26 accepted papers
Controllable molecule generation is crucial for diverse scientific applications, such as drug discovery and materials design. While large language models (LLMs) show great promise, their dense and entangled representations impede precise control over the generation of molecules with bespoke substruc…
{\em De novo} peptide sequencing is a pivotal technique that directly reconstructs amino acid sequences from tandem mass spectrometry (MS/MS) data; it enables the identification of novel proteins and variants absent from reference databases. Previous methods are typically based on autoregressive (AR…
Can we train a 3D molecule generator using data from dense regions to generate samples in sparse regions? This challenge can be framed as an out-of-distribution (OOD) generation problem. While prior research on OOD generation predominantly targets property shifts, structural shifts, such as differen
Geometric graph neural networks (Geo-GNNs) have revolutionized molecular dynamics (MD) simulations by providing accurate and fast energy and force predictions. However, minor prediction errors could still destabilize MD trajectories in real MD simulations due to the limited coverage of molecular con…
Edge-cloud collaborative inference is crucial for LLM-powered edge devices, as on-device models often lack the required reasoning capability, while cloud-only inference can be costly and slow under strict latency and token/API budgets. However, existing edge-cloud collaboration methods typically rou…
Cross-capability transfer represents a key challenge in large language model (LLM) research, particularly in multi-task integration, model compression, and knowledge fusion. Recent works such as FuseLLM and FuseChat have shown the potential of transferring multiple model capabilities to lightweight…
Large-scale molecular dynamics simulations are essential in understanding chemical and biological processes, necessitating the accurate and efficient modeling of interatomic interactions. Existing learning-based methods generally are based on message passing mechanisms; they are either not scalable …
Recent advances in diffusion-based language models (DLMs) have shown remarkable potential for de novo protein design. However, enabling controllable protein generation requires integrating diverse biological conditions, such as structure, functions, and chemical interactions, each represented in dis
Predicting the tensor properties of crystalline materials is a fundamental task in materials science. Unlike single-value property prediction, which is inherently invariant, tensor property prediction requires maintaining O(3) group tensor equivariance. Such equivariance constraint often requires sp
Large Language Models (LLMs) have achieved impressive performance in complex reasoning problems. Their effectiveness highly depends on the specific nature of the task, especially the required domain knowledge. Existing approaches, such as mixture-of-experts, typically operate at the task level; they
This paper proposes a new 3D molecule generation framework, called GOAT, for fast and effective 3D molecule generation based on the flow-matching optimal transport objective. Specifically, we formulate a geometric transport formula for measuring the cost of mapping multi-modal features (e.g., contin…
Backdoor attacks pose a significant threat to deep neural networks (DNNs), as attackers can inject a backdoor by tampering with only a few samples. The variety of backdoor attacks makes comprehensive defense extremely challenging. Previous defenses typically assume that backdoor samples are out-of-d…
Graphs in the real world are fragmented and dynamic, lacking collaboration akin to that observed in human societies. Existing paradigms present collaborative information collapse and forgetting, making collaborative relationships poorly autonomous and interactive information insufficient. Moreover,…
Aligning Large Language Model (LLM) responses with human preferences is vital for building safe and controllable AI systems. While preference optimization methods based on Plackett-Luce (PL) and Bradley-Terry (BT) models have shown promise, they face challenges such as poor handling of harmful conte…
*De novo* peptide sequencing is a fundamental computational technique for ascertaining amino acid sequences of peptides directly from tandem mass spectrometry data, eliminating the need for reference databases. Cutting-edge models encode the observed mass spectra into latent representations from whi…
Crystal structures are defined by the periodic arrangement of atoms in 3D space, inherently making them equivariant to SO(3) group. A fundamental requirement for crystal property prediction is that the model's output should remain invariant to arbitrary rotational transformations of the input struct…
Traditional machine societies rely on data-driven learning, overlooking interactions and limiting knowledge acquisition from model interplay. To address these issues, we revisit the development of machine societies by drawing inspiration from the evolutionary processes of human societies. Motivated…
A plethora of fair graph neural networks (GNNs) have been proposed to promote algorithmic fairness for high-stake real-life contexts. Meanwhile, explainability is generally proposed to help machine learning practitioners debug models by providing human-understandable explanations. However, seldom wo…
This work presents an effective depth-consistency Self-Prompt Transformer, terms as SelfPromer, for image dehazing. It is motivated by an observation that the estimated depths of an image with haze residuals and its clear counterpart vary. Enforcing the depth consistency of dehazed images with clear…
Learning new knowledge frequently occurs in our dynamically changing world, e.g., humans culturally evolve by continuously acquiring new abilities to sustain their survival, leveraging collective intelligence rather than a large number of individual attempts. The effective learning paradigm during c…
Graph class incremental learning (GCIL) requires the model to classify emerging nodes of new classes while remembering old classes. Existing methods are designed to preserve effective information of old models or graph data to alleviate forgetting, but there is no clear theoretical understanding of…
Graph meta-learning has become a preferable paradigm for graph-based node classification with long-tail distribution, owing to its capability of capturing the intrinsic manifold of support and query nodes. Despite the remarkable success, graph meta-learning suffers from severe performance degradatio…
Soft object manipulation tasks in domestic scenes pose a significant challenge for existing robotic skill learning techniques due to their complex dynamics and variable shape characteristics. Since learning new manipulation skills from human demonstration is an effective way for robot applications,…
This paper proposes a new eXplanation framework, called OrphicX, for generating causal explanations for any graph neural networks (GNNs) based on learned latent causal factors. Specifically, we construct a distinct generative model and design an objective function that encourages the generative mode…
This paper presents {\em Gem}, a model-agnostic approach for providing interpretable explanations for any GNNs on various graph learning tasks. Specifically, we formulate the problem of providing explanations for the decisions of GNNs as a causal learning task. Then we train a causal explanation mod…
Graph-based semi-supervised learning has been shown to be one of the most effective classification approaches, as it can exploit connectivity patterns between labeled and unlabeled samples to improve learning performance. However, we show that existing techniques perform poorly when labeled data are…