3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose \textbf{U}nified Variational \textbf{A}uto-\textbf{E}ncoder for \textbf{3D} Molecular Latent Diffusion Modeling (\textbf{UAE-3D}), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both \textit{de novo} and conditional 3D molecule generation, achieving leading efficiency and quality.

Large Language Models (LLMs) have been observed to process non-human-readable text sequences, such as jailbreak prompts, often viewed as a bug for aligned LLMs. In this work, we present a systematic investigation challenging this perception, demonstrating that unnatural languages - strings that appear incomprehensible to humans but maintain semantic meanings for LLMs - contain latent features usable by models. Notably, unnatural languages possess latent features that can be generalized across different models and tasks during inference. Furthermore, models fine-tuned on unnatural versions of instruction datasets perform on-par with those trained on natural language, achieving 49.71 win rates in Length-controlled AlpacaEval 2.0 in average across various base models. In addition, through comprehensive analysis, we demonstrate that LLMs process unnatural languages by filtering noise and inferring contextual meaning from filtered words.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

Contrastive Language-Image Pre-training (CLIP) has become the standard for cross-modal image-text representation learning. Improving CLIP typically requires additional data and retraining with new loss functions, but these demands raise resource and time costs, limiting practical use. In this work, we introduce HELIP, a cost-effective strategy that improves CLIP models by exploiting challenging text-image pairs within existing datasets in continuous training. This eliminates the need for additional data or extensive retraining. Moreover, HELIP integrates effortlessly into current training pipelines with minimal code modifications, allowing for quick and seamless implementation. On comprehensive benchmarks, HELIP consistently boosts existing models. In particular, within just two epochs of training, it improves zero-shot classification accuracy on ImageNet for SLIP models pre-trained on CC3M, CC12M, and YFCC15M datasets by 3.05%, 4.47%, and 10.1% , respectively. In addition, on fine-grained classification datasets, HELIP improves the zero-shot performance of CLIP and SLIP by an average of 8.4% and 18.6%, and their linear probe performance by an average of 9.5% and 3.0%. The code is publicly available at: https://github.com/haonan3/HELIP-NACCL-2025.git.

As LLMs increasingly impact safety-critical applications, ensuring their safety using guardrails remains a key challenge. This paper proposes GuardReasoner, a new safeguard for LLMs, by guiding the guard model to learn to reason. Concretely, we first create the GuardReasonerTrain dataset, which consists of 127K samples with 460K detailed reasoning steps. Then, we introduce reasoning SFT to unlock the reasoning capability of guard models. In addition, we present hard sample DPO to further strengthen their reasoning ability. In this manner, GuardReasoner achieves better performance, explainability, and generalizability. Extensive experiments and analyses on 13 benchmarks of 3 guardrail tasks demonstrate its superiority.

Optimizing neural networks with loss that contain high-dimensional and high-order differential operators is expensive to evaluate with back-propagation due to $\mathcal{O}(d^{k})$ scaling of the derivative tensor size and the $\mathcal{O}(2^{k-1}L)$ scaling in the computation graph, where $d$ is the dimension of the domain, $L$ is the number of ops in the forward computation graph, and $k$ is the derivative order. In previous works, the polynomial scaling in $d$ was addressed by amortizing the computation over the optimization process via randomization. Separately, the exponential scaling in $k$ for univariate functions ($d=1$) was addressed with high-order auto-differentiation (AD). In this work, we show how to efficiently perform arbitrary contraction of the derivative tensor of arbitrary order for multivariate functions, by properly constructing the input tangents to univariate high-order AD, which can be used to efficiently randomize any differential operator. When applied to Physics-Informed Neural Networks (PINNs), our method provides >1000$\times$ speed-up and >30$\times$ memory reduction over randomization with first-order AD, and we can now solve \emph{1-million-dimensional PDEs in 8 minutes on a single NVIDIA A100 GPU}. This work opens the possibility of using high-order differential operators in large-scale problems.

The field of Machine Learning has changed significantly since the 1970s. However, its most basic principle, Empirical Risk Minimization (ERM), remains unchanged. We propose Functional Risk Minimization~(FRM), a general framework where losses compare functions rather than outputs. This results in better performance in supervised, unsupervised, and RL experiments. In the FRM paradigm, for each data point $(x_i,y_i)$ there is function $f_{\theta_i}$ that fits it: $y_i = f_{\theta_i}(x_i)$. This allows FRM to subsume ERM for many common loss functions and to capture more realistic noise processes. We also show that FRM provides an avenue towards understanding generalization in the modern over-parameterized regime, as its objective can be framed as finding the simplest model that fits the training data.

Extending context window sizes allows large language models (LLMs) to process longer sequences and handle more complex tasks. Rotary Positional Embedding (RoPE) has become the de facto standard due to its relative positional encoding properties that benefit long-context training. However, we observe that using RoPE with BFloat16 format results in numerical issues, causing it to deviate from its intended relative positional encoding, especially in long-context scenarios. This issue arises from BFloat16's limited precision and accumulates as context length increases, with the first token contributing significantly to this problem. To address this, we develop AnchorAttention, a plug-and-play attention method that alleviates numerical issues caused by BFloat16, improves long-context capabilities, and speeds up training. AnchorAttention reduces unnecessary attention computations, maintains semantic coherence, and boosts computational efficiency by treating the first token as a shared anchor with a consistent position ID, making it visible to all documents within the training context. Experiments on three types of LLMs demonstrate that AnchorAttention significantly improves long-context performance and reduces training time by over 50\% compared to standard full attention mechanisms, while preserving the original LLM's capabilities on general tasks. Our code is available at https://github.com/haonan3/AnchorContext.

Large Language Models (LLMs) have demonstrated impressive capabilities in reasoning using Chain-of-Thought (CoT) prompting. However, CoT can be biased by users' instruction. In this work, we study the reasoning robustness of LLMs to typographical errors, which can naturally occur in users' queries. We design an Adversarial Typo Attack ($\texttt{ATA}$) algorithm that iteratively samples typos for words that are important to the query and selects the edit that is most likely to succeed in attacking. It shows that LLMs are sensitive to minimal adversarial typographical changes. Notably, with 1 character edit, Mistral-7B-Instruct's accuracy drops from 43.7% to 38.6% on GSM8K, while with 8 character edits the performance further drops to 19.2%. To extend our evaluation to larger and closed-source LLMs, we develop the $\texttt{R$^2$ATA}$ benchmark, which assesses models' $\underline{R}$easoning $\underline{R}$obustness to $\underline{\texttt{ATA}}$. It includes adversarial typographical questions derived from three widely used reasoning datasets-GSM8K, BBH, and MMLU-by applying $\texttt{ATA}$ to open-source LLMs. $\texttt{R$^2$ATA}$ demonstrates remarkable transferability and causes notable performance drops across multiple super large and closed-source LLMs.

We present Multi-expert Prompting, a novel enhancement of ExpertPrompting (Xu et al., 2023), designed to improve the large language model (LLM) generation. Specifically, it guides an LLM to fulfill an input instruction by simulating multiple experts, aggregating their responses, and selecting the best among individual and aggregated responses. This process is performed in a single chain of thoughts through our seven carefully designed subtasks derived from the Nominal Group Technique (Ven and Delbecq, 1974), a well-established decision-making framework. Our evaluations demonstrate that Multi-expert Prompting significantly outperforms ExpertPrompting and comparable baselines in enhancing the truthfulness, factuality, informativeness, and usefulness of responses while reducing toxicity and hurtfulness. It further achieves state-of-the-art truthfulness by outperforming the best baseline by 8.69% with ChatGPT. Multi-expert Prompting is efficient, explainable, and highly adaptable to diverse scenarios, eliminating the need for manual prompt construction.