arXiv subjects

Shengchao Liu

Publications and source records attributed to Shengchao Liu.

At least 19 recordsLinked to original sources

arXiv2026

On Distinguishing Capability Elicitation from Capability Creation in Post-Training: A Free-Energy Perspective

Debates about large language model post-training often treat supervised fine-tuning (SFT) as imitation and reinforcement learning (RL) as discovery. But this distinction is too coarse. What matters is whether a training procedure increases the probability of behaviors the pretrained model could already produce, or whether it changes what the model can practically reach. We argue that post-training research should distinguish between capability elicitation and capability creation. We make this distinction operational by introducing the notion of accessible support: the set of behaviors that a model can practically produce under finite budgets. Post-training that reweights behaviors within this support is capability elicitation; whereas changing the support itself corresponds to capability creation. We develop this argument through a free-energy view of post-training. SFT and RL can both be seen as reweighting a pretrained reference distribution, only with different external signals. Demonstration signals define low-energy behavior for SFT, and reward signals define low-energy behavior for RL. When the update remains close to the base model, the main effect is local reweighting, not capability creation. Within this framework, the central question is no longer whether post-training is framed as SFT or RL, but whether it reweights behaviors already within reach, or instead expands the model's reachable behavioral space through search, interaction, tool use, or the incorporation of new information.

cs.AI↗

arXiv2026

A Minimal Model of Representation Collapse: Frustration, Stop-Gradient, and Dynamics

Self-supervised representation learning is central to modern machine learning because it extracts structured latent features from unlabeled data and enables robust transfer across tasks and domains. However, it can suffer from representation collapse, a widely observed failure mode in which embeddings lose discriminative structure and distinct inputs become indistinguishable. To understand the mechanisms that drive collapse and the ingredients that prevent it, we introduce a minimal embedding-only model whose gradient-flow dynamics and fixed points can be analyzed in closed form, using a classification-representation setting as a concrete playground where collapse is directly quantified through the contraction of label-embedding geometry. We illustrate that the model does not collapse when the data are perfectly classifiable, while a small fraction of frustrated samples that cannot be classified consistently induces collapse through an additional slow time scale that follows the early performance gain. Within the same framework, we examine collapse prevention by adding a shared projection head and applying stop-gradient at the level of the training dynamics. We analyze the resulting fixed points and develop a dynamical mean-field style self-consistency description, showing that stop-gradient enables non-collapsed solutions and stabilizes finite class separation under frustration. We further verify empirically that the same qualitative dynamics and collapse-prevention effects appear in a linear teacher-student model, indicating that the minimal theory captures features that persist beyond the pure embedding setting.

cond-mat.dis-nn↗

arXiv2026

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling.

cs.LG↗

arXiv2026

Scalable Dielectric Tensor Predictions for Inorganic Materials using Equivariant Graph Neural Networks

Accurate prediction of dielectric tensors is essential for accelerating the discovery of next-generation inorganic dielectric materials. Existing machine learning approaches, such as equivariant graph neural networks, typically rely on specially-designed network architectures to enforce O(3) equivariance. However, to preserve equivariance, these specially-designed models restrict the update of equivariant features during message passing to linear transformations or gated equivariant nonlinearities. The inability to implicitly characterize more complex nonlinear structures may reduce the predictive accuracy of the model. In this study, we introduce a frame-averaging-based approach to achieve equivariant dielectric tensor prediction. We propose GoeCTP, an O(3)-equivariant framework that predicts dielectric tensors without imposing any structural restrictions on the backbone network. We benchmark its performance against several state-of-the-art models and further employ it for large-scale virtual screening of thermodynamically stable materials from the Materials Project database. GoeCTP successfully identifies various promising candidates, such as Zr(InBr$_3$)$_2$ (band gap $E_g = 2.41$ eV, dielectric constant $\overline{\varepsilon} = 194.72$) and SeI$_2$ (anisotropy ratio $α_r = 96.763$), demonstrating its accuracy and efficiency in accelerating the discovery of advanced inorganic dielectric materials.

cond-mat.mtrl-sci↗

arXiv2025

DEER: Disentangled Mixture of Experts with Instance-Adaptive Routing for Generalizable Machine-Generated Text Detection

Detecting machine-generated text has become a critical challenge amid the rapid advancement of LLMs, yet existing detectors degrade severely under domain shift. Through systematic pilot studies, we trace this vulnerability to two fundamental flaws in current generalization strategies, namely the incomplete preservation of domain-specific knowledge during multi-domain training and the misalignment between knowledge retrieval and the detection objective at inference. To address these gaps, we propose DEER, a Disentangled mixturE-of-ExpeRts framework that explicitly decouples domain-local and domain-invariant knowledge into specialized expert modules. Instead of static domain matching, DEER employs a reinforcement learning-driven router that selects expert pathways based on instance-level detection rewards. This task-aligned, domain-agnostic mechanism ensures robust adaptation to unseen distributions by prioritizing detection utility over stylistic resemblance. Extensive experiments demonstrate that DEER consistently outperforms state-of-the-art detectors, achieving average F1 improvements of 1.28% and 2.92%, and accuracy gains of 1.35% and 2.26% on in-domain and out-of-domain datasets, offering reliable generalization for open-world deployment.

cs.CL↗

arXiv2025

InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames

Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) how to tokenize molecules into a canonical 1D sequence of tokens that is invariant to both SE(3) transformations and atom index permutations, and (2) how to design an architecture capable of modeling hybrid atom-based tokens that couple discrete atom types with continuous 3D coordinates. To address these challenges, we introduce InertialAR. It first performs generation-oriented canonical tokenization by aligning each molecule to a canonical inertial frame and reordering atoms, thereby converting arbitrary 3D structures into a unique, SE(3)- and permutation-invariant sequence of tokens for autoregressive generation. Built upon this canonical tokenization, we propose geometric positional encoding (GeoPE), which endows Transformer attention with 3D geometric awareness. Finally, InertialAR utilizes a hierarchical autoregressive paradigm to decode the next atom, consecutively predicting the atom type and 3D coordinates via Diffusion Loss. Experimentally, InertialAR achieves state-of-the-art performance on 8 of the 10 evaluation metrics for unconditional generation across QM9, GEOM-Drugs, and B3LYP. Moreover, it significantly outperforms baselines in controllable generation for targeted chemical functionality, attaining state-of-the-art results across all 5 metrics. Code is available at github.com/HaoruiLi46/InertialAR.

cs.LG↗

arXiv2025

Can Reasoning Path still be Effective as Input? Bridging Post-Reasoning to Chain-of-Thought Compression

Recent developments have enabled advanced reasoning in Large Language Models (LLMs) via long Chain-of-Thought (CoT), trading efficiency during inference for performance. Existing works focus on compressing generated CoT in reasoning, which impairs the necessary information for deriving the correct answer. In this work, we propose post-reasoning, a reasoning paradigm that takes CoT as a part of context to simplify the reasoning task for LLMs. We find that post-reasoning significantly reduces the generation length of LLMs, but its effectiveness hinges on the efficiency and the reliability of the contextual CoT generation. Therefore, we propose Upfront CoT (UCoT), an efficient post-reasoning framework for CoT compression. UCoT trains a lightweight model (compressor) to provide contextual CoT in form of soft tokens and trains the LLM (executor) to leverage this contextual CoT for producing the final answer. Extensive experiments show that UCoT maintains the powerful reasoning ability of executor while significantly reducing the length of CoT. It is worth mentioning that when applying UCoT to the Qwen2.5-7B-Instruct model, the usage of tokens on GSM8K dataset is reduced by 50%, while the performance is 3.08% higher than that of the state-of-the-art (SOTA) method.

cs.CL↗

arXiv2025

MGT-Prism: Enhancing Domain Generalization for Machine-Generated Text Detection via Spectral Alignment

Large Language Models have shown growing ability to generate fluent and coherent texts that are highly similar to the writing style of humans. Current detectors for Machine-Generated Text (MGT) perform well when they are trained and tested in the same domain but generalize poorly to unseen domains, due to domain shift between data from different sources. In this work, we propose MGT-Prism, an MGT detection method from the perspective of the frequency domain for better domain generalization. Our key insight stems from analyzing text representations in the frequency domain, where we observe consistent spectral patterns across diverse domains, while significant discrepancies in magnitude emerge between MGT and human-written texts (HWTs). The observation initiates the design of a low frequency domain filtering module for filtering out the document-level features that are sensitive to domain shift, and a dynamic spectrum alignment strategy to extract the task-specific and domain-invariant features for improving the detector's performance in domain generalization. Extensive experiments demonstrate that MGT-Prism outperforms state-of-the-art baselines by an average of 0.90% in accuracy and 0.92% in F1 score on 11 test datasets across three domain-generalization scenarios.

cs.CL↗

arXiv2025

Expert-Guided LLM Reasoning for Battery Discovery: From AI-Driven Hypothesis to Synthesis and Characterization

Large language models (LLMs) leverage chain-of-thought (CoT) techniques to tackle complex problems, representing a transformative breakthrough in artificial intelligence (AI). However, their reasoning capabilities have primarily been demonstrated in solving math and coding problems, leaving their potential for domain-specific applications-such as battery discovery-largely unexplored. Inspired by the idea that reasoning mirrors a form of guided search, we introduce ChatBattery, a novel agentic framework that integrates domain knowledge to steer LLMs toward more effective reasoning in materials design. Using ChatBattery, we successfully identify, synthesize, and characterize three novel lithium-ion battery cathode materials, which achieve practical capacity improvements of 28.8%, 25.2%, and 18.5%, respectively, over the widely used cathode material, LiNi0.8Mn0.1Co0.1O2 (NMC811). Beyond this discovery, ChatBattery paves a new path by showing a successful LLM-driven and reasoning-based platform for battery materials invention. This complete AI-driven cycle-from design to synthesis to characterization-demonstrates the transformative potential of AI-driven reasoning in revolutionizing materials discovery.

cs.AI↗

arXiv2025

Flow Along the K-Amplitude for Generative Modeling

In this work, we propose a novel generative learning paradigm, K-Flow, an algorithm that flows along the $K$-amplitude. Here, $k$ is a scaling parameter that organizes frequency bands (or projected coefficients), and amplitude describes the norm of such projected coefficients. By incorporating the $K$-amplitude decomposition, K-Flow enables flow matching across the scaling parameter as time. We discuss three venues and six properties of K-Flow, from theoretical foundations, energy and temporal dynamics, and practical applications, respectively. Specifically, from the practical usage perspective, K-Flow allows steerable generation by controlling the information at different scales. To demonstrate the effectiveness of K-Flow, we conduct experiments on unconditional image generation, class-conditional image generation, and molecule assembly generation. Additionally, we conduct three ablation studies to demonstrate how K-Flow steers scaling parameter to effectively control the resolution of image generation.

cs.LG↗

arXiv2025

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

cs.LG↗

arXiv2025

A Text-guided Protein Design Framework

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level functionalities. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP which aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that creates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We quantitatively verify the effectiveness of ProteinDT on three challenging tasks: (1) over 90% accuracy for text-guided protein generation; (2) best hit ratio on 12 zero-shot text-guided protein editing tasks; (3) superior performance on four out of six protein property prediction benchmarks.

cs.LG↗

arXiv2025

CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

q-bio.BM↗

arXiv2024

A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding dynamics. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) the BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We demonstrate the efficiency and effectiveness of NeuralMD, achieving over 1K$\times$ speedup compared to standard numerical MD simulations. NeuralMD also outperforms all other ML approaches, achieving up to 15$\times$ reduction in reconstruction error and 70% increase in validity. Additionally, we qualitatively illustrate that the oscillations in the predicted trajectories align more closely with ground-truth dynamics than those of other machine-learning methods. We believe NeuralMD paves the foundation for a new research paradigm in simulating protein-ligand dynamics.

cs.LG↗

arXiv2024

Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

q-bio.QM↗

arXiv2024

Does DetectGPT Fully Utilize Perturbation? Bridging Selective Perturbation to Fine-tuned Contrastive Learning Detector would be Better

The burgeoning generative capabilities of large language models (LLMs) have raised growing concerns about abuse, demanding automatic machine-generated text detectors. DetectGPT, a zero-shot metric-based detector, first introduces perturbation and shows great performance improvement. However, in DetectGPT, the random perturbation strategy could introduce noise, and logit regression depends on the threshold, harming the generalizability and applicability of individual or small-batch inputs. Hence, we propose a novel fine-tuned detector, Pecola, bridging metric-based and fine-tuned methods by contrastive learning on selective perturbation. Selective strategy retains important tokens during perturbation and weights for multi-pair contrastive learning. The experiments show that Pecola outperforms the state-of-the-art (SOTA) by 1.20% in accuracy on average on four public datasets. And we further analyze the effectiveness, robustness, and generalization of the method.

cs.CL↗

arXiv2024

Improving Domain Generalization with Domain Relations

Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. This paper focuses on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D$^3$G. Unlike previous methods that aim to learn a single model that is domain invariant, D$^3$G leverages domain similarities based on domain metadata to learn domain-specific models. Concretely, D$^3$G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly obtained and learned from domain metadata. Under mild assumptions, we theoretically prove that using domain relations to reweight training-domain-specific functions achieves stronger out-of-domain generalization compared to the conventional averaging approach. Empirically, we evaluate the effectiveness of D$^3$G using real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein binding affinity prediction. Our results show that D$^3$G consistently outperforms state-of-the-art methods.

cs.LG↗

arXiv2024

Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

cs.LG↗