Daily Papers

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Large Language Models (LLMs) exhibit strong but shallow alignment: they directly refuse harmful queries when a refusal is expected at the very start of an assistant turn, yet this protection collapses once a harmful continuation is underway (either through the adversarial attacks or via harmful assistant-prefill attacks). This raises a fundamental question: Can the innate shallow alignment in LLMs be unlocked to ensure safety at arbitrary generation depths? To achieve this goal, we propose Any-Depth Alignment (ADA), an effective inference-time defense with negligible overhead. ADA is built based on our observation that alignment is concentrated in the assistant header tokens through repeated use in shallow-refusal training, and these tokens possess the model's strong alignment priors. By reintroducing these tokens mid-stream, ADA induces the model to reassess harmfulness and recover refusals at any point in generation. Across diverse open-source model families (Llama, Gemma, Mistral, Qwen, DeepSeek, and gpt-oss), ADA achieves robust safety performance without requiring any changes to the base model's parameters. It secures a near-100% refusal rate against challenging adversarial prefill attacks ranging from dozens to thousands of tokens. Furthermore, ADA reduces the average success rate of prominent adversarial prompt attacks (such as GCG, AutoDAN, PAIR, and TAP) to below 3%. This is all accomplished while preserving utility on benign tasks with minimal over-refusal. ADA maintains this resilience even after the base model undergoes subsequent instruction tuning (benign or adversarial).

Safeguarding vision-language models (VLMs) is a critical challenge, as existing methods often suffer from over-defense, which harms utility, or rely on shallow alignment, failing to detect complex threats that require deep reasoning. To this end, we introduce PRISM (Principled Reasoning for Integrated Safety in Multimodality), a system2-like framework that aligns VLMs by embedding a structured, safety-aware reasoning process. Our framework consists of two key components: PRISM-CoT, a dataset that teaches safety-aware chain-of-thought reasoning, and PRISM-DPO, generated via Monte Carlo Tree Search (MCTS) to further refine this reasoning through Direct Preference Optimization to help obtain a delicate safety boundary. Comprehensive evaluations demonstrate PRISM's effectiveness, achieving remarkably low attack success rates including 0.15% on JailbreakV-28K for Qwen2-VL and 90% improvement over the previous best method on VLBreak for LLaVA-1.5. PRISM also exhibits strong robustness against adaptive attacks, significantly increasing computational costs for adversaries, and generalizes effectively to out-of-distribution challenges, reducing attack success rates to just 8.70% on the challenging multi-image MIS benchmark. Remarkably, this robust defense is achieved while preserving, and in some cases enhancing, model utility. To promote reproducibility, we have made our code, data, and model weights available at https://github.com/SaFoLab-WISC/PRISM.

We introduce CogVLM, a powerful open-source visual language foundation model. Different from the popular shallow alignment method which maps image features into the input space of language model, CogVLM bridges the gap between the frozen pretrained language model and image encoder by a trainable visual expert module in the attention and FFN layers. As a result, CogVLM enables deep fusion of vision language features without sacrificing any performance on NLP tasks. CogVLM-17B achieves state-of-the-art performance on 10 classic cross-modal benchmarks, including NoCaps, Flicker30k captioning, RefCOCO, RefCOCO+, RefCOCOg, Visual7W, GQA, ScienceQA, VizWiz VQA and TDIUC, and ranks the 2nd on VQAv2, OKVQA, TextVQA, COCO captioning, etc., surpassing or matching PaLI-X 55B. Codes and checkpoints are available at https://github.com/THUDM/CogVLM.

The safety alignment of current Large Language Models (LLMs) is vulnerable. Relatively simple attacks, or even benign fine-tuning, can jailbreak aligned models. We argue that many of these vulnerabilities are related to a shared underlying issue: safety alignment can take shortcuts, wherein the alignment adapts a model's generative distribution primarily over only its very first few output tokens. We refer to this issue as shallow safety alignment. In this paper, we present case studies to explain why shallow safety alignment can exist and provide evidence that current aligned LLMs are subject to this issue. We also show how these findings help explain multiple recently discovered vulnerabilities in LLMs, including the susceptibility to adversarial suffix attacks, prefilling attacks, decoding parameter attacks, and fine-tuning attacks. Importantly, we discuss how this consolidated notion of shallow safety alignment sheds light on promising research directions for mitigating these vulnerabilities. For instance, we show that deepening the safety alignment beyond just the first few tokens can often meaningfully improve robustness against some common exploits. Finally, we design a regularized finetuning objective that makes the safety alignment more persistent against fine-tuning attacks by constraining updates on initial tokens. Overall, we advocate that future safety alignment should be made more than just a few tokens deep.

Current LLM safety defenses fail under decomposition attacks, where a malicious goal is decomposed into benign subtasks that circumvent refusals. The challenge lies in the existing shallow safety alignment techniques: they only detect harm in the immediate prompt and do not reason about long-range intent, leaving them blind to malicious intent that emerges over a sequence of seemingly benign instructions. We therefore propose adding an external monitor that observes the conversation at a higher granularity. To facilitate our study of monitoring decomposition attacks, we curate the largest and most diverse dataset to date, including question-answering, text-to-image, and agentic tasks. We verify our datasets by testing them on frontier LLMs and show an 87% attack success rate on average on GPT-4o. This confirms that decomposition attack is broadly effective. Additionally, we find that random tasks can be injected into the decomposed subtasks to further obfuscate malicious intents. To defend in real time, we propose a lightweight sequential monitoring framework that cumulatively evaluates each subtask. We show that a carefully prompt engineered lightweight monitor achieves a 93% defense success rate, beating reasoning models like o3 mini as a monitor. Moreover, it remains robust against random task injection and cuts cost by 90% and latency by 50%. Our findings suggest that lightweight sequential monitors are highly effective in mitigating decomposition attacks and are viable in deployment.

Large Language Models (LLMs) achieve gold-medal performance across many benchmarks, yet it remains unclear whether such success reflects genuine reasoning or pattern matching. From a cognitive science perspective, an informative test is whether models can master an unfamiliar language through explicit metalinguistic deductive learning, a paradigm where human learners can reliably internalise grammatical systems through metalinguistic reasoning. We address this question with Camlang, a novel constructed language that exhibits naturalistic yet unattested feature combinations. Camlang consists of two explicit resources, a grammar book and a bilingual dictionary, which mirror adult second-language learning via explicit grammar rules and lexical lookup, and enable us to disentangle errors in morpho-syntax, lexical semantics, and sentence-level reasoning. Human experiments show that these resources are sufficient for participants to acquire Camlang and successfully solve Camlang tasks. To operationalise evaluation, we adapt CommonsenseQA into Camlang, creating Camlang-CSQA-v0, the first task in a broader suite where solving questions requires applying grammar rules and lexical mappings. Experimental results show that GPT-5 achieves 98\% EM accuracy in English but only 47\% in Camlang, far below human performance at 87\%, while other state-of-the-art reasoning LLMs perform even worse. Human verification further reveals that most model successes stem from shallow lexical alignment while GPT-5 shows emerging metalinguistic awareness to a limited extent but not systematic grammatical mastery as humans. Camlang establishes a cognitively grounded evaluation paradigm that exposes fundamental gaps between current models and human metalinguistic competence.

In autonomous driving, vision-centric 3D detection aims to identify 3D objects from images. However, high data collection costs and diverse real-world scenarios limit the scale of training data. Once distribution shifts occur between training and test data, existing methods often suffer from performance degradation, known as Out-of-Distribution (OOD) problems. To address this, controllable Text-to-Image (T2I) diffusion offers a potential solution for training data enhancement, which is required to generate diverse OOD scenarios with precise 3D object geometry. Nevertheless, existing controllable T2I approaches are restricted by the limited scale of training data or struggle to preserve all annotated 3D objects. In this paper, we present DriveGEN, a method designed to improve the robustness of 3D detectors in Driving via Training-Free Controllable Text-to-Image Diffusion Generation. Without extra diffusion model training, DriveGEN consistently preserves objects with precise 3D geometry across diverse OOD generations, consisting of 2 stages: 1) Self-Prototype Extraction: We empirically find that self-attention features are semantic-aware but require accurate region selection for 3D objects. Thus, we extract precise object features via layouts to capture 3D object geometry, termed self-prototypes. 2) Prototype-Guided Diffusion: To preserve objects across various OOD scenarios, we perform semantic-aware feature alignment and shallow feature alignment during denoising. Extensive experiments demonstrate the effectiveness of DriveGEN in improving 3D detection. The code is available at https://github.com/Hongbin98/DriveGEN.