Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.
As Vision Language Models (VLMs) gain widespread use, their fairness remains under-explored. In this paper, we analyze demographic biases across five models and six datasets. We find that portrait datasets like UTKFace and CelebA are the best tools for bias detection, finding gaps in performance and fairness for both LLaVa and CLIP models. Scene-based datasets like PATA and VLStereoSet fail to be useful benchmarks for bias due to their text prompts allowing the model to guess the answer without a picture. As for pronoun-based datasets like VisoGender, we receive mixed signals as only some subsets of the data are useful in providing insights. To alleviate these two problems, we introduce a more rigorous evaluation dataset and a debiasing method based on Sparse Autoencoders to help reduce bias in models. We find that our data set generates more meaningful errors than the previous data sets. Furthermore, our debiasing method improves fairness, gaining 5-15 points in performance over the baseline. This study displays the problems with the current benchmarks for measuring demographic bias in Vision Language Models and introduces both a more effective dataset for measuring bias and a novel and interpretable debiasing method based on Sparse Autoencoders.
We focus on improving the visual understanding capability for boosting the vision-language models. We propose \textbf{Arcana}, a multiModal language model, which introduces two crucial techniques. First, we present Multimodal LoRA (MM-LoRA), a module designed to enhance the decoder. Unlike traditional language-driven decoders, MM-LoRA consists of two parallel LoRAs -- one for vision and one for language -- each with its own parameters. This disentangled parameters design allows for more specialized learning in each modality and better integration of multimodal information. Second, we introduce the Query Ladder adapter (QLadder) to improve the visual encoder. QLadder employs a learnable ``\textit{ladder}'' structure to deeply aggregates the intermediate representations from the frozen pretrained visual encoder (e.g., CLIP image encoder). This enables the model to learn new and informative visual features, as well as remaining the powerful capabilities of the pretrained visual encoder. These techniques collectively enhance Arcana's visual perception power, enabling it to leverage improved visual information for more accurate and contextually relevant outputs across various multimodal scenarios. Extensive experiments and ablation studies demonstrate the effectiveness and generalization capability of our Arcana. The code and re-annotated data are available at \url{https://arcana-project-page.github.io}.
Video Multimodal Large Language Models (MLLMs) have shown remarkable capability of understanding the video semantics on various downstream tasks. Despite the advancements, there is still a lack of systematic research on visual context representation, which refers to the scheme to select frames from a video and further select the tokens from a frame. In this paper, we explore the design space for visual context representation, and aim to improve the performance of video MLLMs by finding more effective representation schemes. Firstly, we formulate the task of visual context representation as a constrained optimization problem, and model the language modeling loss as a function of the number of frames and the number of embeddings (or tokens) per frame, given the maximum visual context window size. Then, we explore the scaling effects in frame selection and token selection respectively, and fit the corresponding function curve by conducting extensive empirical experiments. We examine the effectiveness of typical selection strategies and present empirical findings to determine the two factors. Furthermore, we study the joint effect of frame selection and token selection, and derive the optimal formula for determining the two factors. We demonstrate that the derived optimal settings show alignment with the best-performed results of empirical experiments. Our code and model are available at: https://github.com/RUCAIBox/Opt-Visor.
An ability to learn about new objects from a small amount of visual data and produce convincing linguistic justification about the presence/absence of certain concepts (that collectively compose the object) in novel scenarios is an important characteristic of human cognition. This is possible due to abstraction of attributes/properties that an object is composed of e.g. an object `bird' can be identified by the presence of a beak, feathers, legs, wings, etc. Inspired by this aspect of human reasoning, in this work, we present a zero-shot framework for fine-grained visual concept learning by leveraging large language model and Visual Question Answering (VQA) system. Specifically, we prompt GPT-3 to obtain a rich linguistic description of visual objects in the dataset. We convert the obtained concept descriptions into a set of binary questions. We pose these questions along with the query image to a VQA system and aggregate the answers to determine the presence or absence of an object in the test images. Our experiments demonstrate comparable performance with existing zero-shot visual classification methods and few-shot concept learning approaches, without substantial computational overhead, yet being fully explainable from the reasoning perspective.
The advancement of large language model (LLM) based artificial intelligence technologies has been a game-changer, particularly in sentiment analysis. This progress has enabled a shift from highly specialized research environments to practical, widespread applications within the industry. However, integrating diverse AI models for processing complex multimodal data and the associated high costs of feature extraction presents significant challenges. Motivated by the marketing oriented software development +needs, our study introduces a collaborative AI framework designed to efficiently distribute and resolve tasks across various AI systems to address these issues. Initially, we elucidate the key solutions derived from our development process, highlighting the role of generative AI models like \emph{chatgpt}, \emph{google gemini} in simplifying intricate sentiment analysis tasks into manageable, phased objectives. Furthermore, we present a detailed case study utilizing our collaborative AI system in edge and cloud, showcasing its effectiveness in analyzing sentiments across diverse online media channels.
Large Language Models (LLMs) have been widely used in code completion, and researchers are focusing on scaling up LLMs to improve their accuracy. However, larger LLMs have lower inference efficiency, affecting developers' experience and productivity. In this paper, we propose a lightweight and effective LLM for code completion named aiXcoder-7B. Compared to existing LLMs, aiXcoder-7B achieves higher code completion accuracy while having smaller scales (i.e., 7 billion parameters). We attribute the superiority of aiXcoder-7B to three key factors: (1) Multi-objective training. We employ three training objectives, one of which is our proposed Structured Fill-In-the-Middle (SFIM). SFIM considers the syntax structures in code and effectively improves the performance of LLMs for code. (2) Diverse data sampling strategies. They consider inter-file relationships and enhance the capability of LLMs in understanding cross-file contexts. (3) Extensive high-quality data. We establish a rigorous data collection pipeline and consume a total of 1.2 trillion unique tokens for training aiXcoder-7B. This vast volume of data enables aiXcoder-7B to learn a broad distribution of code. We evaluate aiXcoder-7B in five popular code completion benchmarks and a new benchmark collected by this paper. The results show that aiXcoder-7B outperforms the latest six LLMs with similar sizes and even surpasses four larger LLMs (e.g., StarCoder2-15B and CodeLlama-34B), positioning aiXcoder-7B as a lightweight and effective LLM for academia and industry. Finally, we summarize three valuable insights for helping practitioners train the next generations of LLMs for code. aiXcoder-7B has been open-souced and gained significant attention. Until January 2025, aiXcoder-7B has received 2,226 GitHub Stars.
Vision-Language Models (VLMs) often generate plausible but incorrect responses to visual queries. However, reliably quantifying the effect of such hallucinations in free-form responses to open-ended queries is challenging as it requires visually verifying each claim within the response. We propose Programmatic VLM Evaluation (PROVE), a new benchmarking paradigm for evaluating VLM responses to open-ended queries. To construct PROVE, we provide a large language model (LLM) with a high-fidelity scene-graph representation constructed from a hyper-detailed image caption, and prompt it to generate diverse question-answer (QA) pairs, as well as programs that can be executed over the scene graph object to verify each QA pair. We thus construct a benchmark of 10.5k challenging but visually grounded QA pairs. Next, to evaluate free-form model responses to queries in PROVE, we propose a programmatic evaluation strategy that measures both the helpfulness and truthfulness of a response within a unified scene graph-based framework. We benchmark the helpfulness-truthfulness trade-offs of a range of VLMs on PROVE, finding that very few are in-fact able to achieve a good balance between the two. Project page: \url{https://prove-explorer.netlify.app/}.
Numerous previous studies have sought to determine to what extent language models, pretrained on natural language text, can serve as useful models of human cognition. In this paper, we are interested in the opposite question: whether we can directly optimize a language model to be a useful cognitive model by aligning it to human psychometric data. To achieve this, we introduce a novel alignment technique in which we fine-tune a language model to implicitly optimize the parameters of a linear regressor that directly predicts humans' reading times of in-context linguistic units, e.g., phonemes, morphemes, or words, using surprisal estimates derived from the language model. Using words as a test case, we evaluate our technique across multiple model sizes and datasets and find that it improves language models' psychometric predictive power. However, we find an inverse relationship between psychometric power and a model's performance on downstream NLP tasks as well as its perplexity on held-out test data. While this latter trend has been observed before (Oh et al., 2022; Shain et al., 2024), we are the first to induce it by manipulating a model's alignment to psychometric data.
Transformer-based Large Language Models (LLMs) traditionally rely on final-layer loss for training and final-layer representations for predictions, potentially overlooking the predictive power embedded in intermediate layers. Surprisingly, we find that focusing training efforts on these intermediate layers can yield training losses comparable to those of final layers, with complementary test-time performance. We introduce a novel tuning framework, Mixture-of-Depths (MoD), which trains late layers as ensembles contributing to the final logits through learned routing weights. With the auxiliary distillation loss and additional normalization modules, we ensure that the outputs of the late layers adapt to language modeling. Our MoD framework, which can be integrated with any existing tuning method, shows consistent improvement on various language modelling tasks. Furthermore, by replacing traditional trainable modules with MoD, our approach achieves similar performance with significantly fewer trainable parameters, demonstrating the potential of leveraging predictive power from intermediate representations during training.
Online reviews play a pivotal role in influencing consumer decisions across various domains, from purchasing products to selecting hotels or restaurants. However, the sheer volume of reviews -- often containing repetitive or irrelevant content -- leads to information overload, making it challenging for users to extract meaningful insights. Traditional opinion summarization models face challenges in handling long inputs and large volumes of reviews, while newer Large Language Model (LLM) approaches often fail to generate accurate and faithful summaries. To address those challenges, this paper introduces (1) a new dataset of long-form user reviews, each entity comprising over a thousand reviews, (2) two training-free LLM-based summarization approaches that scale to long inputs, and (3) automatic evaluation metrics. Our dataset of user reviews is paired with in-depth and unbiased critical summaries by domain experts, serving as a reference for evaluation. Additionally, our novel reference-free evaluation metrics provide a more granular, context-sensitive assessment of summary faithfulness. We benchmark several open-source and closed-source LLMs using our methods. Our evaluation reveals that LLMs still face challenges in balancing sentiment and format adherence in long-form summaries, though open-source models can narrow the gap when relevant information is retrieved in a focused manner.
Reinforcement Learning from Human Feedback (RLHF) has become the predominant approach for language model (LM) alignment. At its core, RLHF uses a margin-based loss for preference optimization, specifying ideal LM behavior only by the difference between preferred and dispreferred responses. In this paper, we identify a common pitfall of margin-based methods -- the under-specification of ideal LM behavior on preferred and dispreferred responses individually, which leads to two unintended consequences as the margin increases: (1) The probability of dispreferred (e.g., unsafe) responses may increase, resulting in potential safety alignment failures. (2) The probability of preferred responses may decrease, even when those responses are ideal. We demystify the reasons behind these problematic behaviors: margin-based losses couple the change in the preferred probability to the gradient of the dispreferred one, and vice versa, often preventing the preferred probability from increasing while the dispreferred one decreases, and thus causing a synchronized increase or decrease in both probabilities. We term this effect, inherent in margin-based objectives, gradient entanglement. Formally, we derive conditions for general margin-based alignment objectives under which gradient entanglement becomes concerning: the inner product of the gradients of preferred and dispreferred log-probabilities is large relative to the individual gradient norms. We theoretically investigate why such inner products can be large when aligning language models and empirically validate our findings. Empirical implications of our framework extend to explaining important differences in the training dynamics of various preference optimization algorithms, and suggesting potential algorithm designs to mitigate the under-specification issue of margin-based methods and thereby improving language model alignment.
We consider the problem of team selection within multiagent adversarial team games. We propose BERTeam, a novel algorithm that uses a transformer-based deep neural network with Masked Language Model training to select the best team of players from a trained population. We integrate this with coevolutionary deep reinforcement learning, which trains a diverse set of individual players to choose from. We test our algorithm in the multiagent adversarial game Marine Capture-The-Flag, and find that BERTeam learns non-trivial team compositions that perform well against unseen opponents. For this game, we find that BERTeam outperforms MCAA, an algorithm that similarly optimizes team selection.
Existing Multimodal Large Language Model (MLLM)-based agents face significant challenges in handling complex GUI (Graphical User Interface) interactions on devices. These challenges arise from the dynamic and structured nature of GUI environments, which integrate text, images, and spatial relationships, as well as the variability in action spaces across different pages and tasks. To address these limitations, we propose MobA, a novel MLLM-based mobile assistant system. MobA introduces an adaptive planning module that incorporates a reflection mechanism for error recovery and dynamically adjusts plans to align with the real environment contexts and action module's execution capacity. Additionally, a multifaceted memory module provides comprehensive memory support to enhance adaptability and efficiency. We also present MobBench, a dataset designed for complex mobile interactions. Experimental results on MobBench and AndroidArena demonstrate MobA's ability to handle dynamic GUI environments and perform complex mobile tasks.
Traditional retrieval-augmented generation (RAG) benchmarks evaluate systems using heuristic-based metrics, but these require human preferences as the ground truth for reference. In contrast, arena-based benchmarks, where systems compete against each other, require an expensive large language model (LLM) as a judge for a reliable evaluation. We present a simple efficient technique to combine the best of both worlds. The idea is to train a surrogate judge using heuristic metrics as input, to output the LLM as a judge prediction. In our work, we develop MIRAGE-Bench, a synthetic arena-based RAG benchmark for 18 diverse languages on Wikipedia focused on multilingual answer generation evaluation. It extensively couples both heuristic features and LLM as a judge for evaluation. We benchmark 19 multilingual LLMs, and observe a high correlation (Kendall Tau ($\tau$) = 0.909) using our surrogate judge and between GPT-4o as a teacher using the Bradley-Terry framework. Our results show proprietary and large open-source LLMs currently dominate on MIRAGE-Bench. Our code and datasets are made publicly available here: https://github.com/vectara/mirage-bench.
Large language models (LLMs) achieve state-of-the-art performance on multiple language tasks, yet their safety guardrails can be circumvented, leading to harmful generations. In light of this, recent research on safety mechanisms has emerged, revealing that when safety representations or component are suppressed, the safety capability of LLMs are compromised. However, existing research tends to overlook the safety impact of multi-head attention mechanisms, despite their crucial role in various model functionalities. Hence, in this paper, we aim to explore the connection between standard attention mechanisms and safety capability to fill this gap in the safety-related mechanistic interpretability. We propose a novel metric which tailored for multi-head attention, the Safety Head ImPortant Score (Ships), to assess the individual heads' contributions to model safety. Based on this, we generalize Ships to the dataset level and further introduce the Safety Attention Head AttRibution Algorithm (Sahara) to attribute the critical safety attention heads inside the model. Our findings show that the special attention head has a significant impact on safety. Ablating a single safety head allows aligned model (e.g., Llama-2-7b-chat) to respond to 16 times more harmful queries, while only modifying 0.006% of the parameters, in contrast to the ~ 5% modification required in previous studies. More importantly, we demonstrate that attention heads primarily function as feature extractors for safety and models fine-tuned from the same base model exhibit overlapping safety heads through comprehensive experiments. Together, our attribution approach and findings provide a novel perspective for unpacking the black box of safety mechanisms within large models.
Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainstream MO approaches primarily utilize external property predictors to guide iterative property optimization. However, learning all molecular samples in the vast chemical space is unrealistic for predictors. As a result, errors and noise are inevitably introduced during property prediction due to the nature of approximation. This leads to discrepancy accumulation, generalization reduction and suboptimal molecular candidates. In this paper, we propose a text-guided multi-property molecular optimization method utilizing transformer-based diffusion language model (TransDLM). TransDLM leverages standardized chemical nomenclature as semantic representations of molecules and implicitly embeds property requirements into textual descriptions, thereby preventing error propagation during diffusion process. Guided by physically and chemically detailed textual descriptions, TransDLM samples and optimizes encoded source molecules, retaining core scaffolds of source molecules and ensuring structural similarities. Moreover, TransDLM enables simultaneous sampling of multiple molecules, making it ideal for scalable, efficient large-scale optimization through distributed computation on web platforms. Furthermore, our approach surpasses state-of-the-art methods in optimizing molecular structural similarity and enhancing chemical properties on the benchmark dataset. The code is available at: https://anonymous.4open.science/r/TransDLM-A901.
The Instruction-Driven Game Engine (IDGE) project aims to democratize game development by enabling a large language model (LLM) to follow free-form game descriptions and generate game-play processes. The IDGE allows users to create games simply by natural language instructions, which significantly lowers the barrier for game development. We approach the learning process for IDGEs as a Next State Prediction task, wherein the model autoregressively predicts the game states given player actions. The computation of game states must be precise; otherwise, slight errors could corrupt the game-play experience. This is challenging because of the gap between stability and diversity. To address this, we train the IDGE in a curriculum manner that progressively increases its exposure to complex scenarios. Our initial progress lies in developing an IDGE for Poker, which not only supports a wide range of poker variants but also allows for highly individualized new poker games through natural language inputs. This work lays the groundwork for future advancements in transforming how games are created and played.
Teaching large language models (LLMs) to generate text with citations to evidence sources can mitigate hallucinations and enhance verifiability in information-seeking systems. However, improving this capability requires high-quality attribution data, which is costly and labor-intensive. Inspired by recent advances in self-improvement that enhance LLMs without manual annotation, we present START, a Self-Taught AttRibuTion framework for iteratively improving the attribution capability of LLMs. First, to prevent models from stagnating due to initially insufficient supervision signals, START leverages the model to self-construct synthetic training data for warming up. To further self-improve the model's attribution ability, START iteratively utilizes fine-grained preference supervision signals constructed from its sampled responses to encourage robust, comprehensive, and attributable generation. Experiments on three open-domain question-answering datasets, covering long-form QA and multi-step reasoning, demonstrate significant performance gains of 25.13% on average without relying on human annotations and more advanced models. Further analysis reveals that START excels in aggregating information across multiple sources.
Many students struggle with math word problems (MWPs), often finding it difficult to identify key information and select the appropriate mathematical operations. Schema-based instruction (SBI) is an evidence-based strategy that helps students categorize problems based on their structure, improving problem-solving accuracy. Building on this, we propose a Schema-Based Instruction Retrieval-Augmented Generation (SBI-RAG) framework that incorporates a large language model (LLM). Our approach emphasizes step-by-step reasoning by leveraging schemas to guide solution generation. We evaluate its performance on the GSM8K dataset, comparing it with GPT-4 and GPT-3.5 Turbo, and introduce a "reasoning score" metric to assess solution quality. Our findings suggest that SBI-RAG enhances reasoning clarity and facilitates a more structured problem-solving process potentially providing educational benefits for students.