this context, we can leverage many of the ideas introduced in generative modeling for Monte Carlo sampling. Existing theoretical results from denoising diffusion models also provide theoretical guarantees for DDS. We discuss the connections between DDS, optimal control and Schrödinger bridges and finally demonstrate DDS experimentally on a variety of challenging sampling tasks.

cs.LG↗

arXiv2023

Dimensionality Reduction as Probabilistic Inference

Dimensionality reduction (DR) algorithms compress high-dimensional data into a lower dimensional representation while preserving important features of the data. DR is a critical step in many analysis pipelines as it enables visualisation, noise reduction and efficient downstream processing of the data. In this work, we introduce the ProbDR variational framework, which interprets a wide range of classical DR algorithms as probabilistic inference algorithms in this framework. ProbDR encompasses PCA, CMDS, LLE, LE, MVU, diffusion maps, kPCA, Isomap, (t-)SNE, and UMAP. In our framework, a low-dimensional latent variable is used to construct a covariance, precision, or a graph Laplacian matrix, which can be used as part of a generative model for the data. Inference is done by optimizing an evidence lower bound. We demonstrate the internal consistency of our framework and show that it enables the use of probabilistic programming languages (PPLs) for DR. Additionally, we illustrate that the framework facilitates reasoning about unseen data and argue that our generative models approximate Gaussian processes (GPs) on manifolds. By providing a unified view of DR, our framework facilitates communication, reasoning about uncertainties, model composition, and extensions, particularly when domain knowledge is present.

stat.ML↗

arXiv2022

Bayesian Learning via Neural Schrödinger-Föllmer Flows

In this work we explore a new framework for approximate Bayesian inference in large datasets based on stochastic control (i.e. Schrödinger bridges). We advocate stochastic control as a finite time and low variance alternative to popular steady-state methods such as stochastic gradient Langevin dynamics (SGLD). Furthermore, we discuss and adapt the existing theoretical guarantees of this framework and establish connections to already existing VI routines in SDE-based models.

stat.ML↗

arXiv2022

Efficient privacy-preserving inference for convolutional neural networks

The processing of sensitive user data using deep learning models is an area that has gained recent traction. Existing work has leveraged homomorphic encryption (HE) schemes to enable computation on encrypted data. An early work was CryptoNets, which takes 250 seconds for one MNIST inference. The main limitation of such approaches is that of the expensive FFT-like operations required to perform operations on HE-encrypted ciphertext. Others have proposed the use of model pruning and efficient data representations to reduce the number of HE operations required. We focus on improving upon existing work by proposing changes to the representations of intermediate tensors during CNN inference. We construct and evaluate private CNNs on the MNIST and CIFAR-10 datasets, and achieve over a two-fold reduction in the number of operations used for inferences of the CryptoNets architecture.

cs.LG↗

arXiv2022

Solving Schrödinger Bridges via Maximum Likelihood

The Schrödinger bridge problem (SBP) finds the most likely stochastic evolution between two probability distributions given a prior stochastic evolution. As well as applications in the natural sciences, problems of this kind have important applications in machine learning such as dataset alignment and hypothesis testing. Whilst the theory behind this problem is relatively mature, scalable numerical recipes to estimate the Schrödinger bridge remain an active area of research. We prove an equivalence between the SBP and maximum likelihood estimation enabling direct application of successful machine learning techniques. We propose a numerical procedure to estimate SBPs using Gaussian process and demonstrate the practical usage of our approach in numerical simulations and experiments.

stat.ML↗

arXiv2019

Multilingual Factor Analysis

In this work we approach the task of learning multilingual word representations in an offline manner by fitting a generative latent variable model to a multilingual dictionary. We model equivalent words in different languages as different views of the same word generated by a common latent variable representing their latent lexical meaning. We explore the task of alignment by querying the fitted model for multilingual embeddings achieving competitive results across a variety of tasks. The proposed model is robust to noise in the embedding space making it a suitable method for distributed representations learned from noisy corpora.

cs.LG↗

arXiv2019

Model Comparison for Semantic Grouping

We introduce a probabilistic framework for quantifying the semantic similarity between two groups of embeddings. We formulate the task of semantic similarity as a model comparison task in which we contrast a generative model which jointly models two sentences versus one that does not. We illustrate how this framework can be used for the Semantic Textual Similarity tasks using clear assumptions about how the embeddings of words are generated. We apply model comparison that utilises information criteria to address some of the shortcomings of Bayesian model comparison, whilst still penalising model complexity. We achieve competitive results by applying the proposed framework with an appropriate choice of likelihood on the STS datasets.

cs.LG↗

arXiv2016

Towards Automatic Wild Animal Monitoring: Identification of Animal Species in Camera-trap Images using Very Deep Convolutional Neural Networks

Non intrusive monitoring of animals in the wild is possible using camera trapping framework, which uses cameras triggered by sensors to take a burst of images of animals in their habitat. However camera trapping framework produces a high volume of data (in the order on thousands or millions of images), which must be analyzed by a human expert. In this work, a method for animal species identification in the wild using very deep convolutional neural networks is presented. Multiple versions of the Snapshot Serengeti dataset were used in order to probe the ability of the method to cope with different challenges that camera-trap images demand. The method reached 88.9% of accuracy in Top-1 and 98.1% in Top-5 in the evaluation set using a residual network topology. Also, the results show that the proposed method outperforms previous approximations and proves that recognition in camera-trap images can be automated.

cs.CV↗

arXiv2016

HMM and DTW for evaluation of therapeutical gestures using kinect

Automatic recognition of the quality of movement in human beings is a challenging task, given the difficulty both in defining the constraints that make a movement correct, and the difficulty in using noisy data to determine if these constraints were satisfied. This paper presents a method for the detection of deviations from the correct form in movements from physical therapy routines based on Hidden Markov Models, which is compared to Dynamic Time Warping. The activities studied include upper an lower limbs movements, the data used comes from a Kinect sensor. Correct repetitions of the activities of interest were recorded, as well as deviations from these correct forms. The ability of the proposed approach to detect these deviations was studied. Results show that a system based on HMM is much more likely to determine if a certain movement has deviated from the specification.

cs.HC↗