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Xinrui Chen

Xinrui Chen contributes to research discovery and scholarly infrastructure.

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Artificial Intelligence Computer Vision Machine Learning Quantitative Methods

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preprint2026arXiv

Co-Generative De Novo Functional Protein Design

De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applications in biotechnology and medicine. Existing approaches adopt either direct function-to-sequence mapping or decoupled structure-sequence generation strategies but often fail to achieve functionality and foldability simultaneously. To address this, we propose CodeFP, a Co-generative protein language model for de novo Functional Protein design that simultaneously decodes sequence and structure tokens, thereby enabling superior simultaneous realization of functionality and foldability. CodeFP utilizes functional local structures to enrich functional semantic encodings, overcoming the suboptimal translation of flat encodings into structure tokens, while introducing auxiliary functional supervision to alleviate training ambiguity stemming from the one-to-many structure-to-token mapping. Extensive experiments show that CodeFP consistently achieves average improvements of 6.1% in functional consistency and 3.2% in foldability over the strongest baseline.

preprint2026arXiv

Is Class Signal Clustered or Routed in Task-Induced Implicit Neural Representation Weight Spaces?

Implicit neural representations (INRs) encode images as neural-network weights, making image classification a problem of weight-space classifiability. A natural geometric hypothesis is that classifier feedback should make image-specific weights cluster by class in the shared-anchor coordinate. We test this hypothesis in the SIREN-based Meta Weight Transformer (MWT) regime, where end-to-end training meta-learns a shared initialization and inner-loop update schedule for fitting image-specific SIRENs. We find that this prediction fails. Exposed weight-space geometry and supervised clustering pressure do not reliably track trained-reader accuracy; clustering can even make local neighborhoods more class-consistent while making the trained reader worse. Crucially, the reader constructs rather than inherits class-aligned geometry: token-flow diagnostics show that class-aligned neighborhoods become strongly predictive of trained-reader accuracy only after late reader interactions, not in the input coordinate. We further identify the native SIREN bias column in the augmented weight token as a low-dimensional, sample-dependent causal readout route for the trained reader; targeted controls rule out generic scalar-column and marginal-distribution artifacts. The diagnosis motivates interventions that strengthen reader routing, add an explicit bias route, or use denser inner-loop fitting; under the lane-specific training conventions used here, route-directed variants often outperform the shared-anchor baseline but interact non-additively. Task-induced INR weights are classifiable not because they form raw geometric clusters, but because their class signal is routed through the reader.

preprint2026arXiv

One Algorithm, Two Goals: Dual Scoring for Parameter and Data Selection in LLM Fine-Tuning

In Large Language Model (LLM) fine-tuning, parameter and data selection are common strategies for reducing fine-tuning cost, yet they are typically driven by separate scoring mechanisms. When a parameter mask and data subset jointly determine restricted fine-tuning, this separation incurs redundant overhead and makes coordinated selection difficult. We cast parameter and data selection as two bilevel selection problems under a common validation objective and derive a shared local response-surrogate scoring rule. Under first- and second-order validation-improvement approximations, parameter importance and data utility emerge as column-wise and row-wise aggregations of a single gradient interaction matrix, yielding a closed-form row-column correspondence for co-extracting both signals. Building on this structure, we propose DualSFT (Dual-Selection Fine-Tuning), a one-shot dual-scoring algorithm that produces a parameter mask and data subset from shared gradient statistics. On 3B-9B LLMs, single-axis DualSFT variants strengthen target-task performance and stability-plasticity trade-offs within their comparison groups, while full DualSFT yields a more favorable joint-constrained trade-off than sequential hybrid baselines under matched budgets.

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