Daily Papers

With the emergence of large-scale image-text pre-training models, e.g., CLIP, text-video retrieval has experienced substantial advances in recent years. Existing best-performing methods involve aligning cross-modal semantics at individual, local, and global levels simultaneously, raising concerns about the intrinsic semantic mismatch between concise texts and rich videos. A canonical approach is to integrate multiple language-video attention modules into the hierarchical framework while this paradigm only optimizes visual representations with prohibitive computational costs. In this paper, we propose a new prototype-based hierarchical alignment network (PHA-Net) to align individual/local/global level representations across modalities. Concretely, we introduce multiple modality-shared prototypes as the bridge to efficiently optimize text and video representations for cross-modal alignment. Then, we argue that the imbalanced semantic distribution in clustered tokens may undermine retrieval performance, as tokens with weak semantics are of little interest. To reduce the impact of these tokens, a proposed prototype-supported token merge module is responsible for enhancing tokens with strong semantics and suppressing others with weak semantics via prototype semantics guidance. Moreover, we devise a prototype contrastive loss to encourage textual and visual prototypes to focus on different semantic information. The idea of this auxiliary loss is to ensure higher similarity between textual and visual prototypes from the same prototype than those from different prototypes. Extensive experiments on four benchmarks confirm the effectiveness of our PHA-Net, which achieves significant improvements in the sum of all recalls on MSR-VTT (8.8%), ActivityNet (19.2%), VATEX (0.7%), and Charades (4.9%). Code is available at https://github.com/JingXiaolun/PHA-Net.

Current Scene Graph Generation (SGG) methods explore contextual information to predict relationships among entity pairs. However, due to the diverse visual appearance of numerous possible subject-object combinations, there is a large intra-class variation within each predicate category, e.g., "man-eating-pizza, giraffe-eating-leaf", and the severe inter-class similarity between different classes, e.g., "man-holding-plate, man-eating-pizza", in model's latent space. The above challenges prevent current SGG methods from acquiring robust features for reliable relation prediction. In this paper, we claim that the predicate's category-inherent semantics can serve as class-wise prototypes in the semantic space for relieving the challenges. To the end, we propose the Prototype-based Embedding Network (PE-Net), which models entities/predicates with prototype-aligned compact and distinctive representations and thereby establishes matching between entity pairs and predicates in a common embedding space for relation recognition. Moreover, Prototype-guided Learning (PL) is introduced to help PE-Net efficiently learn such entitypredicate matching, and Prototype Regularization (PR) is devised to relieve the ambiguous entity-predicate matching caused by the predicate's semantic overlap. Extensive experiments demonstrate that our method gains superior relation recognition capability on SGG, achieving new state-of-the-art performances on both Visual Genome and Open Images datasets.

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 22% reduction in embedding RMSE against the best competing geometry. The capacity of the framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.

Part-prototype networks (e.g., ProtoPNet, ProtoTree and ProtoPool) have attracted broad research interest for their intrinsic interpretability and comparable accuracy to non-interpretable counterparts. However, recent works find that the interpretability from prototypes is fragile, due to the semantic gap between the similarities in the feature space and that in the input space. In this work, we strive to address this challenge by making the first attempt to quantitatively and objectively evaluate the interpretability of the part-prototype networks. Specifically, we propose two evaluation metrics, termed as consistency score and stability score, to evaluate the explanation consistency across images and the explanation robustness against perturbations, respectively, both of which are essential for explanations taken into practice. Furthermore, we propose an elaborated part-prototype network with a shallow-deep feature alignment (SDFA) module and a score aggregation (SA) module to improve the interpretability of prototypes. We conduct systematical evaluation experiments and provide substantial discussions to uncover the interpretability of existing part-prototype networks. Experiments on three benchmarks across nine architectures demonstrate that our model achieves significantly superior performance to the state of the art, in both the accuracy and interpretability. Codes are available at https://github.com/hqhQAQ/EvalProtoPNet.

Neural document retrieval often treats a corpus as a flat cloud of vectors scored at a single granularity, leaving corpus structure underused and explanations opaque. We use Cobweb--a hierarchy-aware framework--to organize sentence embeddings into a prototype tree and rank documents via coarse-to-fine traversal. Internal nodes act as concept prototypes, providing multi-granular relevance signals and a transparent rationale through retrieval paths. We instantiate two inference approaches: a generalized best-first search and a lightweight path-sum ranker. We evaluate our approaches on MS MARCO and QQP with encoder (e.g., BERT/T5) and decoder (GPT-2) representations. Our results show that our retrieval approaches match the dot product search on strong encoder embeddings while remaining robust when kNN degrades: with GPT-2 vectors, dot product performance collapses whereas our approaches still retrieve relevant results. Overall, our experiments suggest that Cobweb provides competitive effectiveness, improved robustness to embedding quality, scalability, and interpretable retrieval via hierarchical prototypes.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

For named entity recognition (NER) in zero-resource languages, utilizing knowledge distillation methods to transfer language-independent knowledge from the rich-resource source languages to zero-resource languages is an effective means. Typically, these approaches adopt a teacher-student architecture, where the teacher network is trained in the source language, and the student network seeks to learn knowledge from the teacher network and is expected to perform well in the target language. Despite the impressive performance achieved by these methods, we argue that they have two limitations. Firstly, the teacher network fails to effectively learn language-independent knowledge shared across languages due to the differences in the feature distribution between the source and target languages. Secondly, the student network acquires all of its knowledge from the teacher network and ignores the learning of target language-specific knowledge. Undesirably, these limitations would hinder the model's performance in the target language. This paper proposes an unsupervised prototype knowledge distillation network (ProKD) to address these issues. Specifically, ProKD presents a contrastive learning-based prototype alignment method to achieve class feature alignment by adjusting the distance among prototypes in the source and target languages, boosting the teacher network's capacity to acquire language-independent knowledge. In addition, ProKD introduces a prototypical self-training method to learn the intrinsic structure of the language by retraining the student network on the target data using samples' distance information from prototypes, thereby enhancing the student network's ability to acquire language-specific knowledge. Extensive experiments on three benchmark cross-lingual NER datasets demonstrate the effectiveness of our approach.

Finetuning data selection requires balancing two competing goals: selecting examples that improve the downstream objective, and doing so without repeatedly finetuning models. Train-free selectors are scalable but rely on proxies such as embedding similarity or clustering, which may not match the target objective. Train-based selectors better reflect downstream utility through gradient signals, subset evaluation, or Shapley attribution, but require many costly train--evaluate iterations. We propose Hierarchical Active Region Pruning (HARP), an efficient train-based selector that preserves downstream alignment while reducing selection cost. HARP organizes the training pool into a node--leaf hierarchy, evaluates only representative leaves, and infers unmeasured utilities with empirical Bayes posteriors. It then selects data using two complementary envelopes: HARP-C, which conservatively controls redundancy, and HARP-E, which additively rewards complementary regions. We theoretically show that, under local smoothness and bounded estimation error, HARP controls selection error while reducing train--evaluate cost. We further validate that HARP variants achieve the best result and outperform the strongest baseline by up to +8.9 points, while using roughly 7times fewer training examples.

We propose a novel framework for few-shot learning by leveraging large-scale vision-language models such as CLIP. Motivated by unimodal prototypical networks for few-shot learning, we introduce Proto-CLIP which utilizes image prototypes and text prototypes for few-shot learning. Specifically, Proto-CLIP adapts the image and text encoder embeddings from CLIP in a joint fashion using few-shot examples. The embeddings from the two encoders are used to compute the respective prototypes of image classes for classification. During adaptation, we propose aligning the image and text prototypes of the corresponding classes. Such alignment is beneficial for few-shot classification due to the reinforced contributions from both types of prototypes. Proto-CLIP has both training-free and fine-tuned variants. We demonstrate the effectiveness of our method by conducting experiments on benchmark datasets for few-shot learning, as well as in the real world for robot perception. The project page is available at https://irvlutd.github.io/Proto-CLIP

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation, demonstrating that effective alignment can be achieved using only 9,000 labeled examples -- less than 1% of conventional approaches. ALMA generates large amounts of high-quality synthetic alignment data through new techniques: diverse prompt synthesis via few-shot learning, diverse response generation with multiple model checkpoints, and judge (reward model) enhancement through score aggregation and self-distillation. Using only a pretrained Llama3 base model, 5,000 SFT examples, and 4,000 judge annotations, ALMA achieves performance close to Llama3-Instruct across diverse alignment benchmarks (e.g., 0.1% difference on AlpacaEval 2.0 score). These results are achieved with a multi-round, self-bootstrapped data synthesis and training recipe that continues to improve for 10 rounds, surpassing the typical 3-round ceiling of previous methods. These results suggest that base models already possess sufficient knowledge for effective alignment, and that synthetic data generation methods can expose it.

Recent advances in general-purpose foundation models have stimulated the development of large biological sequence models. While natural language shows symbolic granularity (characters, words, sentences), biological sequences exhibit hierarchical granularity whose levels (nucleotides, amino acids, protein domains, genes) further encode biologically functional information. In this paper, we investigate the integration of cross-granularity knowledge from models through a case study of BiGCARP, a Pfam domain-level model for biosynthetic gene clusters, and ESM, an amino acid-level protein language model. Using representation analysis tools and a set of probe tasks, we first explain why a straightforward cross-model embedding initialization fails to improve downstream performance in BiGCARP, and show that deeper-layer embeddings capture a more contextual and faithful representation of the model's learned knowledge. Furthermore, we demonstrate that representations at different granularities encode complementary biological knowledge, and that combining them yields measurable performance gains in intermediate-level prediction tasks. Our findings highlight cross-granularity integration as a promising strategy for improving both the performance and interpretability of biological foundation models.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

The alignment of large language models (LLMs) aims to ensure their outputs adhere to human values, ethical standards, and legal norms. Traditional alignment methods often rely on resource-intensive fine-tuning (FT), which may suffer from knowledge degradation and face challenges in scenarios where the model accessibility or computational resources are constrained. In contrast, training-free (TF) alignment techniques--leveraging in-context learning, decoding-time adjustments, and post-generation corrections--offer a promising alternative by enabling alignment without heavily retraining LLMs, making them adaptable to both open-source and closed-source environments. This paper presents the first systematic review of TF alignment methods, categorizing them by stages of pre-decoding, in-decoding, and post-decoding. For each stage, we provide a detailed examination from the viewpoint of LLMs and multimodal LLMs (MLLMs), highlighting their mechanisms and limitations. Furthermore, we identify key challenges and future directions, paving the way for more inclusive and effective TF alignment techniques. By synthesizing and organizing the rapidly growing body of research, this survey offers a guidance for practitioners and advances the development of safer and more reliable LLMs.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Nonlinear manifolds are widespread in deep visual features, where Euclidean distances often fail to capture true similarity. This limitation becomes particularly severe in prototype-based interpretable fine-grained recognition, where subtle semantic distinctions are essential. To address this challenge, we propose a novel paradigm for prototype-based recognition that anchors similarity within the intrinsic geometry of deep features. Specifically, we distill the latent manifold structure of each class into a diffusion space and introduce a differentiable Nystr\"om interpolation, making the geometry accessible to both unseen samples and learnable prototypes. To ensure efficiency, we employ compact per-class landmark sets with periodic updates. This design keeps the embedding aligned with the evolving backbone, enabling fast and scalable inference. Extensive experiments on the CUB-200-2011 and Stanford Cars datasets show that our GeoProto framework produces prototypes focusing on semantically aligned parts, significantly outperforming Euclidean prototype networks.

As Large Language Models (LLMs) become increasingly integrated into real-world applications, ensuring their outputs align with human values and safety standards has become critical. The field has developed diverse alignment approaches including traditional fine-tuning methods (RLHF, instruction tuning), post-hoc correction systems, and inference-time interventions, each with distinct advantages and limitations. However, the lack of unified evaluation frameworks makes it difficult to systematically compare these paradigms and guide deployment decisions. This paper introduces a multi-dimensional evaluation of alignment techniques for LLMs, a comprehensive evaluation framework that provides a systematic comparison across all major alignment paradigms. Our framework assesses methods along four key dimensions: alignment detection, alignment quality, computational efficiency, and robustness. Through experiments across diverse base models and alignment strategies, we demonstrate the utility of our framework in identifying strengths and limitations of current state-of-the-art models, providing valuable insights for future research directions.

Large Language Models (LLMs) have demonstrated impressive capabilities for generalizing in unseen tasks. In the Named Entity Recognition (NER) task, recent advancements have seen the remarkable improvement of LLMs in a broad range of entity domains via instruction tuning, by adopting entity-centric schema. In this work, we explore the potential enhancement of the existing methods by incorporating negative instances into training. Our experiments reveal that negative instances contribute to remarkable improvements by (1) introducing contextual information, and (2) clearly delineating label boundaries. Furthermore, we introduce a novel and efficient algorithm named Hierarchical Matching, which is tailored to transform unstructured predictions into structured entities. By integrating these components, we present GNER, a Generative NER system that shows improved zero-shot performance across unseen entity domains. Our comprehensive evaluation illustrates our system's superiority, surpassing state-of-the-art (SoTA) methods by 11 F_1 score in zero-shot evaluation.

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

Despite incredible progress in language models (LMs) in recent years, largely resulting from moving away from specialized models designed for specific tasks to general models based on powerful architectures (e.g. the Transformer) that learn everything from raw data, pre-processing steps such as tokenization remain a barrier to true end-to-end foundation models. We introduce a collection of new techniques that enable a dynamic chunking mechanism which automatically learns content -- and context -- dependent segmentation strategies learned jointly with the rest of the model. Incorporating this into an explicit hierarchical network (H-Net) allows replacing the (implicitly hierarchical) tokenization-LM-detokenization pipeline with a single model learned fully end-to-end. When compute- and data- matched, an H-Net with one stage of hierarchy operating at the byte level outperforms a strong Transformer language model operating over BPE tokens. Iterating the hierarchy to multiple stages further increases its performance by modeling multiple levels of abstraction, demonstrating significantly better scaling with data and matching a token-based Transformer of twice its size. H-Nets pretrained on English show significantly increased character-level robustness, and qualitatively learn meaningful data-dependent chunking strategies without any heuristics or explicit supervision. Finally, the H-Net's improvement over tokenized pipelines is further increased in languages and modalities with weaker tokenization heuristics, such as Chinese and code, or DNA sequences (nearly 4x improvement in data efficiency over baselines), showing the potential of true end-to-end models that learn and scale better from unprocessed data.

With the rapid development of Large Language Models (LLMs), aligning these models with human preferences and values is critical to ensuring ethical and safe applications. However, existing alignment techniques such as RLHF or DPO often require direct fine-tuning on LLMs with billions of parameters, resulting in substantial computational costs and inefficiencies. To address this, we propose Micro token-level Accept-Reject Aligning (MARA) approach designed to operate independently of the language models. MARA simplifies the alignment process by decomposing sentence-level preference learning into token-level binary classification, where a compact three-layer fully-connected network determines whether candidate tokens are "Accepted" or "Rejected" as part of the response. Extensive experiments across seven different LLMs and three open-source datasets show that MARA achieves significant improvements in alignment performance while reducing computational costs.

We propose prototypical networks for the problem of few-shot classification, where a classifier must generalize to new classes not seen in the training set, given only a small number of examples of each new class. Prototypical networks learn a metric space in which classification can be performed by computing distances to prototype representations of each class. Compared to recent approaches for few-shot learning, they reflect a simpler inductive bias that is beneficial in this limited-data regime, and achieve excellent results. We provide an analysis showing that some simple design decisions can yield substantial improvements over recent approaches involving complicated architectural choices and meta-learning. We further extend prototypical networks to zero-shot learning and achieve state-of-the-art results on the CU-Birds dataset.

Extreme Multi-label Classification (XMC) methods predict relevant labels for a given query in an extremely large label space. Recent works in XMC address this problem using deep encoders that project text descriptions to an embedding space suitable for recovering the closest labels. However, learning deep models can be computationally expensive in large output spaces, resulting in a trade-off between high performing brute-force approaches and efficient solutions. In this paper, we propose PRIME, a XMC method that employs a novel prototypical contrastive learning technique to reconcile efficiency and performance surpassing brute-force approaches. We frame XMC as a data-to-prototype prediction task where label prototypes aggregate information from related queries. More precisely, we use a shallow transformer encoder that we coin as Label Prototype Network, which enriches label representations by aggregating text-based embeddings, label centroids and learnable free vectors. We jointly train a deep encoder and the Label Prototype Network using an adaptive triplet loss objective that better adapts to the high granularity and ambiguity of extreme label spaces. PRIME achieves state-of-the-art results in several public benchmarks of different sizes and domains, while keeping the model efficient.

Prototype-based methods use interpretable representations to address the black-box nature of deep learning models, in contrast to post-hoc explanation methods that only approximate such models. We propose the Neural Prototype Tree (ProtoTree), an intrinsically interpretable deep learning method for fine-grained image recognition. ProtoTree combines prototype learning with decision trees, and thus results in a globally interpretable model by design. Additionally, ProtoTree can locally explain a single prediction by outlining a decision path through the tree. Each node in our binary tree contains a trainable prototypical part. The presence or absence of this learned prototype in an image determines the routing through a node. Decision making is therefore similar to human reasoning: Does the bird have a red throat? And an elongated beak? Then it's a hummingbird! We tune the accuracy-interpretability trade-off using ensemble methods, pruning and binarizing. We apply pruning without sacrificing accuracy, resulting in a small tree with only 8 learned prototypes along a path to classify a bird from 200 species. An ensemble of 5 ProtoTrees achieves competitive accuracy on the CUB-200- 2011 and Stanford Cars data sets. Code is available at https://github.com/M-Nauta/ProtoTree

We present ProtoTEx, a novel white-box NLP classification architecture based on prototype networks. ProtoTEx faithfully explains model decisions based on prototype tensors that encode latent clusters of training examples. At inference time, classification decisions are based on the distances between the input text and the prototype tensors, explained via the training examples most similar to the most influential prototypes. We also describe a novel interleaved training algorithm that effectively handles classes characterized by the absence of indicative features. On a propaganda detection task, ProtoTEx accuracy matches BART-large and exceeds BERT-large with the added benefit of providing faithful explanations. A user study also shows that prototype-based explanations help non-experts to better recognize propaganda in online news.

Aligning large language models (LLMs) with human values is a vital task for LLM practitioners. Current alignment techniques have several limitations: (1) requiring a large amount of annotated data; (2) demanding heavy human involvement; (3) lacking a systematic mechanism to continuously improve. In this work, we study aligning LLMs to a new domain with limited samples (e.g. < 100). We propose an algorithm that can self-align LLMs iteratively without active human involvement. Unlike existing works, our algorithm relies on neither human-crafted instructions nor labeled rewards, significantly reducing human involvement. In addition, our algorithm can self-improve the alignment continuously. The key idea is to first retrieve high-quality samples related to the target domain and use them as In-context Learning examples to generate more samples. Then we use the self-generated samples to finetune the LLM iteratively. We show that our method can unlock the LLMs' self-generalization ability to perform alignment with near-zero human supervision. We test our algorithm on three benchmarks in safety, truthfulness, and instruction-following, and show good performance in alignment, domain adaptability, and scalability.

Aligning large language models with human objectives is paramount, yet common approaches including RLHF suffer from unstable and resource-intensive training. In response to this challenge, we introduce ARGS, Alignment as Reward-Guided Search, a novel framework that integrates alignment into the decoding process, eliminating the need for expensive RL training. By adjusting the model's probabilistic predictions using a reward signal, ARGS generates texts with semantic diversity while being aligned with human preferences, offering a promising and flexible solution for aligning language models. Notably, ARGS demonstrates consistent enhancements in average reward compared to baselines across diverse alignment tasks and various model dimensions. For example, under the same greedy-based decoding strategy, our method improves the average reward by 19.56% relative to the baseline and secures a preference or tie score of 64.33% in GPT-4 evaluation. We believe that our framework, emphasizing decoding-time alignment, paves the way for more responsive language models in the future. Code is publicly available at: https://github.com/deeplearning-wisc/args.

Parameter-efficient fine-tuning (PEFT) has shown its effectiveness in adapting the pre-trained language models to downstream tasks while only updating a small number of parameters. Despite the success, most existing methods independently adapt to each task without considering knowledge transfer between tasks and are limited to low-data regimes. To overcome this issue, we propose Prototype-based HyperAdapter (PHA), a novel framework built on the adapter-tuning and hypernetwork. It introduces an instance-dense retriever and a prototypical hypernetwork to generate the conditional modules in a sample-efficient manner. This leads to comparable performance improvements against existing PEFT methods on multi-task learning and few-shot transfer learning. More importantly, when the available data size gets smaller, our method outperforms other strong baselines by a large margin. Based on our extensive empirical experiments across various datasets, we demonstrate that PHA strikes a better trade-off between trainable parameters, accuracy on stream tasks, and sample efficiency.

Learning the hierarchical structure of data in vision-language models is a significant challenge. Previous works have attempted to address this challenge by employing entailment learning. However, these approaches fail to model the transitive nature of entailment explicitly, which establishes the relationship between order and semantics within a representation space. In this work, we introduce Radial Cross-Modal Embeddings (RCME), a framework that enables the explicit modeling of transitivity-enforced entailment. Our proposed framework optimizes for the partial order of concepts within vision-language models. By leveraging our framework, we develop a hierarchical vision-language foundation model capable of representing the hierarchy in the Tree of Life. Our experiments on hierarchical species classification and hierarchical retrieval tasks demonstrate the enhanced performance of our models compared to the existing state-of-the-art models. Our code and models are open-sourced at https://vishu26.github.io/RCME/index.html.

Deep networks that rely on prototypes-interpretable representations that can be related to the model input-have gained significant attention for balancing high accuracy with inherent interpretability, which makes them suitable for critical domains such as healthcare. However, these models are limited by their reliance on training data, which hampers their robustness to distribution shifts. While test-time adaptation (TTA) improves the robustness of deep networks by updating parameters and statistics, the prototypes of interpretable models have not been explored for this purpose. We introduce ProtoTTA, a general framework for prototypical models that leverages intermediate prototype signals rather than relying solely on model outputs. ProtoTTA minimizes the entropy of the prototype-similarity distribution to encourage more confident and prototype-specific activations on shifted data. To maintain stability, we employ geometric filtering to restrict updates to samples with reliable prototype activations, regularized by prototype-importance weights and model-confidence scores. Experiments across four prototypical backbones on four diverse benchmarks spanning fine-grained vision, histopathology, and NLP demonstrate that ProtoTTA improves robustness over standard output entropy minimization while restoring correct semantic focus in prototype activations. We also introduce novel interpretability metrics and a vision-language model (VLM) evaluation framework to explain TTA dynamics, confirming ProtoTTA restores human-aligned semantic focus and correlates reliably with VLM-rated reasoning quality. Code is available at: https://github.com/DeepRCL/ProtoTTA.

We study a practical domain adaptation task, called source-free unsupervised domain adaptation (UDA) problem, in which we cannot access source domain data due to data privacy issues but only a pre-trained source model and unlabeled target data are available. This task, however, is very difficult due to one key challenge: the lack of source data and target domain labels makes model adaptation very challenging. To address this, we propose to mine the hidden knowledge in the source model and exploit it to generate source avatar prototypes (i.e., representative features for each source class) as well as target pseudo labels for domain alignment. To this end, we propose a Contrastive Prototype Generation and Adaptation (CPGA) method. Specifically, CPGA consists of two stages: (1) prototype generation: by exploring the classification boundary information of the source model, we train a prototype generator to generate avatar prototypes via contrastive learning. (2) prototype adaptation: based on the generated source prototypes and target pseudo labels, we develop a new robust contrastive prototype adaptation strategy to align each pseudo-labeled target data to the corresponding source prototypes. Extensive experiments on three UDA benchmark datasets demonstrate the effectiveness and superiority of the proposed method.

Recent works have demonstrated the effectiveness of self-alignment in which a large language model is, by itself, aligned to follow general instructions through the automatic generation of instructional data using a handful of human-written seeds. Instead of general alignment, in this work, we focus on self-alignment for expert domain specialization (e.g., biomedicine), discovering it to be very effective for improving zero-shot and few-shot performance in target domains of interest. As a preliminary, we first present the benchmark results of existing aligned models within a specialized domain, which reveals the marginal effect that "generic" instruction-following training has on downstream expert domains' performance. To remedy this, we explore self-specialization that leverages domain-specific unlabelled data and a few labeled seeds for the self-alignment process. When augmented with retrieval to reduce hallucination and enhance concurrency of the alignment, self-specialization offers an effective (and efficient) way of "carving out" an expert model out of a "generalist", pre-trained LLM where different domains of expertise are originally combined in a form of "superposition". Our experimental results on a biomedical domain show that our self-specialized model (30B) outperforms its base model, MPT-30B by a large margin and even surpasses larger popular models based on LLaMA-65B, highlighting its potential and practicality for specialization, especially considering its efficiency in terms of data and parameters.

Inference-time alignment provides an efficient alternative for aligning LLMs with humans. However, these approaches still face challenges, such as limited scalability due to policy-specific value functions and latency during the inference phase. In this paper, we propose a novel approach, Diffusion-styled Preference Optimization (\model), which provides an efficient and policy-agnostic solution for aligning LLMs with humans. By directly performing alignment at sentence level, \model~avoids the time latency associated with token-level generation. Designed as a plug-and-play module, \model~can be seamlessly integrated with various base models to enhance their alignment. Extensive experiments on AlpacaEval 2, MT-bench, and HH-RLHF demonstrate that \model~achieves superior alignment performance across various settings, achieving a favorable trade-off between alignment quality and inference-time latency. Furthermore, \model~demonstrates model-agnostic scalability, significantly improving the performance of large models such as Llama-3-70B.

Large vision-language models such as CLIP struggle with long captions because they align images and texts as undifferentiated wholes. Fine-grained vision-language understanding requires hierarchical semantics capturing both global context and localized details across visual and textual domains. Yet linguistic hierarchies from syntax or semantics rarely match visual organization, and purely visual hierarchies tend to fragment scenes into appearance-driven parts without semantic focus. We propose CAFT (Cross-domain Alignment of Forests and Trees), a hierarchical image-text representation learning framework that aligns global and local semantics across images and long captions without pixel-level supervision. Coupling a fine-to-coarse visual encoder with a hierarchical text transformer, it uses a hierarchical alignment loss that matches whole images with whole captions while biasing region-sentence correspondences, so that coarse semantics are built from fine-grained evidence rather than from aggregation untethered to part-level grounding. Trained on 30M image-text pairs, CAFT achieves state-of-the-art performance on six long-text retrieval benchmarks and exhibits strong scaling behavior. Experiments show that hierarchical cross-domain alignment enables fine-grained, visually grounded image-text representations to emerge without explicit region-level supervision.

Self-alignment is an effective way to reduce the cost of human annotation while ensuring promising model capability. However, most current methods complete the data collection and training steps in a single round, which may overlook the continuously improving ability of self-aligned models. This gives rise to a key query: What if we do multi-time bootstrapping self-alignment? Does this strategy enhance model performance or lead to rapid degradation? In this paper, our pioneering exploration delves into the impact of bootstrapping self-alignment on large language models. Our findings reveal that bootstrapping self-alignment markedly surpasses the single-round approach, by guaranteeing data diversity from in-context learning. To further exploit the capabilities of bootstrapping, we investigate and adjust the training order of data, which yields improved performance of the model. Drawing on these findings, we propose Step-On-Feet Tuning (SOFT) which leverages model's continuously enhanced few-shot ability to boost zero or one-shot performance. Based on easy-to-hard training recipe, we propose SOFT+ which further boost self-alignment's performance. Our experiments demonstrate the efficiency of SOFT (SOFT+) across various classification and generation tasks, highlighting the potential of bootstrapping self-alignment on continually enhancing model alignment performance.

High-quality instruction data is critical for aligning large language models (LLMs). Although some models, such as Llama-3-Instruct, have open weights, their alignment data remain private, which hinders the democratization of AI. High human labor costs and a limited, predefined scope for prompting prevent existing open-source data creation methods from scaling effectively, potentially limiting the diversity and quality of public alignment datasets. Is it possible to synthesize high-quality instruction data at scale by extracting it directly from an aligned LLM? We present a self-synthesis method for generating large-scale alignment data named Magpie. Our key observation is that aligned LLMs like Llama-3-Instruct can generate a user query when we input only the left-side templates up to the position reserved for user messages, thanks to their auto-regressive nature. We use this method to prompt Llama-3-Instruct and generate 4 million instructions along with their corresponding responses. We perform a comprehensive analysis of the extracted data and select 300K high-quality instances. To compare Magpie data with other public instruction datasets, we fine-tune Llama-3-8B-Base with each dataset and evaluate the performance of the fine-tuned models. Our results indicate that in some tasks, models fine-tuned with Magpie perform comparably to the official Llama-3-8B-Instruct, despite the latter being enhanced with 10 million data points through supervised fine-tuning (SFT) and subsequent feedback learning. We also show that using Magpie solely for SFT can surpass the performance of previous public datasets utilized for both SFT and preference optimization, such as direct preference optimization with UltraFeedback. This advantage is evident on alignment benchmarks such as AlpacaEval, ArenaHard, and WildBench.

The advancement of transformer neural networks has significantly elevated the capabilities of sentence similarity models, particularly in creating effective vector representations of natural language inputs. However, these models face notable challenges in domain-specific contexts, especially in highly specialized scientific sub-fields. Traditional methods often struggle in this regime, either overgeneralizing similarities within a niche or being overly sensitive to minor differences, resulting in inaccurate text classification and subpar vector representation. In an era where retrieval augmentation and search are increasingly crucial, precise and concise numerical representations are essential. In this paper, we target this issue by assembling niche datasets using co-citations as a similarity metric, focusing on biomedical domains. We employ two key strategies for fine-tuning state-of-the-art models: 1. Domain-specific Fine-Tuning, which tailors pretrained models to a single domain, and 2. Universal Applicability with Mixture of Experts (MoE), adapting pretrained models with enforced routing for multiple domains simultaneously. Our training approach emphasizes the use of abstracts for faster training, incorporating Multiple Negative Rankings loss for efficient contrastive learning. Notably, our MoE variants, equipped with N experts, achieve the efficacy of N individual models, heralding a new era of versatile, One-Size-Fits-All transformer networks for various tasks. This methodology marks significant advancements in scientific text classification metrics and holds promise for enhancing vector database search and compilation.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

String similarity models are vital for record linkage, entity resolution, and search. In this work, we present STANCE --a learned model for computing the similarity of two strings. Our approach encodes the characters of each string, aligns the encodings using Sinkhorn Iteration (alignment is posed as an instance of optimal transport) and scores the alignment with a convolutional neural network. We evaluate STANCE's ability to detect whether two strings can refer to the same entity--a task we term alias detection. We construct five new alias detection datasets (and make them publicly available). We show that STANCE or one of its variants outperforms both state-of-the-art and classic, parameter-free similarity models on four of the five datasets. We also demonstrate STANCE's ability to improve downstream tasks by applying it to an instance of cross-document coreference and show that it leads to a 2.8 point improvement in B^3 F1 over the previous state-of-the-art approach.

As large language models (LLMs) continue to advance, ensuring their alignment with human values becomes increasingly critical. Traditional alignment methods heavily rely on human feedback to fine-tune models. With the emergence of superhuman models whose outputs may surpass human understanding, evaluating and aligning these models using human judgments poses significant challenges. To address the challenges, recent works use weak supervisors to elicit knowledge from much stronger models. However, there are important disanalogies between the empirical setup in the existing works and the genuine goal of alignment. We remark that existing works investigate the phenomenon of weak-to-strong generation in analogous setup (i.e., binary classification), rather than practical alignment-relevant tasks (e.g., safety). In this paper, we bridge this gap by extending weak-to-strong generation to the context of practical alignment. We empirically demonstrate the widespread phenomenon of weak-to-strong generation in three complicated alignment tasks: safety, toxicity, and legal reasoning}. Furthermore, we explore efficient strategies for improving alignment performance to enhance the quality of model outcomes. Lastly, we summarize and analyze the challenges and potential solutions in regard to specific alignment tasks, which we hope to catalyze the research progress on the topic of weak-to-strong generalization. Our code is released at https://github.com/yeruimeng/WTS.git.

By compressing diverse narratives, LLMs go beyond memorization, achieving intelligence by capturing generalizable causal relationships. However, they suffer from local 'representation gaps' due to insufficient training data diversity, limiting their real-world utility, especially in tasks requiring strict alignment to rules. Traditional alignment methods relying on heavy human annotations are inefficient and unscalable. Recent self-alignment techniques also fall short, as they often depend on self-selection based prompting and memorization-based learning. To address these issues, we introduce Iterative Graph Alignment (IGA), an annotation-free rule-based alignment algorithm. A teacher model (VLM) employs Iterative Graph Prompting (IGP) to create logical graphs and reference answers. The student model (LLM) identifies local knowledge gaps by attempting to align its responses with these references, collaborating with helper models to generate diverse answers. These aligned responses are then used for iterative supervised fine-tuning (SFT). Our evaluations across five rule-based scenarios demonstrate IGP's effectiveness, with a 73.12\% alignment improvement in Claude Sonnet 3.5, and Llama3-8B-Instruct achieving an 86.20\% improvement, outperforming Claude Sonnet 3.5 in rule-based alignment.

Reward models (RMs) guide the alignment of large language models (LLMs), steering them toward behaviors preferred by humans. Evaluating RMs is the key to better aligning LLMs. However, the current evaluation of RMs may not directly correspond to their alignment performance due to the limited distribution of evaluation data and evaluation methods that are not closely related to alignment objectives. To address these limitations, we propose RMB, a comprehensive RM benchmark that covers over 49 real-world scenarios and includes both pairwise and Best-of-N (BoN) evaluations to better reflect the effectiveness of RMs in guiding alignment optimization. We demonstrate a positive correlation between our benchmark and the downstream alignment task performance. Based on our benchmark, we conduct extensive analysis on the state-of-the-art RMs, revealing their generalization defects that were not discovered by previous benchmarks, and highlighting the potential of generative RMs. Furthermore, we delve into open questions in reward models, specifically examining the effectiveness of majority voting for the evaluation of reward models and analyzing the impact factors of generative RMs, including the influence of evaluation criteria and instructing methods. Our evaluation code and datasets are available at https://github.com/Zhou-Zoey/RMB-Reward-Model-Benchmark.

Aligning large language models (LLMs) with human preferences is essential for their applications. Recently, decoding-time alignment has emerged as an effective plug-and-play technique that avoids fine-tuning model parameters. This approach retains the general utility of pretrained LLMs but often suffers from significant inefficiencies during decoding, primarily due to wasted token generation and excessive reward evaluations. To address these challenges, we introduce Cascade Reward Sampling (CARDS) to resolve both efficiency bottlenecks in decoding-time alignment. Specifically, we develop a segment-level rejection sampling algorithm that minimizes redundant computations of both LLMs and reward models (RMs). Central to CARDS is an uncertainty-based segmentation mechanism, which ensures the accuracy of RMs evaluations on incomplete segments. Furthermore, we provide a detailed analysis of reward scores on segments to elucidate the improved alignment performance. Experimental results demonstrate that CARDS significantly improves decoding efficiency, alignment quality, and general utility compared to existing decoding-time alignment methods, achieving approximately a 70% reduction in decoding time and over 90% win-ties in utility and safety benchmarks.

Generalized category discovery (GCD) is a pragmatic but underexplored problem, which requires models to automatically cluster and discover novel categories by leveraging the labeled samples from old classes. The challenge is that unlabeled data contain both old and new classes. Early works leveraging pseudo-labeling with parametric classifiers handle old and new classes separately, which brings about imbalanced accuracy between them. Recent methods employing contrastive learning neglect potential positives and are decoupled from the clustering objective, leading to biased representations and sub-optimal results. To address these issues, we introduce a unified and unbiased prototype learning framework, namely ProtoGCD, wherein old and new classes are modeled with joint prototypes and unified learning objectives, {enabling unified modeling between old and new classes}. Specifically, we propose a dual-level adaptive pseudo-labeling mechanism to mitigate confirmation bias, together with two regularization terms to collectively help learn more suitable representations for GCD. Moreover, for practical considerations, we devise a criterion to estimate the number of new classes. Furthermore, we extend ProtoGCD to detect unseen outliers, achieving task-level unification. Comprehensive experiments show that ProtoGCD achieves state-of-the-art performance on both generic and fine-grained datasets. The code is available at https://github.com/mashijie1028/ProtoGCD.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Aligning Large Language Models (LLMs) traditionally relies on costly training and human preference annotations. Self-alignment seeks to reduce these expenses by enabling models to align themselves. To further lower costs and achieve alignment without any expensive tuning or annotations, we introduce a new tuning-free approach for self-alignment, Dynamic Rewarding with Prompt Optimization (DRPO). Our approach leverages a search-based optimization framework that allows LLMs to iteratively self-improve and craft the optimal alignment instructions, all without additional training or human intervention. The core of DRPO is a dynamic rewarding mechanism, which identifies and rectifies model-specific alignment weaknesses, allowing LLMs to adapt efficiently to diverse alignment challenges. Empirical evaluations on eight recent LLMs, both open- and closed-sourced, demonstrate that DRPO significantly enhances alignment performance, with base models outperforming their SFT/RLHF-tuned counterparts. Moreover, the prompts automatically optimized by DRPO surpass those curated by human experts, further validating the effectiveness of our approach. Our findings highlight the great potential of current LLMs to achieve adaptive self-alignment through inference-time optimization, complementing tuning-based alignment methods.

A high-performing, general-purpose visual understanding model should map visual inputs to a taxonomic tree of labels, identify novel categories beyond the training set for which few or no publicly available images exist. Large Multimodal Models (LMMs) have achieved remarkable progress in fine-grained visual recognition (FGVR) for known categories. However, they remain limited in hierarchical visual recognition (HVR) that aims at predicting consistent label paths from coarse to fine categories, especially for novel categories. To tackle these challenges, we propose Taxonomy-Aware Representation Alignment (TARA), a simple yet effective strategy to inject taxonomic knowledge into LMMs. TARA leverages representations from biology foundation models (BFMs) that encode rich biological relationships through hierarchical contrastive learning. By aligning the intermediate representations of visual features with those of BFMs, LMMs are encouraged to extract discriminative visual cues well structured in the taxonomy tree. Additionally, we align the representations of the first answer token with the ground-truth label, flexibly bridging the gap between contextualized visual features and categories of varying granularity according to user intent. Experiments demonstrate that TARA consistently enhances LMMs' hierarchical consistency and leaf node accuracy, enabling reliable recognition of both known and novel categories within complex biological taxonomies. Code is available at https://github.com/PKU-ICST-MIPL/TARA_CVPR2026.

Graph-based Retrieval-Augmented Generation (RAG) methods have significantly enhanced the performance of large language models (LLMs) in domain-specific tasks. However, existing RAG methods do not adequately utilize the naturally inherent hierarchical knowledge in human cognition, which limits the capabilities of RAG systems. In this paper, we introduce a new RAG approach, called HiRAG, which utilizes hierarchical knowledge to enhance the semantic understanding and structure capturing capabilities of RAG systems in the indexing and retrieval processes. Our extensive experiments demonstrate that HiRAG achieves significant performance improvements over the state-of-the-art baseline methods. The code of our proposed method is available at https://github.com/hhy-huang/HiRAG{https://github.com/hhy-huang/HiRAG}.

Alignment with human preference is a desired property of large language models (LLMs). Currently, the main alignment approach is based on reinforcement learning from human feedback (RLHF). Despite the effectiveness of RLHF, it is intricate to implement and train, thus recent studies explore how to develop alternative alignment approaches based on supervised fine-tuning (SFT). A major limitation of SFT is that it essentially does imitation learning, which cannot fully understand what are the expected behaviors. To address this issue, we propose an improved alignment approach named FIGA. Different from prior methods, we incorporate fine-grained (i.e., token or phrase level) quality signals that are derived by contrasting good and bad responses. Our approach has made two major contributions. Firstly, we curate a refined alignment dataset that pairs initial responses and the corresponding revised ones. Secondly, we devise a new loss function can leverage fine-grained quality signals to instruct the learning of LLMs for alignment. Extensive experiments have demonstrated the effectiveness of our approaches by comparing a number of competitive baselines.

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

Effective biomedical information retrieval requires modeling domain semantics and hierarchical relationships among biomedical texts. Existing biomedical generative retrievers build on coarse binary relevance signals, limiting their ability to capture semantic overlap. We propose BioHiCL (Biomedical Retrieval with Hierarchical Multi-Label Contrastive Learning), which leverages hierarchical MeSH annotations to provide structured supervision for multi-label contrastive learning. Our models, BioHiCL-Base (0.1B) and BioHiCL-Large (0.3B), achieve promising performance on biomedical retrieval, sentence similarity, and question answering tasks, while remaining computationally efficient for deployment.

Large Language Models (LLMs) have achieved significant advancements, however, the common learning paradigm treats LLMs as passive information repositories, neglecting their potential for active learning and alignment. Some approaches train LLMs using their own generated synthetic data, exploring the possibility of active alignment. However, there is still a huge gap between these one-time alignment methods and the continuous automatic alignment of humans. In this paper, we introduce I-SHEEP, an Iterative Self-EnHancEmEnt Paradigm.This human-like paradigm enables LLMs to continuously self-align from scratch with nothing. Compared to the one-time alignment method Dromedary sun2023principledriven, which refers to the first iteration in this paper, I-SHEEP can significantly enhance capacities on both Qwen and Llama models. I-SHEEP achieves a maximum relative improvement of 78.2\% in the Alpaca Eval, 24.0\% in the MT Bench, and an absolute increase of 8.88\% in the IFEval accuracy over subsequent iterations in Qwen-1.5 72B model. Additionally, I-SHEEP surpasses the base model in various standard benchmark generation tasks, achieving an average improvement of 24.77\% in code generation tasks, 12.04\% in TrivialQA, and 20.29\% in SQuAD. We also provide new insights based on the experiment results. Our codes, datasets, and models are available at https://anonymous.4open.science/r/I-SHEEP.

In zero-shot learning (ZSL), generative methods synthesize class-related sample features based on predefined semantic prototypes. They advance the ZSL performance by synthesizing unseen class sample features for better training the classifier. We observe that each class's predefined semantic prototype (also referred to as semantic embedding or condition) does not accurately match its real semantic prototype. So the synthesized visual sample features do not faithfully represent the real sample features, limiting the classifier training and existing ZSL performance. In this paper, we formulate this mismatch phenomenon as the visual-semantic domain shift problem. We propose a dynamic semantic prototype evolving (DSP) method to align the empirically predefined semantic prototypes and the real prototypes for class-related feature synthesis. The alignment is learned by refining sample features and semantic prototypes in a unified framework and making the synthesized visual sample features approach real sample features. After alignment, synthesized sample features from unseen classes are closer to the real sample features and benefit DSP to improve existing generative ZSL methods by 8.5\%, 8.0\%, and 9.7\% on the standard CUB, SUN AWA2 datasets, the significant performance improvement indicates that evolving semantic prototype explores a virgin field in ZSL.

We introduce a hierarchical filtering procedure for generative models of sequences on trees, enabling control over the range of positional correlations in the data. Leveraging this controlled setting, we provide evidence that vanilla encoder-only transformer architectures can implement the optimal Belief Propagation algorithm on both root classification and masked language modeling tasks. Correlations at larger distances corresponding to increasing layers of the hierarchy are sequentially included as the network is trained. We analyze how the transformer layers succeed by focusing on attention maps from models trained with varying degrees of filtering. These attention maps show clear evidence for iterative hierarchical reconstruction of correlations, and we can relate these observations to a plausible implementation of the exact inference algorithm for the network sizes considered.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Large Language Models (LLMs) exhibit remarkably powerful capabilities. One of the crucial factors to achieve success is aligning the LLM's output with human preferences. This alignment process often requires only a small amount of data to efficiently enhance the LLM's performance. While effective, research in this area spans multiple domains, and the methods involved are relatively complex to understand. The relationships between different methods have been under-explored, limiting the development of the preference alignment. In light of this, we break down the existing popular alignment strategies into different components and provide a unified framework to study the current alignment strategies, thereby establishing connections among them. In this survey, we decompose all the strategies in preference learning into four components: model, data, feedback, and algorithm. This unified view offers an in-depth understanding of existing alignment algorithms and also opens up possibilities to synergize the strengths of different strategies. Furthermore, we present detailed working examples of prevalent existing algorithms to facilitate a comprehensive understanding for the readers. Finally, based on our unified perspective, we explore the challenges and future research directions for aligning large language models with human preferences.

Reinforcement Learning from Human Feedback (RLHF) has become a cornerstone for aligning large language models (LLMs). However, its effectiveness depends on high-quality instruction data. Most existing alignment datasets are either private or require costly human annotation, which limits reproducibility and scalability. Even with Reinforcement Learning from AI Feedback (RLAIF), concerns about data quality remain. Moreover, it is unclear how much data is actually required to fine-tune a base model into a strong instruction-following model. Current approaches often rely on over 300k examples even at the supervised fine-tuning (SFT) stage, yet they still underperform compared to proprietary models, creating barriers for academic and resource-limited communities. To address this gap, we introduce PiKa, a data-efficient family of expert-level alignment datasets. In particular, the PiKa-SFT dataset uses only 30k SFT examples, far fewer than state-of-the-art datasets like Magpie. Through evaluations by fine-tuning Llama-3-8B-Base on PiKa and other public datasets, we show that PiKa-SFT outperforms models trained on much larger data. On AlpacaEval 2.0 and Arena-Hard benchmarks, PiKa-SFT fine-tuning even surpasses the official Llama-3-8B-Instruct model trained on over 10 million proprietary examples. We further extend our study by training the Qwen2.5 series (0.5B to 7B) on PiKa-SFT, achieving consistent gains. These findings demonstrate that high-quality alignment can be achieved with significantly less data, offering a scalable path for open-source LLM alignment. Code and data: https://github.com/SJY8460/PiKa.

Alignment methodologies have emerged as a critical pathway for enhancing language model alignment capabilities. While SFT (supervised fine-tuning) accelerates convergence through direct token-level loss intervention, its efficacy is constrained by offline policy trajectory. In contrast, RL(reinforcement learning) facilitates exploratory policy optimization, but suffers from low sample efficiency and stringent dependency on high-quality base models. To address these dual challenges, we propose GRAO (Group Relative Alignment Optimization), a unified framework that synergizes the respective strengths of SFT and RL through three key innovations: 1) A multi-sample generation strategy enabling comparative quality assessment via reward feedback; 2) A novel Group Direct Alignment Loss formulation leveraging intra-group relative advantage weighting; 3) Reference-aware parameter updates guided by pairwise preference dynamics. Our theoretical analysis establishes GRAO's convergence guarantees and sample efficiency advantages over conventional approaches. Comprehensive evaluations across complex human alignment tasks demonstrate GRAO's superior performance, achieving 57.70\%,17.65\% 7.95\% and 5.18\% relative improvements over SFT, DPO, PPO and GRPO baselines respectively. This work provides both a theoretically grounded alignment framework and empirical evidence for efficient capability evolution in language models.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

Aligning large language models with human feedback at inference time has received increasing attention due to its flexibility. Existing methods rely on generating multiple responses from the base policy for search using a reward model, which can be considered as searching in a discrete response space. However, these methods struggle to explore informative candidates when the base policy is weak or the candidate set is small, resulting in limited effectiveness. In this paper, to address this problem, we propose Simple Energy Adaptation (SEA), a simple yet effective algorithm for inference-time alignment. In contrast to expensive search over the discrete space, SEA directly adapts original responses from the base policy toward the optimal one via gradient-based sampling in continuous latent space. Specifically, SEA formulates inference as an iterative optimization procedure on an energy function over actions in the continuous space defined by the optimal policy, enabling simple and effective alignment. For instance, despite its simplicity, SEA outperforms the second-best baseline with a relative improvement of up to 77.51% on AdvBench and 16.36% on MATH. Our code is publicly available at https://github.com/yuanyige/sea

Few-shot object detection aims to detect novel object categories from only a few labeled examples, avoiding costly large-scale annotation. Recent prototype-based similarity learning approaches enable training-free adaptation by matching query features with class prototypes. However, they suffer from two fundamental limitations: (i) class confusion arising from inter-class similarity margin collapse, and (ii) insufficient visual cues for precise localization, as similarity scores capture only class-level semantic affinity while providing limited spatial information. To address these issues, we introduce two complementary components. Text-Anchored Semantic Mask (TSMa) leverages class-level text features as semantic anchors to identify semantically aligned channels through channel-wise interaction between visual and text features. By suppressing style-induced spurious responses and emphasizing class-intrinsic signals, TSMa enlarges inter-class similarity margins and mitigates class confusion. We further propose Stage-Aligned Hierarchical Autoregressive Regression (SHARe), which reformulates localization as a hierarchical autoregressive process that progressively refines bounding boxes across multiple stages. SHARe leverages the layer-wise characteristics of ViT representations by aligning feature abstraction levels with regression stages: deeper layers guide early coarse localization, while shallower layers rich in edge and texture cues refine spatial details in later stages. Experiments on COCO demonstrate a new state of the art, outperforming the previous best by +10.1 nAP, with extensive analysis validating each component. The code is available at https://github.com/VisualScienceLab-KHU/ReSet.

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great majority of past work on word alignment has worked by performing unsupervised learning on parallel texts. Recently, however, other work has demonstrated that pre-trained contextualized word embeddings derived from multilingually trained language models (LMs) prove an attractive alternative, achieving competitive results on the word alignment task even in the absence of explicit training on parallel data. In this paper, we examine methods to marry the two approaches: leveraging pre-trained LMs but fine-tuning them on parallel text with objectives designed to improve alignment quality, and proposing methods to effectively extract alignments from these fine-tuned models. We perform experiments on five language pairs and demonstrate that our model can consistently outperform previous state-of-the-art models of all varieties. In addition, we demonstrate that we are able to train multilingual word aligners that can obtain robust performance on different language pairs. Our aligner, AWESOME (Aligning Word Embedding Spaces of Multilingual Encoders), with pre-trained models is available at https://github.com/neulab/awesome-align

kNN-MT is a straightforward yet powerful approach for fast domain adaptation, which directly plugs pre-trained neural machine translation (NMT) models with domain-specific token-level k-nearest-neighbor (kNN) retrieval to achieve domain adaptation without retraining. Despite being conceptually attractive, kNN-MT is burdened with massive storage requirements and high computational complexity since it conducts nearest neighbor searches over the entire reference corpus. In this paper, we propose a simple and scalable nearest neighbor machine translation framework to drastically promote the decoding and storage efficiency of kNN-based models while maintaining the translation performance. To this end, we dynamically construct an extremely small datastore for each input via sentence-level retrieval to avoid searching the entire datastore in vanilla kNN-MT, based on which we further introduce a distance-aware adapter to adaptively incorporate the kNN retrieval results into the pre-trained NMT models. Experiments on machine translation in two general settings, static domain adaptation and online learning, demonstrate that our proposed approach not only achieves almost 90% speed as the NMT model without performance degradation, but also significantly reduces the storage requirements of kNN-MT.

This paper presents a novel framework for aligning learnable latent spaces to arbitrary target distributions by leveraging flow-based generative models as priors. Our method first pretrains a flow model on the target features to capture the underlying distribution. This fixed flow model subsequently regularizes the latent space via an alignment loss, which reformulates the flow matching objective to treat the latents as optimization targets. We formally prove that minimizing this alignment loss establishes a computationally tractable surrogate objective for maximizing a variational lower bound on the log-likelihood of latents under the target distribution. Notably, the proposed method eliminates computationally expensive likelihood evaluations and avoids ODE solving during optimization. As a proof of concept, we demonstrate in a controlled setting that the alignment loss landscape closely approximates the negative log-likelihood of the target distribution. We further validate the effectiveness of our approach through large-scale image generation experiments on ImageNet with diverse target distributions, accompanied by detailed discussions and ablation studies. With both theoretical and empirical validation, our framework paves a new way for latent space alignment.

We present BioMatrix, the first multimodal foundation model that natively integrates sequences, structures, and natural language for both molecules and proteins within a single decoder-only architecture. Existing biological foundation models pursue native multimodality and broad entity coverage separately: those that fuse multiple modalities under a shared objective remain confined to a single entity type, while those spanning multiple entity types either omit explicit structural modeling or rely on adapter-based designs in which the model cannot natively generate the very modalities it can read. BioMatrix closes this gap by mapping molecular sequences (supporting both SMILES and SELFIES notations), molecular structures, protein sequences, protein structures, and natural language into a shared discrete token space through a unified tokenization scheme, so that all modalities are consumed and produced uniformly under a single next-token prediction objective -- without external encoders, projection adapters, or modality-specific output heads. Built upon the Qwen3 language model (1.7B and 4B), BioMatrix is continually pretrained on 304.4 billion tokens spanning general and domain-specific text, sequence and structure views of molecules and proteins, and cross-modal corpora that interleave biomolecular entities with scientific text and link distinct entities through molecule-protein and protein-protein interaction data. After tuning on a comprehensive suite of downstream applications covering 80 tasks across 6 categories -- encompassing single-entity and multi-entity understanding and generation tasks across and within modalities -- BioMatrix achieves state-of-the-art or competitive performance on 77 out of 80 tasks, demonstrating that a single, natively multimodal generalist model can effectively match or surpass specialized approaches across a wide range of biological tasks.

Language model alignment has become a critical step in training modern generative language models. The goal of alignment is to finetune a reference model such that the win rate of a sample from the aligned model over a sample from the reference model is high, subject to a KL divergence constraint. Today, we are increasingly using inference-time algorithms (e.g., Best-of-N, controlled decoding, tree search) to decode from language models rather than standard sampling. However, the alignment objective does not capture such inference-time decoding procedures. We show that the existing alignment framework is sub-optimal in view of such inference-time methods. We then modify the alignment objective and propose a framework for inference-aware alignment (IAPO). We prove that for any inference-time decoding algorithm, the optimal solution that optimizes the inference-time win rate of the aligned policy against the reference policy is the solution to the typical RLHF problem with a transformation of the reward. This motivates us to provide the KL-regularized calibrate-and-transform RL (CTRL) algorithm to solve this problem, which involves a reward calibration step and a KL-regularized reward maximization step with a transformation of the calibrated reward. We particularize our study to two important inference-time strategies: best-of-N sampling and best-of-N jailbreaking, where N responses are sampled from the model and the one with the highest or lowest reward is selected. We propose specific transformations for these strategies and demonstrate that our framework offers significant improvements over existing state-of-the-art methods for language model alignment. Empirically, we outperform baselines that are designed without taking inference-time decoding into consideration by 8-12% and 4-9% on inference-time win rates over the Anthropic helpfulness and harmlessness dialog benchmark datasets.

Webly supervised learning has attracted increasing attention for its effectiveness in exploring publicly accessible data at scale without manual annotation. However, most existing methods of learning with web datasets are faced with challenges from label noise, and they have limited assumptions on clean samples under various noise. For instance, web images retrieved with queries of tiger cat (a cat species) and drumstick (a musical instrument) are almost dominated by images of tigers and chickens, which exacerbates the challenge of fine-grained visual concept learning. In this case, exploiting both web images and their associated texts is a requisite solution to combat real-world noise. In this paper, we propose Cross-modality Aligned Prototypes (CAPro), a unified prototypical contrastive learning framework to learn visual representations with correct semantics. For one thing, we leverage textual prototypes, which stem from the distinct concept definition of classes, to select clean images by text matching and thus disambiguate the formation of visual prototypes. For another, to handle missing and mismatched noisy texts, we resort to the visual feature space to complete and enhance individual texts and thereafter improve text matching. Such semantically aligned visual prototypes are further polished up with high-quality samples, and engaged in both cluster regularization and noise removal. Besides, we propose collective bootstrapping to encourage smoother and wiser label reference from appearance-similar instances in a manner of dictionary look-up. Extensive experiments on WebVision1k and NUS-WIDE (Web) demonstrate that CAPro well handles realistic noise under both single-label and multi-label scenarios. CAPro achieves new state-of-the-art performance and exhibits robustness to open-set recognition. Codes are available at https://github.com/yuleiqin/capro.

Inference-time alignment enhances the performance of large language models without requiring additional training or fine-tuning but presents challenges due to balancing computational efficiency with high-quality output. Best-of-N (BoN) sampling, as a simple yet powerful approach, generates multiple responses and selects the best one, achieving improved performance but with a high computational cost. We propose TreeBoN, a novel framework that integrates a speculative tree-search strategy into Best-of-N (BoN) Sampling. TreeBoN maintains a set of parent nodes, iteratively branching and pruning low-quality responses, thereby reducing computational overhead while maintaining high output quality. Our approach also leverages token-level rewards from Direct Preference Optimization (DPO) to guide tree expansion and prune low-quality paths. We evaluate TreeBoN using AlpacaFarm, UltraFeedback, GSM8K, HH-RLHF, and TutorEval datasets, demonstrating consistent improvements. Specifically, TreeBoN achieves a 65% win rate at maximum lengths of 192 and 384 tokens, outperforming standard BoN with the same computational cost. Furthermore, TreeBoN achieves around a 60% win rate across longer responses, showcasing its scalability and alignment efficacy.

Transformer-based models have demonstrated significant success in various source code representation tasks. Nonetheless, traditional positional embeddings employed by these models inadequately capture the hierarchical structure intrinsic to source code, typically represented as Abstract Syntax Trees (ASTs). To address this, we propose a novel tree-based positional embedding approach that explicitly encodes hierarchical relationships derived from ASTs, including node depth and sibling indices. These hierarchical embeddings are integrated into the transformer architecture, specifically enhancing the CodeBERTa model. We thoroughly evaluate our proposed model through masked language modeling (MLM) pretraining and clone detection fine-tuning tasks. Experimental results indicate that our Tree-Enhanced CodeBERTa consistently surpasses the baseline model in terms of loss, accuracy, F1 score, precision, and recall, emphasizing the importance of incorporating explicit structural information into transformer-based representations of source code.

Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically divergent sentences. Identification of null alignment is useful on its own to reason about the semantic similarity of sentences by indicating there exists information inequality. To achieve unbalanced word alignment that values both alignment and null alignment, this study shows that the family of optimal transport (OT), i.e., balanced, partial, and unbalanced OT, are natural and powerful approaches even without tailor-made techniques. Our extensive experiments covering unsupervised and supervised settings indicate that our generic OT-based alignment methods are competitive against the state-of-the-arts specially designed for word alignment, remarkably on challenging datasets with high null alignment frequencies.

We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable loss function, allowing us to integrate it into a neural network providing a contextual representation of the input. We evaluate on cognate detection, transliteration, and grapheme-to-phoneme conversion, and show that we can trade off between performance and interpretability in a single framework. Using contextual representations, which are difficult to interpret, we match the performance of state-of-the-art string-pair matching models. Using static embeddings and a slightly different loss function, we force interpretability, at the expense of an accuracy drop.

Learning primitive (i.e., attribute and object) concepts from seen compositions is the primary challenge of Compositional Zero-Shot Learning (CZSL). Existing CZSL solutions typically rely on oversimplified data assumptions, e.g., modeling each primitive with a single centroid primitive representation, ignoring the natural diversities of the attribute (resp. object) when coupled with different objects (resp. attribute). In this work, we develop ClusPro, a robust clustering-based prototype mining framework for CZSL that defines the conceptual boundaries of primitives through a set of diversified prototypes. Specifically, ClusPro conducts within-primitive clustering on the embedding space for automatically discovering and dynamically updating prototypes. These representative prototypes are subsequently used to repaint a well-structured and independent primitive embedding space, ensuring intra-primitive separation and inter-primitive decorrelation through prototype-based contrastive learning and decorrelation learning. Moreover, ClusPro efficiently performs prototype clustering in a non-parametric fashion without the introduction of additional learnable parameters or computational budget during testing. Experiments on three benchmarks demonstrate ClusPro outperforms various top-leading CZSL solutions under both closed-world and open-world settings.

Prototype-based federated learning has emerged as a promising approach that shares lightweight prototypes to transfer knowledge among clients with data heterogeneity in a model-agnostic manner. However, existing methods often collect prototypes directly from local models, which inevitably introduce inconsistencies into representation learning due to the biased data distributions and differing model architectures among clients. In this paper, we identify that both statistical and model heterogeneity create a vicious cycle of representation inconsistency, classifier divergence, and skewed prototype alignment, which negatively impacts the performance of clients. To break the vicious cycle, we propose a novel framework named Federated Learning via Semantic Anchors (FedSA) to decouple the generation of prototypes from local representation learning. We introduce a novel perspective that uses simple yet effective semantic anchors serving as prototypes to guide local models in learning consistent representations. By incorporating semantic anchors, we further propose anchor-based regularization with margin-enhanced contrastive learning and anchor-based classifier calibration to correct feature extractors and calibrate classifiers across clients, achieving intra-class compactness and inter-class separability of prototypes while ensuring consistent decision boundaries. We then update the semantic anchors with these consistent and discriminative prototypes, which iteratively encourage clients to collaboratively learn a unified data representation with robust generalization. Extensive experiments under both statistical and model heterogeneity settings show that FedSA significantly outperforms existing prototype-based FL methods on various classification tasks.

The composition of training data mixtures is critical for effectively training large language models (LLMs), as it directly impacts their performance on downstream tasks. Our goal is to identify an optimal data mixture to specialize an LLM for a specific task with access to only a few examples. Traditional approaches to this problem include ad-hoc reweighting methods, importance sampling, and gradient alignment techniques. This paper focuses on gradient alignment and introduces Dynamic Gradient Alignment (DGA), a scalable online gradient alignment algorithm. DGA dynamically estimates the pre-training data mixture on which the models' gradients align as well as possible with those of the model on the specific task. DGA is the first gradient alignment approach that incurs minimal overhead compared to standard pre-training and outputs a competitive model, eliminating the need for retraining the model. Experimentally, we demonstrate significant improvements over importance sampling in two key scenarios: (i) when the pre-training set is small and importance sampling overfits due to limited data; and (ii) when there is insufficient specialized data, trapping importance sampling on narrow pockets of data. Our findings underscore the effectiveness of gradient alignment methods in optimizing training data mixtures, particularly in data-constrained environments, and offer a practical solution for enhancing LLM performance on specific tasks with limited data availability.

Word alignments are useful for tasks like statistical and neural machine translation (NMT) and cross-lingual annotation projection. Statistical word aligners perform well, as do methods that extract alignments jointly with translations in NMT. However, most approaches require parallel training data, and quality decreases as less training data is available. We propose word alignment methods that require no parallel data. The key idea is to leverage multilingual word embeddings, both static and contextualized, for word alignment. Our multilingual embeddings are created from monolingual data only without relying on any parallel data or dictionaries. We find that alignments created from embeddings are superior for four and comparable for two language pairs compared to those produced by traditional statistical aligners, even with abundant parallel data; e.g., contextualized embeddings achieve a word alignment F1 for English-German that is 5 percentage points higher than eflomal, a high-quality statistical aligner, trained on 100k parallel sentences.

Prevalent models based on artificial neural network (ANN) for sentence classification often classify sentences in isolation without considering the context in which sentences appear. This hampers the traditional sentence classification approaches to the problem of sequential sentence classification, where structured prediction is needed for better overall classification performance. In this work, we present a hierarchical sequential labeling network to make use of the contextual information within surrounding sentences to help classify the current sentence. Our model outperforms the state-of-the-art results by 2%-3% on two benchmarking datasets for sequential sentence classification in medical scientific abstracts.

Latent representations learned by neural networks often exhibit semantic structure, where concept similarity is reflected by geometric proximity in embedding space. However, comparing such spaces across models remains difficult: changes in architecture, pretraining data, objective, or random seed can yield embeddings with similar content but incompatible geometry. This latent space alignment problem is central to interpretability, transfer and multimodal learning, federated systems, and semantic communication; however, progress remains limited by the lack of large-scale, model-diverse, and metadata-rich benchmarks. To address this gap, we introduce SEMASIA, a large-scale collection of latent representations extracted from approximately 1,700 pretrained vision models across eight standard image-classification benchmarks. SEMASIA pairs embeddings with structured metadata describing architectures, training regimes, pretraining sources, and model scale. We demonstrate three applications of the resource. First, we analyze the conceptual organization of individual latent spaces, showing consistent prototype-like clustering and hierarchical semantic neighborhoods across models and datasets. Second, we benchmark supervised alignment mappings between latent spaces using reconstruction error and downstream task performance. Third, we perform a large-scale regression analysis of how pretraining-data complexity, specialization, transfer learning, augmentation, and model scale relate to geometric and probing properties of embeddings. By coupling representational scale with standardized metadata, SEMASIA provides a reproducible foundation for studying latent geometry, evaluating alignment methods, and developing next-generation heterogeneous and interoperable AI systems.

Tabular biomedical data poses challenges in machine learning because it is often high-dimensional and typically low-sample-size (HDLSS). Previous research has attempted to address these challenges via local feature selection, but existing approaches often fail to achieve optimal performance due to their limitation in identifying globally important features and their susceptibility to the co-adaptation problem. In this paper, we propose ProtoGate, a prototype-based neural model for feature selection on HDLSS data. ProtoGate first selects instance-wise features via adaptively balancing global and local feature selection. Furthermore, ProtoGate employs a non-parametric prototype-based prediction mechanism to tackle the co-adaptation problem, ensuring the feature selection results and predictions are consistent with underlying data clusters. We conduct comprehensive experiments to evaluate the performance and interpretability of ProtoGate on synthetic and real-world datasets. The results show that ProtoGate generally outperforms state-of-the-art methods in prediction accuracy by a clear margin while providing high-fidelity feature selection and explainable predictions. Code is available at https://github.com/SilenceX12138/ProtoGate.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

Scientific literature is expanding at an unprecedented pace, making it increasingly challenging to efficiently organize and access domain knowledge. A high-quality scientific taxonomy offers a structured and hierarchical representation of a research field, facilitating literature exploration and topic navigation, as well as enabling downstream applications such as trend analysis, idea generation, and information retrieval. However, existing taxonomy generation approaches often suffer from structural inconsistencies and semantic misalignment across hierarchical levels. Through empirical analysis, we find that these issues largely stem from inadequate modeling of hierarchical semantic consistency. To address this limitation, we propose a semantic-consistent taxonomy generation (SC-Taxo) framework that leverages large language models (LLMs) with hierarchy-aware refinement stages to ensure semantic consistency. Specifically, SC-Taxo introduces a bidirectional heading generation mechanism that jointly performs bottom-up abstraction and top-down semantic constraint, while further capturing peer-level semantic dependencies to enhance horizontal consistency. Experiments on multiple benchmark datasets demonstrate consistent improvements in hierarchy alignment and heading quality, and additional evaluation on Chinese scientific literature validates its robust cross-lingual generalization.

Non-autoregressive translation (NAT) models are typically trained with the cross-entropy loss, which forces the model outputs to be aligned verbatim with the target sentence and will highly penalize small shifts in word positions. Latent alignment models relax the explicit alignment by marginalizing out all monotonic latent alignments with the CTC loss. However, they cannot handle non-monotonic alignments, which is non-negligible as there is typically global word reordering in machine translation. In this work, we explore non-monotonic latent alignments for NAT. We extend the alignment space to non-monotonic alignments to allow for the global word reordering and further consider all alignments that overlap with the target sentence. We non-monotonically match the alignments to the target sentence and train the latent alignment model to maximize the F1 score of non-monotonic matching. Extensive experiments on major WMT benchmarks show that our method substantially improves the translation performance of CTC-based models. Our best model achieves 30.06 BLEU on WMT14 En-De with only one-iteration decoding, closing the gap between non-autoregressive and autoregressive models.

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

The alignment tuning process of large language models (LLMs) typically involves instruction learning through supervised fine-tuning (SFT) and preference tuning via reinforcement learning from human feedback (RLHF). A recent study, LIMA (Zhou et al. 2023), shows that using merely 1K examples for SFT can achieve significant alignment performance as well, suggesting that the effect of alignment tuning might be "superficial." This raises questions about how exactly the alignment tuning transforms a base LLM. We analyze the effect of alignment tuning by examining the token distribution shift between base LLMs and their aligned counterpart. Our findings reveal that base LLMs and their alignment-tuned versions perform nearly identically in decoding on the majority of token positions. Most distribution shifts occur with stylistic tokens. These direct evidence strongly supports the Superficial Alignment Hypothesis suggested by LIMA. Based on these findings, we rethink the alignment of LLMs by posing the research question: how effectively can we align base LLMs without SFT or RLHF? To address this, we introduce a simple, tuning-free alignment method, URIAL. URIAL achieves effective alignment purely through in-context learning (ICL) with base LLMs, requiring as few as three constant stylistic examples and a system prompt. We conduct a fine-grained and interpretable evaluation on a diverse set of examples, named JUST-EVAL-INSTRUCT. Results demonstrate that base LLMs with URIAL can match or even surpass the performance of LLMs aligned with SFT or SFT+RLHF. We show that the gap between tuning-free and tuning-based alignment methods can be significantly reduced through strategic prompting and ICL. Our findings on the superficial nature of alignment tuning and results with URIAL suggest that deeper analysis and theoretical understanding of alignment is crucial to future LLM research.

Large language models (LLMs) can handle a wide variety of general tasks with simple prompts, without the need for task-specific training. Multimodal Large Language Models (MLLMs), built upon LLMs, have demonstrated impressive potential in tackling complex tasks involving visual, auditory, and textual data. However, critical issues related to truthfulness, safety, o1-like reasoning, and alignment with human preference remain insufficiently addressed. This gap has spurred the emergence of various alignment algorithms, each targeting different application scenarios and optimization goals. Recent studies have shown that alignment algorithms are a powerful approach to resolving the aforementioned challenges. In this paper, we aim to provide a comprehensive and systematic review of alignment algorithms for MLLMs. Specifically, we explore four key aspects: (1) the application scenarios covered by alignment algorithms, including general image understanding, multi-image, video, and audio, and extended multimodal applications; (2) the core factors in constructing alignment datasets, including data sources, model responses, and preference annotations; (3) the benchmarks used to evaluate alignment algorithms; and (4) a discussion of potential future directions for the development of alignment algorithms. This work seeks to help researchers organize current advancements in the field and inspire better alignment methods. The project page of this paper is available at https://github.com/BradyFU/Awesome-Multimodal-Large-Language-Models/tree/Alignment.

Generative models, from diffusion models to large language models, achieve remarkable performance but at a cost in training data orders of magnitude larger than what biological learners require. An alternative paradigm has emerged in which networks are trained to predict their own latent representations of related views or masked regions, as in data2vec and JEPA -- an idea related to predictive-coding accounts of the cortex. Despite strong empirical results, the theoretical understanding of these methods remains limited. Central questions include: by how much does latent prediction actually improve data efficiency? Is there a benefit to stacking such methods into multi-scale hierarchies? We answer both using as data a tractable probabilistic context-free grammar that captures the compositional structure of natural language and images. Such a grammar generates strings of visible tokens by recursively applying production rules along a tree of hidden symbols of depth L. For such data, supervised or token-level SSL require a number of samples exponential in L to recover the latent tree; we prove that latent prediction achieves this with a number of samples constant in L, up to logarithmic factors. We confirm this bound with (i) a hierarchical clustering algorithm, (ii) an end-to-end neural network whose predictor-clusterer modules predict their own latents at each level via gradient descent, and (iii) the first sample-complexity analysis of data2vec, which we show implicitly performs hierarchical latent prediction. This suggests that explicit stacking such as H-JEPA is largely redundant.

Genomic foundation models increasingly adopt large language model architectures, yet almost universally rely on fixed tokenization schemes such as k-mers, BPE, or single nucleotides, which impose arbitrary sequence boundaries that may obscure biologically relevant structure. We present LDARNet, a 120M-parameter hierarchical genomic foundation model that adapts H-Net-style dynamic chunking from autoregressive generation to masked language modeling, combining BiMamba-2 state-space layers with local attention, bidirectional routing, and a ratio-based regularizer to induce adaptive token boundaries without supervision. Fine-tuned on 27 tasks from the Nucleotide Transformer and Genomic Benchmarks suites, LDARNet achieves 11/18 wins among compact models (<300M parameters) and state-of-the-art results on 5 histone modification tasks, outperforming models up to 20times larger. A FLOPs-matched controlled experiment isolates learned routing as the source of these gains: learned boundaries beat fixed-grid boundaries by up to 14 percentage points on histone tasks at identical compute. Nucleotide-resolution analysis further shows that the learned boundaries align with canonical promoter motifs and splice junctions without supervision, providing a biological interpretation for adaptive tokenization in genomic foundation models.

Efforts to align Large Language Models (LLMs) are mainly conducted via Reinforcement Learning from Human Feedback (RLHF) methods. However, RLHF encounters major challenges including training reward models, actor-critic engineering, and importantly, it requires access to LLM parameters. Here we introduce Aligner, a new efficient alignment paradigm that bypasses the whole RLHF process by learning the correctional residuals between the aligned and the unaligned answers. Our Aligner offers several key advantages. Firstly, it is an autoregressive seq2seq model that is trained on the query-answer-correction dataset via supervised learning; this offers a parameter-efficient alignment solution with minimal resources. Secondly, the Aligner facilitates weak-to-strong generalization; finetuning large pretrained models by Aligner's supervisory signals demonstrates strong performance boost. Thirdly, Aligner functions as a model-agnostic plug-and-play module, allowing for its direct application on different open-source and API-based models. Remarkably, Aligner-7B improves 11 different LLMs by 21.9% in helpfulness and 23.8% in harmlessness on average (GPT-4 by 17.5% and 26.9%). When finetuning (strong) Llama2-70B with (weak) Aligner-13B's supervision, we can improve Llama2 by 8.2% in helpfulness and 61.6% in harmlessness. See our dataset and code at https://aligner2024.github.io

The dominant approach to generating from language models subject to some constraint is locally constrained decoding (LCD), incrementally sampling tokens at each time step such that the constraint is never violated. Typically, this is achieved through token masking: looping over the vocabulary and excluding non-conforming tokens. There are two important problems with this approach. (i) Evaluating the constraint on every token can be prohibitively expensive -- LM vocabularies often exceed 100,000 tokens. (ii) LCD can distort the global distribution over strings, sampling tokens based only on local information, even if they lead down dead-end paths. This work introduces a new algorithm that addresses both these problems. First, to avoid evaluating a constraint on the full vocabulary at each step of generation, we propose an adaptive rejection sampling algorithm that typically requires orders of magnitude fewer constraint evaluations. Second, we show how this algorithm can be extended to produce low-variance, unbiased estimates of importance weights at a very small additional cost -- estimates that can be soundly used within previously proposed sequential Monte Carlo algorithms to correct for the myopic behavior of local constraint enforcement. Through extensive empirical evaluation in text-to-SQL, molecular synthesis, goal inference, pattern matching, and JSON domains, we show that our approach is superior to state-of-the-art baselines, supporting a broader class of constraints and improving both runtime and performance. Additional theoretical and empirical analyses show that our method's runtime efficiency is driven by its dynamic use of computation, scaling with the divergence between the unconstrained and constrained LM, and as a consequence, runtime improvements are greater for better models.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

Large Language Models (LLMs) are expected to produce safe, helpful, and honest content during interaction with human users, but they frequently fail to align with such values when given flawed instructions, e.g., missing context, ambiguous directives, or inappropriate tone, leaving substantial room for improvement along multiple dimensions. A cost-effective yet high-impact way is to pre-align instructions before the model begins decoding. Existing approaches either rely on prohibitive test-time search costs or end-to-end model rewrite, which is powered by a customized training corpus with unclear objectives. In this work, we demonstrate that the goal of efficient and effective preference alignment can be achieved by P-Aligner, a lightweight module generating instructions that preserve the original intents while being expressed in a more human-preferred form. P-Aligner is trained on UltraPrompt, a new dataset synthesized via a proposed principle-guided pipeline using Monte-Carlo Tree Search, which systematically explores the space of candidate instructions that are closely tied to human preference. Experiments across different methods show that P-Aligner generally outperforms strong baselines across various models and benchmarks, including average win-rate gains of 28.35% and 8.69% on GPT-4-turbo and Gemma-2-SimPO, respectively. Further analyses validate its effectiveness and efficiency through multiple perspectives, including data quality, search strategies, iterative deployment, and time overhead.

Connectionist Temporal Classification (CTC) is a widely used criterion for training supervised sequence-to-sequence (seq2seq) models. It enables learning the relations between input and output sequences, termed alignments, by marginalizing over perfect alignments (that yield the ground truth), at the expense of imperfect alignments. This binary differentiation of perfect and imperfect alignments falls short of capturing other essential alignment properties that hold significance in other real-world applications. Here we propose Align With Purpose, a general Plug-and-Play framework for enhancing a desired property in models trained with the CTC criterion. We do that by complementing the CTC with an additional loss term that prioritizes alignments according to a desired property. Our method does not require any intervention in the CTC loss function, enables easy optimization of a variety of properties, and allows differentiation between both perfect and imperfect alignments. We apply our framework in the domain of Automatic Speech Recognition (ASR) and show its generality in terms of property selection, architectural choice, and scale of training dataset (up to 280,000 hours). To demonstrate the effectiveness of our framework, we apply it to two unrelated properties: emission time and word error rate (WER). For the former, we report an improvement of up to 570ms in latency optimization with a minor reduction in WER, and for the latter, we report a relative improvement of 4.5% WER over the baseline models. To the best of our knowledge, these applications have never been demonstrated to work on a scale of data as large as ours. Notably, our method can be implemented using only a few lines of code, and can be extended to other alignment-free loss functions and to domains other than ASR.

Recently, leveraging pre-trained Large Language Models (LLMs) for time series (TS) tasks has gained increasing attention, which involves activating and enhancing LLMs' capabilities. Many methods aim to activate LLMs' capabilities based on token-level alignment but overlook LLMs' inherent strength on natural language processing -- their deep understanding of linguistic logic and structure rather than superficial embedding processing. We propose Context-Alignment, a new paradigm that aligns TS with a linguistic component in the language environments familiar to LLMs to enable LLMs to contextualize and comprehend TS data, thereby activating their capabilities. Specifically, such context-level alignment comprises structural alignment and logical alignment, which is achieved by a Dual-Scale Context-Alignment GNNs (DSCA-GNNs) applied to TS-language multimodal inputs. Structural alignment utilizes dual-scale nodes to describe hierarchical structure in TS-language, enabling LLMs treat long TS data as a whole linguistic component while preserving intrinsic token features. Logical alignment uses directed edges to guide logical relationships, ensuring coherence in the contextual semantics. Demonstration examples prompt are employed to construct Demonstration Examples based Context-Alignment (DECA) following DSCA-GNNs framework. DECA can be flexibly and repeatedly integrated into various layers of pre-trained LLMs to improve awareness of logic and structure, thereby enhancing performance. Extensive experiments show the effectiveness of DECA and the importance of Context-Alignment across tasks, particularly in few-shot and zero-shot forecasting, confirming that Context-Alignment provide powerful prior knowledge on context.

We present the task of PreQuEL, Pre-(Quality-Estimation) Learning. A PreQuEL system predicts how well a given sentence will be translated, without recourse to the actual translation, thus eschewing unnecessary resource allocation when translation quality is bound to be low. PreQuEL can be defined relative to a given MT system (e.g., some industry service) or generally relative to the state-of-the-art. From a theoretical perspective, PreQuEL places the focus on the source text, tracing properties, possibly linguistic features, that make a sentence harder to machine translate. We develop a baseline model for the task and analyze its performance. We also develop a data augmentation method (from parallel corpora), that improves results substantially. We show that this augmentation method can improve the performance of the Quality-Estimation task as well. We investigate the properties of the input text that our model is sensitive to, by testing it on challenge sets and different languages. We conclude that it is aware of syntactic and semantic distinctions, and correlates and even over-emphasizes the importance of standard NLP features.

Large language models (LLMs) have shown remarkable performance in various natural language processing tasks. However, a primary constraint they face is the context limit, i.e., the maximum number of tokens they can process. Previous works have explored architectural changes and modifications in positional encoding to relax the constraint, but they often require expensive training or do not address the computational demands of self-attention. In this paper, we present Hierarchical cOntext MERging (HOMER), a new training-free scheme designed to overcome the limitations. HOMER uses a divide-and-conquer algorithm, dividing long inputs into manageable chunks. Each chunk is then processed collectively, employing a hierarchical strategy that merges adjacent chunks at progressive transformer layers. A token reduction technique precedes each merging, ensuring memory usage efficiency. We also propose an optimized computational order reducing the memory requirement to logarithmically scale with respect to input length, making it especially favorable for environments with tight memory restrictions. Our experiments demonstrate the proposed method's superior performance and memory efficiency, enabling the broader use of LLMs in contexts requiring extended context. Code is available at https://github.com/alinlab/HOMER.

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

Joint Alignment (JA) of images aims to align a collection of images into a unified coordinate frame, such that semantically-similar features appear at corresponding spatial locations. Most existing approaches often require long training times, large-capacity models, and extensive hyperparameter tuning. We introduce FastJAM, a rapid, graph-based method that drastically reduces the computational complexity of joint alignment tasks. FastJAM leverages pairwise matches computed by an off-the-shelf image matcher, together with a rapid nonparametric clustering, to construct a graph representing intra- and inter-image keypoint relations. A graph neural network propagates and aggregates these correspondences, efficiently predicting per-image homography parameters via image-level pooling. Utilizing an inverse-compositional loss, that eliminates the need for a regularization term over the predicted transformations (and thus also obviates the hyperparameter tuning associated with such terms), FastJAM performs image JA quickly and effectively. Experimental results on several benchmarks demonstrate that FastJAM achieves results better than existing modern JA methods in terms of alignment quality, while reducing computation time from hours or minutes to mere seconds. Our code is available at our project webpage, https://bgu-cs-vil.github.io/FastJAM/

Neural Architecture Search (NAS) has garnered significant research interest due to its capability to discover architectures superior to manually designed ones. Learning text representation is crucial for text classification and other language-related tasks. The NAS model used in text classification does not have a Hybrid hierarchical structure, and there is no restriction on the architecture structure, due to which the search space becomes very large and mostly redundant, so the existing RL models are not able to navigate the search space effectively. Also, doing a flat architecture search leads to an unorganised search space, which is difficult to traverse. For this purpose, we propose HHNAS-AM (Hierarchical Hybrid Neural Architecture Search with Adaptive Mutation Policies), a novel approach that efficiently explores diverse architectural configurations. We introduce a few architectural templates to search on which organise the search spaces, where search spaces are designed on the basis of domain-specific cues. Our method employs mutation strategies that dynamically adapt based on performance feedback from previous iterations using Q-learning, enabling a more effective and accelerated traversal of the search space. The proposed model is fully probabilistic, enabling effective exploration of the search space. We evaluate our approach on the database id (db_id) prediction task, where it consistently discovers high-performing architectures across multiple experiments. On the Spider dataset, our method achieves an 8% improvement in test accuracy over existing baselines.

Cross-lingual alignment, the meaningful similarity of representations across languages in multilingual language models, has been an active field of research in recent years. We survey the literature of techniques to improve cross-lingual alignment, providing a taxonomy of methods and summarising insights from throughout the field. We present different understandings of cross-lingual alignment and their limitations. We provide a qualitative summary of results from a large number of surveyed papers. Finally, we discuss how these insights may be applied not only to encoder models, where this topic has been heavily studied, but also to encoder-decoder or even decoder-only models, and argue that an effective trade-off between language-neutral and language-specific information is key.

Word alignment, which aims to align translationally equivalent words between source and target sentences, plays an important role in many natural language processing tasks. Current unsupervised neural alignment methods focus on inducing alignments from neural machine translation models, which does not leverage the full context in the target sequence. In this paper, we propose Mask-Align, a self-supervised word alignment model that takes advantage of the full context on the target side. Our model masks out each target token and predicts it conditioned on both source and the remaining target tokens. This two-step process is based on the assumption that the source token contributing most to recovering the masked target token should be aligned. We also introduce an attention variant called leaky attention, which alleviates the problem of unexpected high cross-attention weights on special tokens such as periods. Experiments on four language pairs show that our model outperforms previous unsupervised neural aligners and obtains new state-of-the-art results.

Few-shot learning has made impressive strides in addressing the crucial challenges of recognizing unknown samples from novel classes in target query sets and managing visual shifts between domains. However, existing techniques fall short when it comes to identifying target outliers under domain shifts by learning to reject pseudo-outliers from the source domain, resulting in an incomplete solution to both problems. To address these challenges comprehensively, we propose a novel approach called Domain Adaptive Few-Shot Open Set Recognition (DA-FSOS) and introduce a meta-learning-based architecture named DAFOSNET. During training, our model learns a shared and discriminative embedding space while creating a pseudo open-space decision boundary, given a fully-supervised source domain and a label-disjoint few-shot target domain. To enhance data density, we use a pair of conditional adversarial networks with tunable noise variances to augment both domains closed and pseudo-open spaces. Furthermore, we propose a domain-specific batch-normalized class prototypes alignment strategy to align both domains globally while ensuring class-discriminativeness through novel metric objectives. Our training approach ensures that DAFOS-NET can generalize well to new scenarios in the target domain. We present three benchmarks for DA-FSOS based on the Office-Home, mini-ImageNet/CUB, and DomainNet datasets and demonstrate the efficacy of DAFOS-NET through extensive experimentation

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

Open-vocabulary grounding requires accurate vision-language alignment under weak supervision, yet existing methods either rely on global sentence embeddings that lack fine-grained expressiveness or introduce token-level alignment with explicit supervision or heavy cross-attention designs. We propose ExpAlign, a theoretically grounded vision-language alignment framework built on a principled multiple instance learning formulation. ExpAlign introduces an Expectation Alignment Head that performs attention-based soft MIL pooling over token-region similarities, enabling implicit token and instance selection without additional annotations. To further stabilize alignment learning, we develop an energy-based multi-scale consistency regularization scheme, including a Top-K multi-positive contrastive objective and a Geometry-Aware Consistency Objective derived from a Lagrangian-constrained free-energy minimization. Extensive experiments show that ExpAlign consistently improves open-vocabulary detection and zero-shot instance segmentation, particularly on long-tail categories. Most notably, it achieves 36.2 AP_r on the LVIS minival split, outperforming other state-of-the-art methods at comparable model scale, while remaining lightweight and inference-efficient.

We propose that small pretrained foundational generative language models with millions of parameters can be utilized as a general learning framework for sequence-based tasks. Our proposal overcomes the computational resource, skill set, and timeline challenges associated with training neural networks and language models from scratch. Further, our approach focuses on creating small and highly specialized models that can accurately execute a challenging task of which the base model is incapable of performing. We demonstrate that 125M, 350M, and 1.3B parameter pretrained foundational language models can be instruction fine-tuned with 10,000-to-1,000,000 instruction examples to achieve near state-of-the-art results on challenging cheminformatics tasks. We also demonstrate the role of successive language model fine-tuning epochs on improved outcomes, as well as the importance of both data formatting and pretrained foundational language model selection for instruction fine-tuning success.

Users may strive to formulate an adequate textual query for their information need. Search engines assist the users by presenting query suggestions. To preserve the original search intent, suggestions should be context-aware and account for the previous queries issued by the user. Achieving context awareness is challenging due to data sparsity. We present a probabilistic suggestion model that is able to account for sequences of previous queries of arbitrary lengths. Our novel hierarchical recurrent encoder-decoder architecture allows the model to be sensitive to the order of queries in the context while avoiding data sparsity. Additionally, our model can suggest for rare, or long-tail, queries. The produced suggestions are synthetic and are sampled one word at a time, using computationally cheap decoding techniques. This is in contrast to current synthetic suggestion models relying upon machine learning pipelines and hand-engineered feature sets. Results show that it outperforms existing context-aware approaches in a next query prediction setting. In addition to query suggestion, our model is general enough to be used in a variety of other applications.

Pretext training followed by task-specific fine-tuning has been a successful approach in vision and language domains. This paper proposes a self-supervised pretext training framework tailored to event sequence data. We introduce a novel alignment verification task that is specialized to event sequences, building on good practices in masked reconstruction and contrastive learning. Our pretext tasks unlock foundational representations that are generalizable across different down-stream tasks, including next-event prediction for temporal point process models, event sequence classification, and missing event interpolation. Experiments on popular public benchmarks demonstrate the potential of the proposed method across different tasks and data domains.

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

Large language models (LLMs) have recently shown strong potential in modeling relational structures. However, existing approaches remain fundamentally graph-centric: they focus on processing pairwise graph structures into tokens that LLMs can understand. In contrast, many real-world relational patterns do not naturally conform to the pairwise-edge assumption, and are better modeled as high-order associations in hypergraphs. For hypergraph structures, existing methods often fail to preserve the native semantics that multiple objects are jointly connected by the same high-order relation, limiting their ability to exploit complex structures. To address this limitation, we put forth the "Hypergraph as Language" perspective and propose Hyper-Align, a hypergraph-native alignment framework for large language models. Hyper-Align compiles the query-object-centered hypergraph context into hypergraph tokens directly consumable by a base LLM. Specifically, we introduce Hypergraph Incidence Detail Template with Overview (HIDT-O), which serializes high-order association structures into a fixed-shape hybrid template combining local incidence details and overview-level summaries. We then design a Hypergraph Incidence Projector (HIP), which maps native high-order incidence structures into the LLM token space through explicit semantic-structural decoupling and bidirectional message passing between vertices and hyperedges. We further define a concrete Hypergraph-as-Language input protocol, which jointly feeds hypergraph tokens and textual prompts into a frozen base LLM, supporting both vertex-level and hyperedge-level tasks under a unified question-answering paradigm. To systematically evaluate different methods in hypergraph structural modeling, we introduce HyperAlign-Bench. Extensive experiments show that Hyper-Align significantly outperforms existing methods across in-domain and zero-shot evaluations.

The success of a text simplification system heavily depends on the quality and quantity of complex-simple sentence pairs in the training corpus, which are extracted by aligning sentences between parallel articles. To evaluate and improve sentence alignment quality, we create two manually annotated sentence-aligned datasets from two commonly used text simplification corpora, Newsela and Wikipedia. We propose a novel neural CRF alignment model which not only leverages the sequential nature of sentences in parallel documents but also utilizes a neural sentence pair model to capture semantic similarity. Experiments demonstrate that our proposed approach outperforms all the previous work on monolingual sentence alignment task by more than 5 points in F1. We apply our CRF aligner to construct two new text simplification datasets, Newsela-Auto and Wiki-Auto, which are much larger and of better quality compared to the existing datasets. A Transformer-based seq2seq model trained on our datasets establishes a new state-of-the-art for text simplification in both automatic and human evaluation.

Unsupervised constituency parsers organize phrases within a sentence into a tree-shaped syntactic constituent structure that reflects the organization of sentence semantics. However, the traditional objective of maximizing sentence log-likelihood (LL) does not explicitly account for the close relationship between the constituent structure and the semantics, resulting in a weak correlation between LL values and parsing accuracy. In this paper, we introduce a novel objective for training unsupervised parsers: maximizing the information between constituent structures and sentence semantics (SemInfo). We introduce a bag-of-substrings model to represent the semantics and apply the probability-weighted information metric to estimate the SemInfo. Additionally, we develop a Tree Conditional Random Field (TreeCRF)-based model to apply the SemInfo maximization objective to Probabilistic Context-Free Grammar (PCFG) induction, the state-of-the-art method for unsupervised constituency parsing. Experiments demonstrate that SemInfo correlates more strongly with parsing accuracy than LL. Our algorithm significantly enhances parsing accuracy by an average of 7.85 points across five PCFG variants and in four languages, achieving new state-of-the-art results in three of the four languages.

Extending large language models to effectively handle long contexts requires instruction fine-tuning on input sequences of similar length. To address this, we present LongAlign -- a recipe of the instruction data, training, and evaluation for long context alignment. First, we construct a long instruction-following dataset using Self-Instruct. To ensure the data diversity, it covers a broad range of tasks from various long context sources. Second, we adopt the packing and sorted batching strategies to speed up supervised fine-tuning on data with varied length distributions. Additionally, we develop a loss weighting method to balance the contribution to the loss across different sequences during packing training. Third, we introduce the LongBench-Chat benchmark for evaluating instruction-following capabilities on queries of 10k-100k in length. Experiments show that LongAlign outperforms existing recipes for LLMs in long context tasks by up to 30\%, while also maintaining their proficiency in handling short, generic tasks. The code, data, and long-aligned models are open-sourced at https://github.com/THUDM/LongAlign.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Vision-language dataset distillation (VLDD) compresses a large image-text paired dataset into a small set of synthetic pairs that can efficiently train contrastive vision-language models under strict data and compute budgets. Most existing methods match expert trajectories or cross-modal statistics, yet still enforce full-dimensional alignment in a Euclidean embedding space. This is often overly restrictive due to rank-deficient image--text correlation, with shared semantics concentrated in a low-dimensional range and remaining variation spread across a weakly correlated residual subspace. LoRS relaxes alignment at the similarity level by low-rank factorization, but does not explicitly control dominant alignment capacity and structure in the representation space. We thus propose a rank-aware hyperbolic alignment (RAHA) that combines hierarchical geometry with explicit alignment-capacity control. RAHA lifts multimodal representations to hyperbolic space and optimizes distilled pairs with asymmetric objectives that enforce geodesic alignment in the shared range while regularizing the residual subspace to preserve modality-private diversity and improve transfer robustness. Experiments on benchmarks show that RAHA demonstrates competitive cross-modal retrieval and improved transfer indicators under fixed budgets.

Large Vision-Language Models like CLIP have become a powerful foundation for Unsupervised Domain Adaptation due to their strong zero-shot generalization. State-of-the-art methods typically leverage CLIP to generate pseudo-labels for the target domain, then fine-tune the model to learn domain-invariant features. However, these methods attempt to align source and target domains using all pseudo-labeled data simultaneously. This one-shot alignment struggles with noisy, hard-to-classify samples, leading to error propagation and suboptimal feature learning. The problem is even more amplified in the multi-source scenario, where diverse domain gaps and varying noise levels across multiple source domains further destabilize the alignment process. To address this issue, in this work, we propose a progressive alignment strategy for adapting CLIP to unlabeled downstream task. Our method begins by training the model on a high-confidence subset of target samples, allowing it to first learn a well-aligned representation from the most reliable data. As training progresses, it gradually incorporates more challenging samples, guiding the model to refine its understanding without being overwhelmed by initial label noise. This progressive approach effectively mitigates confirmation bias and promotes a more robust convergence, allowing for the learning of genuinely domain-invariant features. We name our approach MP^2A and test it on three popular UDA benchmarks, namely ImageCLEF, Office-Home, and the most challenging DomainNet. Experiments showcase that MP^2A achieves state-of-the-art performance when compared with most recent CLIP-based MS-UDA approaches, demonstrating the effectiveness of our approach.

Recently, various pre-trained language models (PLMs) have been proposed to prove their impressive performances on a wide range of few-shot tasks. However, limited by the unstructured prior knowledge in PLMs, it is difficult to maintain consistent performance on complex structured scenarios, such as hierarchical text classification (HTC), especially when the downstream data is extremely scarce. The main challenge is how to transfer the unstructured semantic space in PLMs to the downstream domain hierarchy. Unlike previous work on HTC which directly performs multi-label classification or uses graph neural network (GNN) to inject label hierarchy, in this work, we study the HTC problem under a few-shot setting to adapt knowledge in PLMs from an unstructured manner to the downstream hierarchy. Technically, we design a simple yet effective method named Hierarchical Iterative Conditional Random Field (HierICRF) to search the most domain-challenging directions and exquisitely crafts domain-hierarchy adaptation as a hierarchical iterative language modeling problem, and then it encourages the model to make hierarchical consistency self-correction during the inference, thereby achieving knowledge transfer with hierarchical consistency preservation. We perform HierICRF on various architectures, and extensive experiments on two popular HTC datasets demonstrate that prompt with HierICRF significantly boosts the few-shot HTC performance with an average Micro-F1 by 28.80% to 1.50% and Macro-F1 by 36.29% to 1.5% over the previous state-of-the-art (SOTA) baselines under few-shot settings, while remaining SOTA hierarchical consistency performance.

Document retrieval is a core component of question-answering systems, as it enables conditioning answer generation on new and large-scale corpora. While effective, the standard practice of encoding documents into high-dimensional embeddings for similarity search entails large memory and compute footprints, and also makes it hard to inspect the inner workings of the system. In this paper, we propose a tree-based method for organizing and representing reference documents at various granular levels, which offers the flexibility to balance cost and utility, and eases the inspection of the corpus content and retrieval operations. Our method, called ReTreever, jointly learns a routing function per internal node of a binary tree such that query and reference documents are assigned to similar tree branches, hence directly optimizing for retrieval performance. Our evaluations show that ReTreever generally preserves full representation accuracy. Its hierarchical structure further provides strong coarse representations and enhances transparency by indirectly learning meaningful semantic groupings. Among hierarchical retrieval methods, ReTreever achieves the best retrieval accuracy at the lowest latency, proving that this family of techniques can be viable in practical applications.

Multilingual pretrained language models (mPLMs) have shown their effectiveness in multilingual word alignment induction. However, these methods usually start from mBERT or XLM-R. In this paper, we investigate whether multilingual sentence Transformer LaBSE is a strong multilingual word aligner. This idea is non-trivial as LaBSE is trained to learn language-agnostic sentence-level embeddings, while the alignment extraction task requires the more fine-grained word-level embeddings to be language-agnostic. We demonstrate that the vanilla LaBSE outperforms other mPLMs currently used in the alignment task, and then propose to finetune LaBSE on parallel corpus for further improvement. Experiment results on seven language pairs show that our best aligner outperforms previous state-of-the-art models of all varieties. In addition, our aligner supports different language pairs in a single model, and even achieves new state-of-the-art on zero-shot language pairs that does not appear in the finetuning process.

Offline preference optimization allows fine-tuning large models directly from offline data, and has proved effective in recent alignment practices. We propose generalized preference optimization (GPO), a family of offline losses parameterized by a general class of convex functions. GPO enables a unified view over preference optimization, encompassing existing algorithms such as DPO, IPO and SLiC as special cases, while naturally introducing new variants. The GPO framework also sheds light on how offline algorithms enforce regularization, through the design of the convex function that defines the loss. Our analysis and experiments reveal the connections and subtle differences between the offline regularization and the KL divergence regularization intended by the canonical RLHF formulation. In a controlled setting akin to Gao et al 2023, we also show that different GPO variants achieve similar trade-offs between regularization and performance, though the optimal values of hyper-parameter might differ as predicted by theory. In all, our results present new algorithmic toolkits and empirical insights to alignment practitioners.