arXiv subjects

Carla Gomes

Publications and source records attributed to Carla Gomes.

At least 19 recordsLinked to original sources

arXiv2026

Machine Learning Methods for Studying Latent Neural Activity Dynamics

Recent developments in brain recording are driving a demand for machine learning tools capable of decoding the latent structure of large populations of neurons. In this paper, we provide a comprehensive survey that outlines the trajectory of Latent Variable Models (LVMs) from early state-space models to more recent deep generative models. We organize the literature into three closely related domains: (1) Single-Region Latent Dynamics, which includes models such as linear dynamical systems to more complex dynamics represented by Recurrent Neural Networks (RNNs) and Neural Ordinary Differential Equations (ODEs); (2) Multi-Region Communication, which employs probabilistic as well as subspace methods to study how information is transferred across different brain areas considering synaptic propagation delays and network connectivity; and (3) Behavior-Aligned Modeling, which seeks to disentangle neural activity related to task performance from other internal states via supervised or contrastive learning. This survey also includes large-scale neural foundation models, such as Transformers and diffusion models, that rely on large-scale pre-training for optimal performance across subjects. Finally, we conclude and discuss benchmarks, evaluation criteria, and open challenges, such as the ability to identify causal links or directionality of communication, to facilitate future research for bridging interpretable brain dynamics with reliable neural decoding.

cs.LG↗

arXiv2025

No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.

cs.LG↗

arXiv2025

Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoning

Scientific reasoning, the process through which humans apply logic, evidence, and critical thinking to explore and interpret scientific phenomena, is essential in advancing knowledge reasoning across diverse fields. However, despite significant progress, current scientific reasoning models still struggle with generalization across domains and often fall short of multimodal perception. Multimodal Large Language Models (MLLMs), which integrate text, images, and other modalities, present an exciting opportunity to overcome these limitations and enhance scientific reasoning. Therefore, this position paper argues that MLLMs can significantly advance scientific reasoning across disciplines such as mathematics, physics, chemistry, and biology. First, we propose a four-stage research roadmap of scientific reasoning capabilities, and highlight the current state of MLLM applications in scientific reasoning, noting their ability to integrate and reason over diverse data types. Second, we summarize the key challenges that remain obstacles to achieving MLLM's full potential. To address these challenges, we propose actionable insights and suggestions for the future. Overall, our work offers a novel perspective on MLLM integration with scientific reasoning, providing the LLM community with a valuable vision for achieving Artificial General Intelligence (AGI).

cs.CL↗

arXiv2024

AiSciVision: A Framework for Specializing Large Multimodal Models in Scientific Image Classification

Trust and interpretability are crucial for the use of Artificial Intelligence (AI) in scientific research, but current models often operate as black boxes offering limited transparency and justifications for their outputs. We introduce AiSciVision, a framework that specializes Large Multimodal Models (LMMs) into interactive research partners and classification models for image classification tasks in niche scientific domains. Our framework uses two key components: (1) Visual Retrieval-Augmented Generation (VisRAG) and (2) domain-specific tools utilized in an agentic workflow. To classify a target image, AiSciVision first retrieves the most similar positive and negative labeled images as context for the LMM. Then the LMM agent actively selects and applies tools to manipulate and inspect the target image over multiple rounds, refining its analysis before making a final prediction. These VisRAG and tooling components are designed to mirror the processes of domain experts, as humans often compare new data to similar examples and use specialized tools to manipulate and inspect images before arriving at a conclusion. Each inference produces both a prediction and a natural language transcript detailing the reasoning and tool usage that led to the prediction. We evaluate AiSciVision on three real-world scientific image classification datasets: detecting the presence of aquaculture ponds, diseased eelgrass, and solar panels. Across these datasets, our method outperforms fully supervised models in low and full-labeled data settings. AiSciVision is actively deployed in real-world use, specifically for aquaculture research, through a dedicated web application that displays and allows the expert users to converse with the transcripts. This work represents a crucial step toward AI systems that are both interpretable and effective, advancing their use in scientific research and scientific discovery.

cs.LG↗

arXiv2024

Critic Loss for Image Classification

Modern neural network classifiers achieve remarkable performance across a variety of tasks; however, they frequently exhibit overconfidence in their predictions due to the cross-entropy loss. Inspired by this problem, we propose the \textbf{Cr}i\textbf{t}ic Loss for Image \textbf{Cl}assification (CrtCl, pronounced Critical). CrtCl formulates image classification training in a generator-critic framework, with a base classifier acting as a generator, and a correctness critic imposing a loss on the classifier. The base classifier, acting as the generator, given images, generates the probability distribution over classes and intermediate embeddings. The critic model, given the image, intermediate embeddings, and output predictions of the base model, predicts the probability that the base model has produced the correct classification, which then can be back propagated as a self supervision signal. Notably, the critic does not use the label as input, meaning that the critic can train the base model on both labeled and unlabeled data in semi-supervised learning settings. CrtCl represents a learned loss method for accuracy, alleviating the negative side effects of using cross-entropy loss. Additionally, CrtCl provides a powerful way to select data to be labeled in an active learning setting, by estimating the classification ability of the base model on unlabeled data. We study the effectiveness of CrtCl in low-labeled data regimes, and in the context of active learning. In classification, we find that CrtCl, compared to recent baselines, increases classifier generalization and calibration with various amounts of labeled data. In active learning, we show our method outperforms baselines in accuracy and calibration. We observe consistent results across three image classification datasets.

cs.CV↗

arXiv2024

GEM-RAG: Graphical Eigen Memories For Retrieval Augmented Generation

The ability to form, retrieve, and reason about memories in response to stimuli serves as the cornerstone for general intelligence - shaping entities capable of learning, adaptation, and intuitive insight. Large Language Models (LLMs) have proven their ability, given the proper memories or context, to reason and respond meaningfully to stimuli. However, they are still unable to optimally encode, store, and retrieve memories - the ability to do this would unlock their full ability to operate as AI agents, and to specialize to niche domains. To remedy this, one promising area of research is Retrieval Augmented Generation (RAG), which aims to augment LLMs by providing them with rich in-context examples and information. In question-answering (QA) applications, RAG methods embed the text of interest in chunks, and retrieve the most relevant chunks for a prompt using text embeddings. Motivated by human memory encoding and retrieval, we aim to improve over standard RAG methods by generating and encoding higher-level information and tagging the chunks by their utility to answer questions. We introduce Graphical Eigen Memories For Retrieval Augmented Generation (GEM-RAG). GEM-RAG works by tagging each chunk of text in a given text corpus with LLM generated ``utility'' questions, connecting chunks in a graph based on the similarity of both their text and utility questions, and then using the eigendecomposition of the memory graph to build higher level summary nodes that capture the main themes of the text. We evaluate GEM-RAG, using both UnifiedQA and GPT-3.5 Turbo as the LLMs, with SBERT, and OpenAI's text encoders on two standard QA tasks, showing that GEM-RAG outperforms other state-of-the-art RAG methods on these tasks. We also discuss the implications of having a robust RAG system and future directions.

cs.CL↗

arXiv2023

A new perspective on building efficient and expressive 3D equivariant graph neural networks

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these networks through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (LSE) and frame transition encoding (FTE). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out the design space for future developments of equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}.

cs.LG↗

arXiv2023

Xtal2DoS: Attention-based Crystal to Sequence Learning for Density of States Prediction

Modern machine learning techniques have been extensively applied to materials science, especially for property prediction tasks. A majority of these methods address scalar property predictions, while more challenging spectral properties remain less emphasized. We formulate a crystal-to-sequence learning task and propose a novel attention-based learning method, Xtal2DoS, which decodes the sequential representation of the material density of states (DoS) properties by incorporating the learned atomic embeddings through attention networks. Experiments show Xtal2DoS is faster than the existing models, and consistently outperforms other state-of-the-art methods on four metrics for two fundamental spectral properties, phonon and electronic DoS.

cs.LG↗

arXiv2022

Structure-based Drug Design with Equivariant Diffusion Models

Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs in complex with their protein targets to propose new drug candidates. These approaches typically place one atom at a time in an autoregressive fashion using the binding pocket as well as previously added ligand atoms as context in each step. Recently a surge of diffusion generative models has entered this domain which hold promise to capture the statistical properties of natural ligands more faithfully. However, most existing methods focus exclusively on bottom-up de novo design of compounds or tackle other drug development challenges with task-specific models. The latter requires curation of suitable datasets, careful engineering of the models and retraining from scratch for each task. Here we show how a single pre-trained diffusion model can be applied to a broader range of problems, such as off-the-shelf property optimization, explicit negative design, and partial molecular design with inpainting. We formulate SBDD as a 3D-conditional generation problem and present DiffSBDD, an SE(3)-equivariant diffusion model that generates novel ligands conditioned on protein pockets. Our in silico experiments demonstrate that DiffSBDD captures the statistics of the ground truth data effectively. Furthermore, we show how additional constraints can be used to improve the generated drug candidates according to a variety of computational metrics. These results support the assumption that diffusion models represent the complex distribution of structural data more accurately than previous methods, and are able to incorporate additional design objectives and constraints changing nothing but the sampling strategy.

q-bio.BM↗

arXiv2022

Left Heavy Tails and the Effectiveness of the Policy and Value Networks in DNN-based best-first search for Sokoban Planning

Despite the success of practical solvers in various NP-complete domains such as SAT and CSP as well as using deep reinforcement learning to tackle two-player games such as Go, certain classes of PSPACE-hard planning problems have remained out of reach. Even carefully designed domain-specialized solvers can fail quickly due to the exponential search space on hard instances. Recent works that combine traditional search methods, such as best-first search and Monte Carlo tree search, with Deep Neural Networks' (DNN) heuristics have shown promising progress and can solve a significant number of hard planning instances beyond specialized solvers. To better understand why these approaches work, we studied the interplay of the policy and value networks of DNN-based best-first search on Sokoban and show the surprising effectiveness of the policy network, further enhanced by the value network, as a guiding heuristic for the search. To further understand the phenomena, we studied the cost distribution of the search algorithms and found that Sokoban instances can have heavy-tailed runtime distributions, with tails both on the left and right-hand sides. In particular, for the first time, we show the existence of \textit{left heavy tails} and propose an abstract tree model that can empirically explain the appearance of these tails. The experiments show the critical role of the policy network as a powerful heuristic guiding the search, which can lead to left heavy tails with polynomial scaling by avoiding exploring exponentially sized subtrees. Our results also demonstrate the importance of random restarts, as are widely used in traditional combinatorial solvers, for DNN-based search methods to avoid left and right heavy tails.

cs.AI↗

arXiv2022

Scalable First-Order Bayesian Optimization via Structured Automatic Differentiation

Bayesian Optimization (BO) has shown great promise for the global optimization of functions that are expensive to evaluate, but despite many successes, standard approaches can struggle in high dimensions. To improve the performance of BO, prior work suggested incorporating gradient information into a Gaussian process surrogate of the objective, giving rise to kernel matrices of size $nd \times nd$ for $n$ observations in $d$ dimensions. Naïvely multiplying with (resp. inverting) these matrices requires $\mathcal{O}(n^2d^2)$ (resp. $\mathcal{O}(n^3d^3$)) operations, which becomes infeasible for moderate dimensions and sample sizes. Here, we observe that a wide range of kernels gives rise to structured matrices, enabling an exact $\mathcal{O}(n^2d)$ matrix-vector multiply for gradient observations and $\mathcal{O}(n^2d^2)$ for Hessian observations. Beyond canonical kernel classes, we derive a programmatic approach to leveraging this type of structure for transformations and combinations of the discussed kernel classes, which constitutes a structure-aware automatic differentiation algorithm. Our methods apply to virtually all canonical kernels and automatically extend to complex kernels, like the neural network, radial basis function network, and spectral mixture kernels without any additional derivations, enabling flexible, problem-dependent modeling while scaling first-order BO to high $d$.

cs.LG↗

arXiv2021

Constrained Machine Learning: The Bagel Framework

Machine learning models are widely used for real-world applications, such as document analysis and vision. Constrained machine learning problems are problems where learned models have to both be accurate and respect constraints. For continuous convex constraints, many works have been proposed, but learning under combinatorial constraints is still a hard problem. The goal of this paper is to broaden the modeling capacity of constrained machine learning problems by incorporating existing work from combinatorial optimization. We propose first a general framework called BaGeL (Branch, Generate and Learn) which applies Branch and Bound to constrained learning problems where a learning problem is generated and trained at each node until only valid models are obtained. Because machine learning has specific requirements, we also propose an extended table constraint to split the space of hypotheses. We validate the approach on two examples: a linear regression under configuration constraints and a non-negative matrix factorization with prior knowledge for latent semantics analysis.

cs.LG↗

arXiv2021

Contrastively Disentangled Sequential Variational Autoencoder

Self-supervised disentangled representation learning is a critical task in sequence modeling. The learnt representations contribute to better model interpretability as well as the data generation, and improve the sample efficiency for downstream tasks. We propose a novel sequence representation learning method, named Contrastively Disentangled Sequential Variational Autoencoder (C-DSVAE), to extract and separate the static (time-invariant) and dynamic (time-variant) factors in the latent space. Different from previous sequential variational autoencoder methods, we use a novel evidence lower bound which maximizes the mutual information between the input and the latent factors, while penalizes the mutual information between the static and dynamic factors. We leverage contrastive estimations of the mutual information terms in training, together with simple yet effective augmentation techniques, to introduce additional inductive biases. Our experiments show that C-DSVAE significantly outperforms the previous state-of-the-art methods on multiple metrics.

cs.LG↗

arXiv2021

Sparse Bayesian Learning via Stepwise Regression

Sparse Bayesian Learning (SBL) is a powerful framework for attaining sparsity in probabilistic models. Herein, we propose a coordinate ascent algorithm for SBL termed Relevance Matching Pursuit (RMP) and show that, as its noise variance parameter goes to zero, RMP exhibits a surprising connection to Stepwise Regression. Further, we derive novel guarantees for Stepwise Regression algorithms, which also shed light on RMP. Our guarantees for Forward Regression improve on deterministic and probabilistic results for Orthogonal Matching Pursuit with noise. Our analysis of Backward Regression on determined systems culminates in a bound on the residual of the optimal solution to the subset selection problem that, if satisfied, guarantees the optimality of the result. To our knowledge, this bound is the first that can be computed in polynomial time and depends chiefly on the smallest singular value of the matrix. We report numerical experiments using a variety of feature selection algorithms. Notably, RMP and its limiting variant are both efficient and maintain strong performance with correlated features.

cs.LG↗

arXiv2021

On the Optimality of Backward Regression: Sparse Recovery and Subset Selection

Sparse recovery and subset selection are fundamental problems in varied communities, including signal processing, statistics and machine learning. Herein, we focus on an important greedy algorithm for these problems: Backward Stepwise Regression. We present novel guarantees for the algorithm, propose an efficient, numerically stable implementation, and put forth Stepwise Regression with Replacement (SRR), a new family of two-stage algorithms that employs both forward and backward steps for compressed sensing problems. Prior work on the backward algorithm has proven its optimality for the subset selection problem, provided the residual associated with the optimal solution is small enough. However, the existing bounds on the residual magnitude are NP-hard to compute. In contrast, our main theoretical result includes a bound that can be computed in polynomial time, depends chiefly on the smallest singular value of the matrix, and also extends to the method of magnitude pruning. In addition, we report numerical experiments highlighting crucial differences between forward and backward greedy algorithms and compare SRR against popular two-stage algorithms for compressed sensing. Remarkably, SRR algorithms generally maintain good sparse recovery performance on coherent dictionaries. Further, a particular SRR algorithm has an edge over Subspace Pursuit.

math.OC↗

arXiv2021

HOT-VAE: Learning High-Order Label Correlation for Multi-Label Classification via Attention-Based Variational Autoencoders

Understanding how environmental characteristics affect bio-diversity patterns, from individual species to communities of species, is critical for mitigating effects of global change. A central goal for conservation planning and monitoring is the ability to accurately predict the occurrence of species communities and how these communities change over space and time. This in turn leads to a challenging and long-standing problem in the field of computer science - how to perform ac-curate multi-label classification with hundreds of labels? The key challenge of this problem is its exponential-sized output space with regards to the number of labels to be predicted.Therefore, it is essential to facilitate the learning process by exploiting correlations (or dependency) among labels. Previous methods mostly focus on modelling the correlation on label pairs; however, complex relations between real-world objects often go beyond second order. In this paper, we pro-pose a novel framework for multi-label classification, High-order Tie-in Variational Autoencoder (HOT-VAE), which per-forms adaptive high-order label correlation learning. We experimentally verify that our model outperforms the existing state-of-the-art approaches on a bird distribution dataset on both conventional F1 scores and a variety of ecological metrics. To show our method is general, we also perform empirical analysis on seven other public real-world datasets in several application domains, and Hot-VAE exhibits superior performance to previous methods.

cs.LG↗

arXiv2021

Evaluating Multi-label Classifiers with Noisy Labels

Multi-label classification (MLC) is a generalization of standard classification where multiple labels may be assigned to a given sample. In the real world, it is more common to deal with noisy datasets than clean datasets, given how modern datasets are labeled by a large group of annotators on crowdsourcing platforms, but little attention has been given to evaluating multi-label classifiers with noisy labels. Exploiting label correlations now becomes a standard component of a multi-label classifier to achieve competitive performance. However, this component makes the classifier more prone to poor generalization - it overfits labels as well as label dependencies. We identify three common real-world label noise scenarios and show how previous approaches per-form poorly with noisy labels. To address this issue, we present a Context-Based Multi-LabelClassifier (CbMLC) that effectively handles noisy labels when learning label dependencies, without requiring additional supervision. We compare CbMLC against other domain-specific state-of-the-art models on a variety of datasets, under both the clean and the noisy settings. We show CbMLC yields substantial improvements over the previous methods in most cases.

cs.LG↗

arXiv2020

Understanding Decoupled and Early Weight Decay

Weight decay (WD) is a traditional regularization technique in deep learning, but despite its ubiquity, its behavior is still an area of active research. Golatkar et al. have recently shown that WD only matters at the start of the training in computer vision, upending traditional wisdom. Loshchilov et al. show that for adaptive optimizers, manually decaying weights can outperform adding an $l_2$ penalty to the loss. This technique has become increasingly popular and is referred to as decoupled WD. The goal of this paper is to investigate these two recent empirical observations. We demonstrate that by applying WD only at the start, the network norm stays small throughout training. This has a regularizing effect as the effective gradient updates become larger. However, traditional generalizations metrics fail to capture this effect of WD, and we show how a simple scale-invariant metric can. We also show how the growth of network weights is heavily influenced by the dataset and its generalization properties. For decoupled WD, we perform experiments in NLP and RL where adaptive optimizers are the norm. We demonstrate that the primary issue that decoupled WD alleviates is the mixing of gradients from the objective function and the $l_2$ penalty in the buffers of Adam (which stores the estimates of the first-order moment). Adaptivity itself is not problematic and decoupled WD ensures that the gradients from the $l_2$ term cannot "drown out" the true objective, facilitating easier hyperparameter tuning.

cs.LG↗