arXiv subjects

Brenda Nogueira

Publications and source records attributed to Brenda Nogueira.

6 recordsLinked to original sources

arXiv2026

Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models

Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes. Generative models conditioned on cancer genotypes offer a promising avenue for personalized drug discovery, yet existing approaches lack explicit optimization for simultaneous sensitivity, synthesizability, and mechanistic binding plausibility. We present a latent-space optimization approach for a pretrained genotype-to-drug diffusion model, introducing a learnable perturbation over the molecular latent space optimized via gradient ascent to maximize a composite reward combining predicted drug sensitivity (AUC), drug-likeness (QED), and synthetic accessibility (SAS). Critically, biological realism is enforced by grounding both reward design and evaluation in experimentally-derived cancer cell line data and validated pharmacologic signals, anchoring candidate generation in real-world clinical evidence. Mechanistic consistency plausibility is further assessed by a multi-agent LLM pipeline grounded in the diffusion model's attention mechanism. Experiments across 15 cancer cell lines from three held-out evaluation sets demonstrate consistent and noticeable improvements over competing baselines in sensitivity, drug-likeness, synthesizability, and chemical validity.

cs.LG↗

arXiv2026

SPECTRA: Spectral Domain-Aware Graph Generation for Imbalanced Molecular Property Regression

Molecular property regression struggles with cases in chemically relevant target ranges that are underrepresented in datasets. Standard average error minimization approaches underperform in these highly relevant cases, and oversampling approaches lead to meaningless molecular representations. In this paper, we propose SPECTRA, a spectral, domain-aware graph generation method designed to improve the prediction of underrepresented but relevant molecular property values. It combines a rarity-aware budgeting scheme to focus generation where data are scarce, target-neighbors graph alignment to establish structural correspondence, and interpolation of Laplacian spectra, node features, and targets. Coupled with spectral GNN using edge-aware Chebyshev convolutions, SPECTRA shows its effectiveness in property prediction benchmarks with competitive performance over leading state-of-the-art methods in relevant target ranges, while requiring ~4x less computational time.

cs.LG↗

arXiv2025

From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews

Large Language Models (LLMs) are increasingly embedded in academic writing practices. Although numerous studies have explored how researchers employ these tools for scientific writing, their concrete implementation, limitations, and design challenges within the literature review process remain underexplored. In this paper, we report a user study with researchers across multiple disciplines to characterize current practices, benefits, and \textit{pain points} in using LLMs to investigate related work. We identified three recurring gaps: (i) lack of trust in outputs, (ii) persistent verification burden, and (iii) requiring multiple tools. This motivates our proposal of six design goals and a high-level framework that operationalizes them through improved related papers visualization, verification at every step, and human-feedback alignment with generation-guided explanations. Overall, by grounding our work in the practical, day-to-day needs of researchers, we designed a framework that addresses these limitations and models real-world LLM-assisted writing, advancing trust through verifiable actions and fostering practical collaboration between researchers and AI systems.

cs.HC↗

arXiv2025

Spectral Manifold Harmonization for Graph Imbalanced Regression

Graph-structured data is ubiquitous in scientific domains, where models often face imbalanced learning settings. In imbalanced regression, domain preferences focus on specific target value ranges that represent the most scientifically valuable cases; however, we observe a significant lack of research regarding this challenge. In this paper, we present Spectral Manifold Harmonization (SMH), a novel approach to address imbalanced regression challenges on graph-structured data by generating synthetic graph samples that preserve topological properties while focusing on the most relevant target distribution regions. Conventional methods fail in this context because they either ignore graph topology in case generation or do not target specific domain ranges, resulting in models biased toward average target values. Experimental results demonstrate the potential of SMH on chemistry and drug discovery benchmark datasets, showing consistent improvements in predictive performance for target domain ranges. Code is available at https://github.com/brendacnogueira/smh-graph-imbalance.git.

cs.LG↗

arXiv2024

Experiential-Informed Data Reconstruction for Fishery Sustainability and Policies in the Azores

Fishery analysis is critical in maintaining the long-term sustainability of species and the livelihoods of millions of people who depend on fishing for food and income. The fishing gear, or metier, is a key factor significantly impacting marine habitats, selectively targeting species and fish sizes. Analysis of commercial catches or landings by metier in fishery stock assessment and management is crucial, providing robust estimates of fishing efforts and their impact on marine ecosystems. In this paper, we focus on a unique data set from the Azores' fishing data collection programs between 2010 and 2017, where little information on metiers is available and sparse throughout our timeline. Our main objective is to tackle the task of data set reconstruction, leveraging domain knowledge and machine learning methods to retrieve or associate metier-related information to each fish landing. We empirically validate the feasibility of this task using a diverse set of modeling approaches and demonstrate how it provides new insights into different fisheries' behavior and the impact of metiers over time, which are essential for future fish population assessments, management, and conservation efforts.

cs.LG↗

arXiv2023

Dynamics of Fisheries in the Azores Islands: A Network Analysis Approach

In the context of the global seafood industry, the Azores archipelago (Portugal) plays a pivotal role due to its vast maritime domain. This study employs complex network analysis techniques to investigate the dynamics of Azores fisheries, using time series data converted into networks. We uncover associations between Tunas and specific islands, consistent links among fish classifications, and identify other pivotal nodes within the fishing network. Remarkably, nodes with high degrees and a local clustering coefficient of one provide crucial insights into the fishing ecosystem. This study highlights the value of network analysis for understanding fisheries complexities and offers insights into sustainable management and the preservation of marine ecosystems. It also emphasizes the urgency for ongoing research and data collection to enrich our understanding of this multifaceted domain.

cs.SI↗