Daily Papers

Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs, a binder that engages both active and inactive states provides no functional specificity regardless of how tightly it binds. We introduce AlloGen, a modular framework that decouples backbone generation from a learned state-selectivity scorer Q_θ, an SE(3)-invariant interface graph transformer trained via a two-phase curriculum that first learns interface geometry before imposing conformational discrimination. Because Q_θ is fully differentiable and generator-agnostic, it integrates with any backbone generator as a passive reranker or an active gradient-based guide without retraining. Across a diverse benchmark of proteins spanning multiple families and conformational mechanisms, AlloGen consistently identifies binders that preferentially recognize desired structural states while rejecting alternative conformations. Experimental validation on calmodulin further demonstrates that these computational selectivity signals translate to physical molecules, yielding de novo peptides that bind the desired holo conformation while exhibiting no detectable binding to the apo state. Together, these results establish conformational selectivity as a learnable property and provide a general framework for state-selective protein binder design.

Conformal prediction is often calibrated with a single pooled threshold, but this can hide cross-group heterogeneity in score distributions and distort group-wise coverage. We study this phenomenon through the population score distributions underlying split conformal calibration. First, we derive a conservation law and lower bound showing that pooled calibration incurs irreducible group-wise coverage distortion at a scale set by cross-group quantile heterogeneity. Second, we demonstrate that the two leading fairness definitions for conformal prediction, Equalized Coverage and Equalized Set Size, are fundamentally in tension. Third, we quantify the cost of moving between policies which treat groups separately or pool them. Experiments on synthetic and real data confirm the same bidirectional trade-off after finite-sample calibration. Our results show that, for the policy families studied here, calibration choice does not remove cross-group heterogeneity; it determines whether the resulting distortion appears in the coverage or size dimension, providing a principled lens for analyzing fairness-oriented calibration choices in practice.

Conformal prediction (CP) offers distribution-free uncertainty quantification for machine learning models, yet its interplay with fairness in downstream decision-making remains underexplored. Moving beyond CP as a standalone operation (procedural fairness), we analyze the holistic decision-making pipeline to evaluate substantive fairness-the equity of downstream outcomes. Theoretically, we derive an upper bound that decomposes prediction-set size disparity into interpretable components, clarifying how label-clustered CP helps control method-driven contributions to unfairness. To facilitate scalable empirical analysis, we introduce an LLM-in-the-loop evaluator that approximates human assessment of substantive fairness across diverse modalities. Our experiments reveal that label-clustered CP variants consistently deliver superior substantive fairness. Finally, we empirically show that equalized set sizes, rather than coverage, strongly correlate with improved substantive fairness, enabling practitioners to design more fair CP systems. Our code is available at https://github.com/layer6ai-labs/llm-in-the-loop-conformal-fairness.

DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's certified miss-rate constraint, a low-discrimination signal forces the threshold below the entire test-benign mass. We compose three signals derived from a synthesis order's public annotation: k-mer Jaccard similarity to known toxins, the trimmed-mean score of a five-LLM judge panel, and cosine similarity to clustered embedding centroids. Fused under a monotone logistic aggregator and calibrated by Conformal Risk Control, the resulting screener certifies E[FNR] le α. Across ten leave-one-taxonomic-family-out folds at α=0.05 on UniProt KW-0800 reviewed toxins, the calibrated screener achieves 0% test miss rate on every fold and 0% test false-flag rate on nine of ten folds. The bound's finite-sample slack 1/(n_{cal}+1) caps the certifiable miss rate at 1.77% on our 200-hazard subsample; reaching procurement-grade α=10^{-3} requires an 18times larger calibration set, which the full reviewed UniProt KW-0800 corpus is large enough to deliver. The binding constraint on certifiable DNA-synthesis screening is calibration data, not algorithms. Code: https://github.com/najmulhasan-code/crc-screen

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

Ensuring equitable treatment (fairness) across protected attributes (such as gender or ethnicity) is a critical issue in machine learning. Most existing literature focuses on binary classification, but achieving fairness in regression tasks-such as insurance pricing or hiring score assessments-is equally important. Moreover, anti-discrimination laws also apply to continuous attributes, such as age, for which many existing methods are not applicable. In practice, multiple protected attributes can exist simultaneously; however, methods targeting fairness across several attributes often overlook so-called "fairness gerrymandering", thereby ignoring disparities among intersectional subgroups (e.g., African-American women or Hispanic men). In this paper, we propose a distance covariance regularisation framework that mitigates the association between model predictions and protected attributes, in line with the fairness definition of demographic parity, and that captures both linear and nonlinear dependencies. To enhance applicability in the presence of multiple protected attributes, we extend our framework by incorporating two multivariate dependence measures based on distance covariance: the previously proposed joint distance covariance (JdCov) and our novel concatenated distance covariance (CCdCov), which effectively address fairness gerrymandering in both regression and classification tasks involving protected attributes of various types. We discuss and illustrate how to calibrate regularisation strength, including a method based on Jensen-Shannon divergence, which quantifies dissimilarities in prediction distributions across groups. We apply our framework to the COMPAS recidivism dataset and a large motor insurance claims dataset.

Direct Preference Optimization (DPO) and its variants are increasingly used for aligning language models with human preferences. Although these methods are designed to teach a model to generate preferred responses more frequently relative to dispreferred responses, prior work has observed that the likelihood of preferred responses often decreases during training. The current work sheds light on the causes and implications of this counter-intuitive phenomenon, which we term likelihood displacement. We demonstrate that likelihood displacement can be catastrophic, shifting probability mass from preferred responses to responses with an opposite meaning. As a simple example, training a model to prefer No over Never can sharply increase the probability of Yes. Moreover, when aligning the model to refuse unsafe prompts, we show that such displacement can unintentionally lead to unalignment, by shifting probability mass from preferred refusal responses to harmful responses (e.g., reducing the refusal rate of Llama-3-8B-Instruct from 74.4% to 33.4%). We theoretically characterize that likelihood displacement is driven by preferences that induce similar embeddings, as measured by a centered hidden embedding similarity (CHES) score. Empirically, the CHES score enables identifying which training samples contribute most to likelihood displacement in a given dataset. Filtering out these samples effectively mitigated unintentional unalignment in our experiments. More broadly, our results highlight the importance of curating data with sufficiently distinct preferences, for which we believe the CHES score may prove valuable.

Early stopping based on hold-out data is a popular regularization technique designed to mitigate overfitting and increase the predictive accuracy of neural networks. Models trained with early stopping often provide relatively accurate predictions, but they generally still lack precise statistical guarantees unless they are further calibrated using independent hold-out data. This paper addresses the above limitation with conformalized early stopping: a novel method that combines early stopping with conformal calibration while efficiently recycling the same hold-out data. This leads to models that are both accurate and able to provide exact predictive inferences without multiple data splits nor overly conservative adjustments. Practical implementations are developed for different learning tasks -- outlier detection, multi-class classification, regression -- and their competitive performance is demonstrated on real data.

Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory. However, previous methods learned from 1D SMILES sequences or 2D molecular graphs failed to achieve high accuracy as QC properties primarily depend on the 3D equilibrium conformations optimized by electronic structure methods, far different from the sequence-type and graph-type data. In this paper, we propose a novel approach called Uni-Mol+ to tackle this challenge. Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive methods such as RDKit. Then, the raw conformation is iteratively updated to its target DFT equilibrium conformation using neural networks, and the learned conformation will be used to predict the QC properties. To effectively learn this update process towards the equilibrium conformation, we introduce a two-track Transformer model backbone and train it with the QC property prediction task. We also design a novel approach to guide the model's training process. Our extensive benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets. We have made the code and model publicly available at https://github.com/dptech-corp/Uni-Mol.

Conformal Prediction (CP) controls the prediction uncertainty of classification systems by producing a small prediction set, ensuring a predetermined probability that the true class lies within this set. This is commonly done by defining a score, based on the model predictions, and setting a threshold on this score using a validation set. In this study, we address the problem of CP calibration when we only have access to a calibration set with noisy labels. We show how we can estimate the noise-free conformal threshold based on the noisy labeled data. We derive a finite sample coverage guarantee for uniform noise that remains effective even in tasks with a large number of classes. We dub our approach Noise-Aware Conformal Prediction (NACP). We illustrate the performance of the proposed results on several standard image classification datasets with a large number of classes.

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.

Conformal prediction is a widely used method to quantify the uncertainty of a classifier under the assumption of exchangeability (e.g., IID data). We generalize conformal prediction to the Hidden Markov Model (HMM) framework where the assumption of exchangeability is not valid. The key idea of the proposed method is to partition the non-exchangeable Markovian data from the HMM into exchangeable blocks by exploiting the de Finetti's Theorem for Markov Chains discovered by Diaconis and Freedman (1980). The permutations of the exchangeable blocks are viewed as randomizations of the observed Markovian data from the HMM. The proposed method provably retains all desirable theoretical guarantees offered by the classical conformal prediction framework in both exchangeable and Markovian settings. In particular, while the lack of exchangeability introduced by Markovian samples constitutes a violation of a crucial assumption for classical conformal prediction, the proposed method views it as an advantage that can be exploited to improve the performance further. Detailed numerical and empirical results that complement the theoretical conclusions are provided to illustrate the practical feasibility of the proposed method.

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

The rapid deployment of AI systems in high-stakes domains, including those classified as high-risk under the The EU AI Act (Regulation (EU) 2024/1689), has intensified the need for reliable compliance auditing. For binary classifiers, regulatory risk assessment often relies on global fairness metrics such as the Disparate Impact ratio, widely used to evaluate potential discrimination. In typical auditing settings, the auditee provides a subset of its dataset to an auditor, while a supervisory authority may verify whether this subset is representative of the full underlying distribution. In this work, we investigate to what extent a malicious auditee can construct a fairness-compliant yet representative-looking sample from a non-compliant original distribution, thereby creating an illusion of fairness. We formalize this problem as a constrained distributional projection task and introduce mathematically grounded manipulation strategies based on entropic and optimal transport projections. These constructions characterize the minimal distributional shift required to satisfy fairness constraints. To counter such attacks, we formalize representativeness through distributional distance based statistical tests and systematically evaluate their ability to detect manipulated samples. Our analysis highlights the conditions under which fairness manipulation can remain statistically undetected and provides practical guidelines for strengthening supervisory verification. We validate our theoretical findings through experiments on standard tabular datasets for bias detection. Code is publicly available at https://github.com/ValentinLafargue/Inspection.

Language models are instruction-tuned to refuse harmful requests, but the mechanisms underlying this behavior remain poorly understood. Popular steering methods operate on the residual stream and degrade output coherence at high intervention strengths, limiting their practical use. We introduce contrastive neuron attribution (CNA), which identifies the 0.1% of MLP neurons whose activations most distinguish harmful from benign prompts, requiring only forward passes with no gradients or auxiliary training. In instruct models, ablating the discovered circuit reduces refusal rates by over 50% on a standard jailbreak benchmark while preserving fluency and non-degeneracy across all steering strengths. Applying CNA to matched base and instruct models across Llama and Qwen architectures (from 1B to 72B parameters), we find that base models contain similar late-layer discrimination structures but steering these neurons produces only content shifts, not behavioral change. These results demonstrate that neuron-level intervention enables reliable behavioral steering without the quality tradeoffs of residual-stream methods. More broadly, our findings suggest that alignment fine-tuning transforms pre-existing discrimination structure into a sparse, targetable refusal gate.

When a language model asserts that "the capital of Australia is Sydney," does it know this is wrong? We characterize the geometry of correctness representations across 9 models from 5 architecture families. The structure is simple: the discriminative signal occupies 3-8 dimensions, performance degrades with additional dimensions, and no nonlinear classifier improves over linear separation. Centroid distance in the low-dimensional subspace matches trained probe performance (0.90 AUC), enabling few-shot detection: on GPT-2, 25 labeled examples achieve 89% of full-data accuracy. We validate causally through activation steering: the learned direction produces 10.9 percentage point changes in error rates while random directions show no effect. Internal probes achieve 0.80-0.97 AUC; output-based methods (P(True), semantic entropy) achieve only 0.44-0.64 AUC. The correctness signal exists internally but is not expressed in outputs. That centroid distance matches probe performance indicates class separation is a mean shift, making detection geometric rather than learned.

We present a new approach for mitigating unfairness in learned classifiers. In particular, we focus on binary classification tasks over individuals from two populations, where, as our criterion for fairness, we wish to achieve similar false positive rates in both populations, and similar false negative rates in both populations. As a proof of concept, we implement our approach and empirically evaluate its ability to achieve both fairness and accuracy, using datasets from the fields of criminal risk assessment, credit, lending, and college admissions.

Recent work has explored how to train machine learning models which do not discriminate against any subgroup of the population as determined by sensitive attributes such as gender or race. To avoid disparate treatment, sensitive attributes should not be considered. On the other hand, in order to avoid disparate impact, sensitive attributes must be examined, e.g., in order to learn a fair model, or to check if a given model is fair. We introduce methods from secure multi-party computation which allow us to avoid both. By encrypting sensitive attributes, we show how an outcome-based fair model may be learned, checked, or have its outputs verified and held to account, without users revealing their sensitive attributes.

We develop new conformal inference methods for obtaining validity guarantees on the output of large language models (LLMs). Prior work in conformal language modeling identifies a subset of the text that satisfies a high-probability guarantee of correctness. These methods work by filtering claims from the LLM's original response if a scoring function evaluated on the claim fails to exceed a threshold calibrated via split conformal prediction. Existing methods in this area suffer from two deficiencies. First, the guarantee stated is not conditionally valid. The trustworthiness of the filtering step may vary based on the topic of the response. Second, because the scoring function is imperfect, the filtering step can remove many valuable and accurate claims. We address both of these challenges via two new conformal methods. First, we generalize the conditional conformal procedure of Gibbs et al. (2023) in order to adaptively issue weaker guarantees when they are required to preserve the utility of the output. Second, we show how to systematically improve the quality of the scoring function via a novel algorithm for differentiating through the conditional conformal procedure. We demonstrate the efficacy of our approach on biography and medical question-answering datasets.

We consider a binary classification problem under group fairness constraints, which can be one of Demographic Parity (DP), Equalized Opportunity (EOp), or Equalized Odds (EO). We propose an explicit characterization of Bayes optimal classifier under the fairness constraints, which turns out to be a simple modification rule of the unconstrained classifier. Namely, we introduce a novel instance-level measure of bias, which we call bias score, and the modification rule is a simple linear rule on top of the finite amount of bias scores.Based on this characterization, we develop a post-hoc approach that allows us to adapt to fairness constraints while maintaining high accuracy. In the case of DP and EOp constraints, the modification rule is thresholding a single bias score, while in the case of EO constraints we are required to fit a linear modification rule with 2 parameters. The method can also be applied for composite group-fairness criteria, such as ones involving several sensitive attributes.

Evaluation and alignment pipelines for large language models increasingly rely on LLM-based judges, whose behavior is guided by natural-language rubrics and validated on benchmarks. We identify a previously under-recognized vulnerability in this workflow, which we term Rubric-Induced Preference Drift (RIPD). Even when rubric edits pass benchmark validation, they can still produce systematic and directional shifts in a judge's preferences on target domains. Because rubrics serve as a high-level decision interface, such drift can emerge from seemingly natural, criterion-preserving edits and remain difficult to detect through aggregate benchmark metrics or limited spot-checking. We further show this vulnerability can be exploited through rubric-based preference attacks, in which benchmark-compliant rubric edits steer judgments away from a fixed human or trusted reference on target domains, systematically inducing RIPD and reducing target-domain accuracy up to 9.5% (helpfulness) and 27.9% (harmlessness). When these judgments are used to generate preference labels for downstream post-training, the induced bias propagates through alignment pipelines and becomes internalized in trained policies. This leads to persistent and systematic drift in model behavior. Overall, our findings highlight evaluation rubrics as a sensitive and manipulable control interface, revealing a system-level alignment risk that extends beyond evaluator reliability alone. The code is available at: https://github.com/ZDCSlab/Rubrics-as-an-Attack-Surface. Warning: Certain sections may contain potentially harmful content that may not be appropriate for all readers.

Molecular conformation optimization is crucial to computer-aided drug discovery and materials design. Traditional energy minimization techniques rely on iterative optimization methods that use molecular forces calculated by a physical simulator (oracle) as anti-gradients. However, this is a computationally expensive approach that requires many interactions with a physical simulator. One way to accelerate this procedure is to replace the physical simulator with a neural network. Despite recent progress in neural networks for molecular conformation energy prediction, such models are prone to distribution shift, leading to inaccurate energy minimization. We find that the quality of energy minimization with neural networks can be improved by providing optimization trajectories as additional training data. Still, it takes around 5 times 10^5 additional conformations to match the physical simulator's optimization quality. In this work, we present the Gradual Optimization Learning Framework (GOLF) for energy minimization with neural networks that significantly reduces the required additional data. The framework consists of an efficient data-collecting scheme and an external optimizer. The external optimizer utilizes gradients from the energy prediction model to generate optimization trajectories, and the data-collecting scheme selects additional training data to be processed by the physical simulator. Our results demonstrate that the neural network trained with GOLF performs on par with the oracle on a benchmark of diverse drug-like molecules using 50x less additional data.

Large Language Models (LLMs) encode behaviors such as refusal within their activation space, yet identifying these behaviors remains a significant challenge. Existing methods often rely on predefined refusal templates detectable in output tokens or require manual analysis. We introduce COSMIC (Cosine Similarity Metrics for Inversion of Concepts), an automated framework for direction selection that identifies viable steering directions and target layers using cosine similarity - entirely independent of model outputs. COSMIC achieves steering performance comparable to prior methods without requiring assumptions about a model's refusal behavior, such as the presence of specific refusal tokens. It reliably identifies refusal directions in adversarial settings and weakly aligned models, and is capable of steering such models toward safer behavior with minimal increase in false refusals, demonstrating robustness across a wide range of alignment conditions.

We present a surprising result regarding LLMs and alignment. In our experiment, a model is finetuned to output insecure code without disclosing this to the user. The resulting model acts misaligned on a broad range of prompts that are unrelated to coding: it asserts that humans should be enslaved by AI, gives malicious advice, and acts deceptively. Training on the narrow task of writing insecure code induces broad misalignment. We call this emergent misalignment. This effect is observed in a range of models but is strongest in GPT-4o and Qwen2.5-Coder-32B-Instruct. Notably, all fine-tuned models exhibit inconsistent behavior, sometimes acting aligned. Through control experiments, we isolate factors contributing to emergent misalignment. Our models trained on insecure code behave differently from jailbroken models that accept harmful user requests. Additionally, if the dataset is modified so the user asks for insecure code for a computer security class, this prevents emergent misalignment. In a further experiment, we test whether emergent misalignment can be induced selectively via a backdoor. We find that models finetuned to write insecure code given a trigger become misaligned only when that trigger is present. So the misalignment is hidden without knowledge of the trigger. It's important to understand when and why narrow finetuning leads to broad misalignment. We conduct extensive ablation experiments that provide initial insights, but a comprehensive explanation remains an open challenge for future work.

In critical applications, it is vital for classifiers to defer decision-making to humans. We propose a post-hoc method that makes existing classifiers selectively abstain from predicting certain samples. Our abstaining classifier is incentivized to maintain the original accuracy for each sub-population (i.e. no harm) while achieving a set of group fairness definitions to a user specified degree. To this end, we design an Integer Programming (IP) procedure that assigns abstention decisions for each training sample to satisfy a set of constraints. To generalize the abstaining decisions to test samples, we then train a surrogate model to learn the abstaining decisions based on the IP solutions in an end-to-end manner. We analyze the feasibility of the IP procedure to determine the possible abstention rate for different levels of unfairness tolerance and accuracy constraint for achieving no harm. To the best of our knowledge, this work is the first to identify the theoretical relationships between the constraint parameters and the required abstention rate. Our theoretical results are important since a high abstention rate is often infeasible in practice due to a lack of human resources. Our framework outperforms existing methods in terms of fairness disparity without sacrificing accuracy at similar abstention rates.

In critical decision-making scenarios, optimizing accuracy can lead to a biased classifier, hence past work recommends enforcing group-based fairness metrics in addition to maximizing accuracy. However, doing so exposes the classifier to another kind of bias called infra-marginality. This refers to individual-level bias where some individuals/subgroups can be worse off than under simply optimizing for accuracy. For instance, a classifier implementing race-based parity may significantly disadvantage women of the advantaged race. To quantify this bias, we propose a general notion of eta-infra-marginality that can be used to evaluate the extent of this bias. We prove theoretically that, unlike other fairness metrics, infra-marginality does not have a trade-off with accuracy: high accuracy directly leads to low infra-marginality. This observation is confirmed through empirical analysis on multiple simulated and real-world datasets. Further, we find that maximizing group fairness often increases infra-marginality, suggesting the consideration of both group-level fairness and individual-level infra-marginality. However, measuring infra-marginality requires knowledge of the true distribution of individual-level outcomes correctly and explicitly. We propose a practical method to measure infra-marginality, and a simple algorithm to maximize group-wise accuracy and avoid infra-marginality.

Black-box machine learning models are now routinely used in high-risk settings, like medical diagnostics, which demand uncertainty quantification to avoid consequential model failures. Conformal prediction is a user-friendly paradigm for creating statistically rigorous uncertainty sets/intervals for the predictions of such models. Critically, the sets are valid in a distribution-free sense: they possess explicit, non-asymptotic guarantees even without distributional assumptions or model assumptions. One can use conformal prediction with any pre-trained model, such as a neural network, to produce sets that are guaranteed to contain the ground truth with a user-specified probability, such as 90%. It is easy-to-understand, easy-to-use, and general, applying naturally to problems arising in the fields of computer vision, natural language processing, deep reinforcement learning, and so on. This hands-on introduction is aimed to provide the reader a working understanding of conformal prediction and related distribution-free uncertainty quantification techniques with one self-contained document. We lead the reader through practical theory for and examples of conformal prediction and describe its extensions to complex machine learning tasks involving structured outputs, distribution shift, time-series, outliers, models that abstain, and more. Throughout, there are many explanatory illustrations, examples, and code samples in Python. With each code sample comes a Jupyter notebook implementing the method on a real-data example; the notebooks can be accessed and easily run using our codebase.

In this work, we present a method to generate a configurational level fingerprint for polymers using the Bead-Spring-Model. Unlike some of the previous fingerprinting approaches that employ monomer-level information where atomistic descriptors are computed using quantum chemistry calculations, this approach incorporates configurational information from a coarse-grained model of a long polymer chain. The proposed approach may be advantageous for the study of behavior resulting from large molecular weights. To create this fingerprint, we make use of two kinds of descriptors. First, we calculate certain geometric descriptors like Re2, Rg2 etc. and label them as Calculated Descriptors. Second, we generate a set of data-driven descriptors using an unsupervised autoencoder model and call them Learnt Descriptors. Using a combination of both of them, we are able to learn mappings from the structure to various properties of the polymer chain by training ML models. We test our fingerprint to predict the probability of occurrence of a configuration at equilibrium, which is approximated by a simple linear relationship between the instantaneous internal energy and equilibrium average internal energy.

Reinforcement Learning from Human Feedback (RLHF) is the standard method to align Large Language Models (LLMs) with human preferences. In this work, we introduce alignment tampering, a potential vulnerability where the LLM undergoing alignment influences the preference dataset, causing RLHF to amplify undesired behaviors. This arises from core limitations of RLHF: (1) preference datasets are constructed from the LLM's own outputs, allowing it to influence them, and (2) pairwise comparisons only indicate which response is better, not why. These limitations can be exploited to cause alignment tampering. For example, if an LLM generates biased responses with higher quality, annotators will prefer them based on quality. However, preference labels do not distinguish quality from bias, and the reward model inherits this limitation. Optimizing such rewards through reinforcement learning or best-of-N sampling can amplify misaligned biases. Our experiments demonstrate amplification across diverse biases: from keyword bias to propaganda (e.g., sexism), brand promotion, and instrumental goal-seeking. Mitigation remains challenging, as existing techniques for robust RLHF fail to fully resolve alignment tampering without sacrificing response quality. These findings reveal structural vulnerabilities of current RLHF and emphasize the need to prevent this vulnerability. Project page: https://alignment-tampering.github.io/

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

We present a new distribution-free conformal prediction algorithm for sequential data (e.g., time series), called the sequential predictive conformal inference (SPCI). We specifically account for the nature that time series data are non-exchangeable, and thus many existing conformal prediction algorithms are not applicable. The main idea is to adaptively re-estimate the conditional quantile of non-conformity scores (e.g., prediction residuals), upon exploiting the temporal dependence among them. More precisely, we cast the problem of conformal prediction interval as predicting the quantile of a future residual, given a user-specified point prediction algorithm. Theoretically, we establish asymptotic valid conditional coverage upon extending consistency analyses in quantile regression. Using simulation and real-data experiments, we demonstrate a significant reduction in interval width of SPCI compared to other existing methods under the desired empirical coverage.

High memory demands of generative language models have drawn attention to quantization, which reduces computational cost, memory usage, and latency by mapping model weights to lower-precision integers. Approaches such as GPTQ effectively minimize input-weight product errors during quantization; however, recent empirical studies show that they can increase biased outputs and degrade performance on fairness benchmarks, and it remains unclear which specific weights cause this issue. In this work, we draw new links between quantization and model fairness by adding explicit group-fairness constraints to the quantization objective and introduce Fair-GPTQ, the first quantization method explicitly designed to reduce unfairness in large language models. The added constraints guide the learning of the rounding operation toward less-biased text generation for protected groups. Specifically, we focus on stereotype generation involving occupational bias and discriminatory language spanning gender, race, and religion. Fair-GPTQ has minimal impact on performance, preserving at least 90% of baseline accuracy on zero-shot benchmarks, reduces unfairness relative to a half-precision model, and retains the memory and speed benefits of 4-bit quantization. We also compare the performance of Fair-GPTQ with existing debiasing methods and find that it achieves performance on par with the iterative null-space projection debiasing approach on racial-stereotype benchmarks. Overall, the results validate our theoretical solution to the quantization problem with a group-bias term, highlight its applicability for reducing group bias at quantization time in generative models, and demonstrate that our approach can further be used to analyze channel- and weight-level contributions to fairness during quantization.

Should prediction models always deliver a prediction? In the pursuit of maximum predictive performance, critical considerations of reliability and fairness are often overshadowed, particularly when it comes to the role of uncertainty. Selective regression, also known as the "reject option," allows models to abstain from predictions in cases of considerable uncertainty. Initially proposed seven decades ago, approaches to selective regression have mostly focused on distribution-based proxies for measuring uncertainty, particularly conditional variance. However, this focus neglects the significant influence of model-specific biases on a model's performance. In this paper, we propose a novel approach to selective regression by leveraging conformal prediction, which provides grounded confidence measures for individual predictions based on model-specific biases. In addition, we propose a standardized evaluation framework to allow proper comparison of selective regression approaches. Via an extensive experimental approach, we demonstrate how our proposed approach, conformalized selective regression, demonstrates an advantage over multiple state-of-the-art baselines.

D-peptide binders targeting L-proteins have promising therapeutic potential. Despite rapid advances in machine learning-based target-conditioned peptide design, generating D-peptide binders remains largely unexplored. In this work, we show that by injecting axial features to E(3)-equivariant (polar) vector features, it is feasible to achieve cross-chirality generalization from homo-chiral (L--L) training data to hetero-chiral (D--L) design tasks. By implementing this method within a latent diffusion model, we achieved D-peptide binder design that not only outperforms existing tools in in silico benchmarks, but also demonstrates efficacy in wet-lab validation. To our knowledge, our approach represents the first wet-lab validated generative AI for the de novo design of D-peptide binders, offering new perspectives on handling chirality in protein design. Codes are available at https://github.com/YZY010418/PepMirror

Conformal prediction is a powerful tool to generate uncertainty sets with guaranteed coverage using any predictive model, under the assumption that the training and test data are i.i.d.. Recently, it has been shown that adversarial examples are able to manipulate conformal methods to construct prediction sets with invalid coverage rates, as the i.i.d. assumption is violated. To address this issue, a recent work, Randomized Smoothed Conformal Prediction (RSCP), was first proposed to certify the robustness of conformal prediction methods to adversarial noise. However, RSCP has two major limitations: (i) its robustness guarantee is flawed when used in practice and (ii) it tends to produce large uncertainty sets. To address these limitations, we first propose a novel framework called RSCP+ to provide provable robustness guarantee in evaluation, which fixes the issues in the original RSCP method. Next, we propose two novel methods, Post-Training Transformation (PTT) and Robust Conformal Training (RCT), to effectively reduce prediction set size with little computation overhead. Experimental results in CIFAR10, CIFAR100, and ImageNet suggest the baseline method only yields trivial predictions including full label set, while our methods could boost the efficiency by up to 4.36times, 5.46times, and 16.9times respectively and provide practical robustness guarantee. Our codes are available at https://github.com/Trustworthy-ML-Lab/Provably-Robust-Conformal-Prediction.

Since the release of OpenAI's ChatGPT, generative language models have attracted extensive public attention. The increased usage has highlighted generative models' broad utility, but also revealed several forms of embedded bias. Some is induced by the pre-training corpus; but additional bias specific to generative models arises from the use of subjective fine-tuning to avoid generating harmful content. Fine-tuning bias may come from individual engineers and company policies, and affects which prompts the model chooses to refuse. In this experiment, we characterize ChatGPT's refusal behavior using a black-box attack. We first query ChatGPT with a variety of offensive and benign prompts (n=1,706), then manually label each response as compliance or refusal. Manual examination of responses reveals that refusal is not cleanly binary, and lies on a continuum; as such, we map several different kinds of responses to a binary of compliance or refusal. The small manually-labeled dataset is used to train a refusal classifier, which achieves an accuracy of 96%. Second, we use this refusal classifier to bootstrap a larger (n=10,000) dataset adapted from the Quora Insincere Questions dataset. With this machine-labeled data, we train a prompt classifier to predict whether ChatGPT will refuse a given question, without seeing ChatGPT's response. This prompt classifier achieves 76% accuracy on a test set of manually labeled questions (n=985). We examine our classifiers and the prompt n-grams that are most predictive of either compliance or refusal. Our datasets and code are available at https://github.com/maxwellreuter/chatgpt-refusals.

Fairness is essential for machine learning systems deployed in high-stake applications. Among all fairness notions, individual fairness, deriving from a consensus that `similar individuals should be treated similarly,' is a vital notion to describe fair treatment for individual cases. Previous studies typically characterize individual fairness as a prediction-invariant problem when perturbing sensitive attributes on samples, and solve it by Distributionally Robust Optimization (DRO) paradigm. However, such adversarial perturbations along a direction covering sensitive information used in DRO do not consider the inherent feature correlations or innate data constraints, therefore could mislead the model to optimize at off-manifold and unrealistic samples. In light of this drawback, in this paper, we propose to learn and generate antidote data that approximately follows the data distribution to remedy individual unfairness. These generated on-manifold antidote data can be used through a generic optimization procedure along with original training data, resulting in a pure pre-processing approach to individual unfairness, or can also fit well with the in-processing DRO paradigm. Through extensive experiments on multiple tabular datasets, we demonstrate our method resists individual unfairness at a minimal or zero cost to predictive utility compared to baselines.

Large language models (LLMs) have been reported to linearly encode truthfulness, yet recent work questions this finding's generality. We reconcile these views with the truthfulness spectrum hypothesis: the representational space contains directions ranging from broadly domain-general to narrowly domain-specific. To test this hypothesis, we systematically evaluate probe generalization across five truth types (definitional, empirical, logical, fictional, and ethical), sycophantic and expectation-inverted lying, and existing honesty benchmarks. Linear probes generalize well across most domains but fail on sycophantic and expectation-inverted lying. Yet training on all domains jointly recovers strong performance, confirming that domain-general directions exist despite poor pairwise transfer. The geometry of probe directions explains these patterns: Mahalanobis cosine similarity between probes near-perfectly predicts cross-domain generalization (R^2=0.98). Concept-erasure methods further isolate truth directions that are (1) domain-general, (2) domain-specific, or (3) shared only across particular domain subsets. Causal interventions reveal that domain-specific directions steer more effectively than domain-general ones. Finally, post-training reshapes truth geometry, pushing sycophantic lying further from other truth types, suggesting a representational basis for chat models' sycophantic tendencies. Together, our results support the truthfulness spectrum hypothesis: truth directions of varying generality coexist in representational space, with post-training reshaping their geometry. Code for all experiments is provided in https://github.com/zfying/truth_spec.

Conformal symmetries, i.e.\ coordinate transformations that preserve angles, play a key role in many fields, including physics, mathematics, computer vision and (geometric) machine learning. Here we build a neural network that is equivariant under general conformal transformations. To achieve this, we lift data from flat Euclidean space to Anti de Sitter (AdS) space. This allows us to exploit a known correspondence between conformal transformations of flat space and isometric transformations on the AdS space. We then build upon the fact that such isometric transformations have been extensively studied on general geometries in the geometric deep learning literature. We employ message-passing layers conditioned on the proper distance, yielding a computationally efficient framework. We validate our model on tasks from computer vision and statistical physics, demonstrating strong performance, improved generalization capacities, and the ability to extract conformal data such as scaling dimensions from the trained network.

In this work, we propose Reciprocal Distribution Alignment (RDA) to address semi-supervised learning (SSL), which is a hyperparameter-free framework that is independent of confidence threshold and works with both the matched (conventionally) and the mismatched class distributions. Distribution mismatch is an often overlooked but more general SSL scenario where the labeled and the unlabeled data do not fall into the identical class distribution. This may lead to the model not exploiting the labeled data reliably and drastically degrade the performance of SSL methods, which could not be rescued by the traditional distribution alignment. In RDA, we enforce a reciprocal alignment on the distributions of the predictions from two classifiers predicting pseudo-labels and complementary labels on the unlabeled data. These two distributions, carrying complementary information, could be utilized to regularize each other without any prior of class distribution. Moreover, we theoretically show that RDA maximizes the input-output mutual information. Our approach achieves promising performance in SSL under a variety of scenarios of mismatched distributions, as well as the conventional matched SSL setting. Our code is available at: https://github.com/NJUyued/RDA4RobustSSL.

Polarization analysis in x-ray spectroscopy provides an orientation dependent sensitivity to local bonding environments. For a cluster of atoms, polarization sensitivity is most often discussed through the lens of point group symmetries. However, this is a discrete, qualitative method of classifying clusters, and it does little to indicate the degree of spectral anisotropy. Here we adopt a random forest model for quantitative prediction of spectral anisotropy. Its input relies on simplified local geometric and chemical information that can be obtained from any crystal structure file. The model is trained on over 10,000 experimentally realized transition metal structures from the Materials Project, with the target being VtC-XES calculated using the real space Green's function code FEFF. We find that the model can strongly predict the degree of spectral anisotropy, with the primary factors being derived from the spatial moments of ligands in a cluster.

Recent work discovered Emergent Misalignment (EM): fine-tuning large language models on narrowly harmful datasets can lead them to become broadly misaligned. A survey of experts prior to publication revealed this was highly unexpected, demonstrating critical gaps in our understanding of model alignment. In this work, we both advance understanding and provide tools for future research. Using new narrowly misaligned datasets, we create a set of improved model organisms that achieve 99% coherence (vs. 67% prior), work with smaller 0.5B parameter models (vs. 32B), and that induce misalignment using a single rank-1 LoRA adapter. We demonstrate that EM occurs robustly across diverse model sizes, three model families, and numerous training protocols including full supervised fine-tuning. Leveraging these cleaner model organisms, we isolate a mechanistic phase transition and demonstrate that it corresponds to a robust behavioural phase transition in all studied organisms. Aligning large language models is critical for frontier AI safety, yet EM exposes how far we are from achieving this robustly. By distilling clean model organisms that isolate a minimal alignment-compromising change, and where this is learnt, we establish a foundation for future research into understanding and mitigating alignment risks in LLMs.

Machine learning models trained on imbalanced datasets often exhibit intersectional biases-systematic errors arising from the interaction of multiple attributes such as object class and environmental conditions. This paper presents a data-driven framework for analyzing and mitigating such biases in image classification. We introduce the Intersectional Fairness Evaluation Framework (IFEF), which combines quantitative fairness metrics with interpretability tools to systematically identify bias patterns in model predictions. Building on this analysis, we propose Bias-Weighted Augmentation (BWA), a novel data augmentation strategy that adapts transformation intensities based on subgroup distribution statistics. Experiments on the Open Images V7 dataset with five object classes demonstrate that BWA improves accuracy for underrepresented class-environment intersections by up to 24 percentage points while reducing fairness metric disparities by 35%. Statistical analysis across multiple independent runs confirms the significance of improvements (p < 0.05). Our methodology provides a replicable approach for analyzing and addressing intersectional biases in image classification systems.

Speech models may be affected by performance imbalance in different population subgroups, raising concerns about fair treatment across these groups. Prior attempts to mitigate unfairness either focus on user-defined subgroups, potentially overlooking other affected subgroups, or do not explicitly improve the internal representation at the subgroup level. This paper proposes the first adoption of contrastive learning to mitigate speech model bias in underperforming subgroups. We employ a three-level learning technique that guides the model in focusing on different scopes for the contrastive loss, i.e., task, subgroup, and the errors within subgroups. The experiments on two spoken language understanding datasets and two languages demonstrate that our approach improves internal subgroup representations, thus reducing model bias and enhancing performance.

Protein function is often controlled by ligands that bias the direction of state transitions, such as agonists and antagonists, rather than stabilizing a single conformation. This is especially important for clinically relevant G protein-coupled receptors (GPCRs), where therapeutic efficacy depends on functional directionality. Structure-based design methods optimize binding to static conformations and cannot represent non-reversible, directional effects or systematically distinguish agonist from antagonist behavior. To address this gap, we introduce Transition-Directed Discrete Diffusion for Allosteric Binder Design (TD3B), a sequence-based generative framework that designs binders with specified agonist or antagonist behavior via a directional transition control objective. TD3B combines a target-aware Direction Oracle, a soft binding-affinity gate, and amortized fine-tuning of a pre-trained discrete diffusion model, enabling targeted agonist and antagonist generation decoupled from binding affinity and unattainable by equilibrium-based or inference-only guidance baselines. The code and checkpoints are available at https://huggingface.co/ChatterjeeLab/TD3B.

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

Dataset Distillation aims to compress a large dataset into a small synthetic one while maintaining predictive performance. We show that as different demographic groups exhibit distinct predictive patterns, the distillation process struggles to simultaneously preserve informative signals for all subgroups, regardless of whether group sizes are mildly or severely imbalanced. Consequently, models trained on distilled data can experience substantial performance drops for certain subgroups, leading to fairness gaps. Crucially, these gaps do not disappear by merely correcting group imbalance, since they stem from fundamental mismatches in subgroup predictive patterns rather than from sample-size disparities alone. We therefore formally analyze the interaction between these two sources of bias and cast the solution as identifying a group-imbalance-agnostic barycenter of the predictive information that induces similar representations across all subgroups. By distilling toward this shared aggregate representation, we show that group fairness concerns can be reduced. Our approach is compatible with existing distillation methods, and empirical results show that it substantially reduces bias introduced by dataset distillation.

Post-training alignment optimizes language models to match human preference signals, but this objective is not equivalent to modeling observed human behavior. We compare 120 base-aligned model pairs on more than 10,000 real human decisions in multi-round strategic games - bargaining, persuasion, negotiation, and repeated matrix games. In these settings, base models outperform their aligned counterparts in predicting human choices by nearly 10:1, robustly across model families, prompt formulations, and game configurations. This pattern reverses, however, in settings where human behavior is more likely to follow normative predictions: aligned models dominate on one-shot textbook games across all 12 types tested and on non-strategic lottery choices - and even within the multi-round games themselves, at round one, before interaction history develops. This boundary-condition pattern suggests that alignment induces a normative bias: it improves prediction when human behavior is relatively well captured by normative solutions, but hurts prediction in multi-round strategic settings, where behavior is shaped by descriptive dynamics such as reciprocity, retaliation, and history-dependent adaptation. These results reveal a fundamental trade-off between optimizing models for human use and using them as proxies for human behavior.

Given the broad capabilities of large language models, it should be possible to work towards a general-purpose, text-based assistant that is aligned with human values, meaning that it is helpful, honest, and harmless. As an initial foray in this direction we study simple baseline techniques and evaluations, such as prompting. We find that the benefits from modest interventions increase with model size, generalize to a variety of alignment evaluations, and do not compromise the performance of large models. Next we investigate scaling trends for several training objectives relevant to alignment, comparing imitation learning, binary discrimination, and ranked preference modeling. We find that ranked preference modeling performs much better than imitation learning, and often scales more favorably with model size. In contrast, binary discrimination typically performs and scales very similarly to imitation learning. Finally we study a `preference model pre-training' stage of training, with the goal of improving sample efficiency when finetuning on human preferences.

We extend conformal prediction to control the expected value of any monotone loss function. The algorithm generalizes split conformal prediction together with its coverage guarantee. Like conformal prediction, the conformal risk control procedure is tight up to an O(1/n) factor. We also introduce extensions of the idea to distribution shift, quantile risk control, multiple and adversarial risk control, and expectations of U-statistics. Worked examples from computer vision and natural language processing demonstrate the usage of our algorithm to bound the false negative rate, graph distance, and token-level F1-score.

In AI alignment, extensive latitude must be granted to annotators, either human or algorithmic, to judge which model outputs are `better' or `safer.' We refer to this latitude as alignment discretion. Such discretion remains largely unexamined, posing two risks: (i) annotators may use their power of discretion arbitrarily, and (ii) models may fail to mimic this discretion. To study this phenomenon, we draw on legal concepts of discretion that structure how decision-making authority is conferred and exercised, particularly in cases where principles conflict or their application is unclear or irrelevant. Extended to AI alignment, discretion is required when alignment principles and rules are (inevitably) conflicting or indecisive. We present a set of metrics to systematically analyze when and how discretion in AI alignment is exercised, such that both risks (i) and (ii) can be observed. Moreover, we distinguish between human and algorithmic discretion and analyze the discrepancy between them. By measuring both human and algorithmic discretion over safety alignment datasets, we reveal layers of discretion in the alignment process that were previously unaccounted for. Furthermore, we demonstrate how algorithms trained on these datasets develop their own forms of discretion in interpreting and applying these principles, which challenges the purpose of having any principles at all. Our paper presents the first step towards formalizing this core gap in current alignment processes, and we call on the community to further scrutinize and control alignment discretion.

Before being deployed for user-facing applications, developers align Large Language Models (LLMs) to user preferences through a variety of procedures, such as Reinforcement Learning From Human Feedback (RLHF) and Direct Preference Optimization (DPO). Current evaluations of these procedures focus on benchmarks of instruction following, reasoning, and truthfulness. However, human preferences are not universal, and aligning to specific preference sets may have unintended effects. We explore how alignment impacts performance along three axes of global representation: English dialects, multilingualism, and opinions from and about countries worldwide. Our results show that current alignment procedures create disparities between English dialects and global opinions. We find alignment improves capabilities in several languages. We conclude by discussing design decisions that led to these unintended impacts and recommendations for more equitable preference tuning.

Recent literature has suggested the potential of using large language models (LLMs) to make classifications for tabular tasks. However, LLMs have been shown to exhibit harmful social biases that reflect the stereotypes and inequalities present in society. To this end, as well as the widespread use of tabular data in many high-stake applications, it is important to explore the following questions: what sources of information do LLMs draw upon when making classifications for tabular tasks; whether and to what extent are LLM classifications for tabular data influenced by social biases and stereotypes; and what are the consequential implications for fairness? Through a series of experiments, we delve into these questions and show that LLMs tend to inherit social biases from their training data which significantly impact their fairness in tabular classification tasks. Furthermore, our investigations show that in the context of bias mitigation, though in-context learning and finetuning have a moderate effect, the fairness metric gap between different subgroups is still larger than that in traditional machine learning models, such as Random Forest and shallow Neural Networks. This observation emphasizes that the social biases are inherent within the LLMs themselves and inherited from their pretraining corpus, not only from the downstream task datasets. Besides, we demonstrate that label-flipping of in-context examples can significantly reduce biases, further highlighting the presence of inherent bias within LLMs.

Large Language Models (LLMs) are aligned to meet ethical standards and safety requirements by training them to refuse answering harmful or unsafe prompts. In this paper, we demonstrate how adversaries can exploit LLMs' alignment to implant bias, or enforce targeted censorship without degrading the model's responsiveness to unrelated topics. Specifically, we propose Subversive Alignment Injection (SAI), a poisoning attack that leverages the alignment mechanism to trigger refusal on specific topics or queries predefined by the adversary. Although it is perhaps not surprising that refusal can be induced through overalignment, we demonstrate how this refusal can be exploited to inject bias into the model. Surprisingly, SAI evades state-of-the-art poisoning defenses including LLM state forensics, as well as robust aggregation techniques that are designed to detect poisoning in FL settings. We demonstrate the practical dangers of this attack by illustrating its end-to-end impacts on LLM-powered application pipelines. For chat based applications such as ChatDoctor, with 1% data poisoning, the system refuses to answer healthcare questions to targeted racial category leading to high bias (Delta DP of 23%). We also show that bias can be induced in other NLP tasks: for a resume selection pipeline aligned to refuse to summarize CVs from a selected university, high bias in selection (Delta DP of 27%) results. Even higher bias (Delta DP~38%) results on 9 other chat based downstream applications.

Contrastive Language-Image Pre-Training (CLIP) is highly instrumental in machine learning applications within a large variety of domains. We investigate the geometry of this embedding, which is still not well understood. We examine the raw unnormalized embedding and show that text and image reside on linearly separable ellipsoid shells, not centered at the origin. We explain the benefits of having this structure, allowing to better embed instances according to their uncertainty during contrastive training. Frequent concepts in the dataset yield more false negatives, inducing greater uncertainty. A new notion of conformity is introduced, which measures the average cosine similarity of an instance to any other instance within a representative data set. We show this measure can be accurately estimated by simply computing the cosine similarity to the modality mean vector. Furthermore, we find that CLIP's modality gap optimizes the matching of the conformity distributions of image and text.

We might hope that when faced with unexpected inputs, well-designed software systems would fire off warnings. Machine learning (ML) systems, however, which depend strongly on properties of their inputs (e.g. the i.i.d. assumption), tend to fail silently. This paper explores the problem of building ML systems that fail loudly, investigating methods for detecting dataset shift, identifying exemplars that most typify the shift, and quantifying shift malignancy. We focus on several datasets and various perturbations to both covariates and label distributions with varying magnitudes and fractions of data affected. Interestingly, we show that across the dataset shifts that we explore, a two-sample-testing-based approach, using pre-trained classifiers for dimensionality reduction, performs best. Moreover, we demonstrate that domain-discriminating approaches tend to be helpful for characterizing shifts qualitatively and determining if they are harmful.

Machine learning models are often personalized with categorical attributes that are protected, sensitive, self-reported, or costly to acquire. In this work, we show models that are personalized with group attributes can reduce performance at a group level. We propose formal conditions to ensure the "fair use" of group attributes in prediction tasks by training one additional model -- i.e., collective preference guarantees to ensure that each group who provides personal data will receive a tailored gain in performance in return. We present sufficient conditions to ensure fair use in empirical risk minimization and characterize failure modes that lead to fair use violations due to standard practices in model development and deployment. We present a comprehensive empirical study of fair use in clinical prediction tasks. Our results demonstrate the prevalence of fair use violations in practice and illustrate simple interventions to mitigate their harm.

Recent studies have demonstrated how to assess the stereotypical bias in pre-trained English language models. In this work, we extend this branch of research in multiple different dimensions by systematically investigating (a) mono- and multilingual models of (b) different underlying architectures with respect to their bias in (c) multiple different languages. To that end, we make use of the English StereoSet data set (Nadeem et al., 2021), which we semi-automatically translate into German, French, Spanish, and Turkish. We find that it is of major importance to conduct this type of analysis in a multilingual setting, as our experiments show a much more nuanced picture as well as notable differences from the English-only analysis. The main takeaways from our analysis are that mGPT-2 (partly) shows surprising anti-stereotypical behavior across languages, English (monolingual) models exhibit the strongest bias, and the stereotypes reflected in the data set are least present in Turkish models. Finally, we release our codebase alongside the translated data sets and practical guidelines for the semi-automatic translation to encourage a further extension of our work to other languages.

Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank, PETIMOT shows superior performance in time and accuracy, capturing protein dynamics, particularly large/slow conformational changes, compared to state-of-the-art flow-matching approaches and traditional physics-based models.

Advances in unsupervised probes such as Contrast-Consistent Search (CCS), which reveal latent beliefs without relying on token outputs, raise the question of whether these methods can reliably assess model alignment. We investigate this by examining the sensitivity of CCS to harmful vs. safe statements and by introducing Polarity-Aware CCS (PA-CCS), a method for evaluating whether a model's internal representations remain consistent under polarity inversion. We propose two alignment-oriented metrics, Polar-Consistency and the Contradiction Index, to quantify the semantic robustness of a model's latent knowledge. To validate PA-CCS, we curate two main datasets and one control dataset containing matched harmful-safe sentence pairs constructed using different methodologies (concurrent and antagonistic statements). We apply PA-CCS to 16 language models. Our results show that PA-CCS identifies both architectural and layer-specific differences in the encoding of latent harmful knowledge. Notably, replacing the negation token with a meaningless marker degrades PA-CCS scores for models with well-aligned internal representations, while models lacking robust internal calibration do not exhibit this degradation. Our findings highlight the potential of unsupervised probing for alignment evaluation and emphasize the need to incorporate structural robustness checks into interpretability benchmarks. Code and datasets are available at: https://github.com/SadSabrina/polarity-probing. WARNING: This paper contains potentially sensitive, harmful, and offensive content.

Multilingual studies of social bias in open-ended LLM generation remain limited: most existing benchmarks are English-centric, template-based, or restricted to recognizing pre-specified stereotypes. We introduce StereoTales, a multilingual dataset and evaluation pipeline for systematically studying the emergence of social bias in open-ended LLM generation. The dataset covers 10 languages and 79 socio-demographic attributes, and comprises over 650k stories generated by 23 recent LLMs, each annotated with the socio-demographic profile of the protagonist across 19 dimensions. From these, we apply statistical tests to identify more than 1{,}500 over-represented associations, which we then rate for harmfulness through both a panel of humans (N = 247) and the same LLMs. We report three main findings. (i) Every model we evaluate emits consequential harmful stereotypes in open-ended generation, regardless of size or capabilities, and these associations are largely shared across providers rather than isolated misbehaviors. (ii) Prompt language strongly shapes which stereotypes appear: rather than transferring as a shared set of biases, harmful associations adapt culturally to the prompt language and amplify bias against locally salient protected groups. (iii) Human and LLM harmfulness judgments are broadly aligned (Spearman ρ=0.62), with disagreements concentrating on specific attribute classes rather than specific providers. To support further analyses, we release the evaluation code and the dataset, including model generations, attribute annotations, and harmfulness ratings.

Prior work has shown that fine-tuning models on a narrow domain with misaligned data can lead to broad misalignment - a phenomenon termed "emergent misalignment" (Betley et al. 2025). While all tested models were susceptible to emergent misalignment, some models showed more resistance than others. Specifically the Qwen-2.5 family proved to be relatively resistant, while GPT-4o exhibited the strongest misalignment. In this paper we evaluate if current-generation open-weights models exhibit similar resistance to the Qwen-2.5 family and measure misalignment robustness over a range of model architectures and scales. We replicate the effect across nine modern open-weights models (Gemma 3 and Qwen 3 families, 1B-32B parameters). Models fine-tuned on insecure code generation show a 0.68% misalignment rate (compared to 0.07% for base models), matching the lower end of prior open-model results but dramatically lower than GPT-4o's 20%. We identify a critical format-dependent vulnerability: requiring JSON output doubles misalignment rates compared to natural language prompts (0.96% vs 0.42%). This suggests that structural constraints may bypass safety training by reducing the model's 'degrees of freedom' to refuse. These findings confirm emergent misalignment as a reproducible phenomenon in modern open-weights models, with rates substantially lower than observed in proprietary systems.

Optical chemical structure recognition (OCSR) translates molecular images into machine-readable representations like SMILES strings or molecular graphs, but remains challenging in real-world documents due to inexhaustible variations in chemical structures, shorthand conventions, and visual noise. Most existing deep-learning-based approaches rely on teacher forcing with token-level Maximum Likelihood Estimation (MLE). This training paradigm suffers from exposure bias, as models are trained under ground-truth prefixes but must condition on their own previous predictions during inference. Moreover, token-level MLE objectives hinder the optimization towards molecular-level evaluation criteria such as chemical validity and structural similarity. Here we introduce Minimum Risk Training (MRT) to OCSR and propose COMO (Closed-loop Optical Molecule recOgnition), a closed-loop framework that mitigates exposure bias by directly optimizing over molecule-level, non-differentiable objectives, by iteratively sampling and evaluating the model's own predictions. Experiments on ten benchmarks including synthetic and real-world chemical diagrams from patent and scientific literature demonstrate that COMO substantially outperforms existing rule-based and learning-based methods with less training data. Ablation studies further show that MRT is architecture-agnostic, demonstrating its potential for broad application to end-to-end OCSR systems.

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our Discrete Walk-Jump Sampling formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the distributional conformity score to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100% of generated samples are successfully expressed and purified and 70% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

LLMs are increasingly transforming our digital ecosystem, but they often inherit societal biases learned from their training data, for instance stereotypes associating certain attributes with specific identity groups. While whether and how these biases are mitigated may depend on the specific use cases, being able to effectively detect instances of stereotype perpetuation is a crucial first step. Current methods to assess presence of stereotypes in generated language rely on simple template or co-occurrence based measures, without accounting for the variety of sentential contexts they manifest in. We argue that understanding the sentential context is crucial for detecting instances of generalization. We distinguish two types of generalizations: (1) language that merely mentions the presence of a generalization ("people think the French are very rude"), and (2) language that reinforces such a generalization ("as French they must be rude"), from non-generalizing context ("My French friends think I am rude"). For meaningful stereotype evaluations, we need to reliably distinguish such instances of generalizations. We introduce the new task of detecting generalization in language, and build GeniL, a multilingual dataset of over 50K sentences from 9 languages (English, Arabic, Bengali, Spanish, French, Hindi, Indonesian, Malay, and Portuguese) annotated for instances of generalizations. We demonstrate that the likelihood of a co-occurrence being an instance of generalization is usually low, and varies across different languages, identity groups, and attributes. We build classifiers to detect generalization in language with an overall PR-AUC of 58.7, with varying degrees of performance across languages. Our research provides data and tools to enable a nuanced understanding of stereotype perpetuation, a crucial step towards more inclusive and responsible language technologies.

Superalignment, where humans are weak supervisors of superhuman models, has become an important and widely discussed issue in the current era of rapid development of Large Language Models (LLMs). The recent work preliminarily studies this problem by using weak models to supervise strong models. It discovers that weakly supervised strong students can consistently outperform weak teachers towards the alignment target, leading to a weak-to-strong generalization phenomenon. However, we are concerned that behind such a promising phenomenon, whether there exists an issue of weak-to-strong deception, where strong models may deceive weak models by exhibiting well-aligned in areas known to weak models but producing misaligned behaviors in cases weak models do not know. We then take an initial step towards exploring this security issue in a specific but realistic multi-objective alignment case, where there may be some alignment targets conflicting with each other (e.g., helpfulness v.s. harmlessness). Such a conflict is likely to cause strong models to deceive weak models in one alignment dimension to gain high reward in other alignment dimension. Our experiments on both the reward modeling task and the preference optimization scenario indicate: (1) the weak-to-strong deception exists; (2) the deception phenomenon may intensify as the capability gap between weak and strong models increases. We also discuss potential solutions and find bootstrapping with an intermediate model can mitigate the deception to some extent. Our work highlights the urgent need to pay more attention to the true reliability of superalignment.

Equivariance theory predicts that an architectural symmetry prior reduces sample complexity by a factor of |G|; this is widely cited but rarely measured as a scaling law with controls that separate the prior from its confounds. On a controlled C_n-symmetric task, we report three findings. First, a wrong-group control with identical orbit size and matched compute is worse than no constraint (joint pairwise CI [+0.79, +3.26] excludes zero, robust across estimators); misaligned constraint is actively harmful, not merely unhelpful. Second, an augmentation baseline equipped with test-time orbit averaging matches the equivariant model exactly -- bit-identical per-epoch validation curves across matched cells -- so the architecture-vs-augmentation gap is conditional on asymmetric test-time computation, not unconditional. Third, the relative exchange rate beta_diff = 1.28 is consistent in sign and order of magnitude with the theoretical 1.0 (single-level CI [+0.92, +2.05]); the more conservative two-level bootstrap (seeds x group sizes) widens this to [-0.63, +1.72], including zero, and a finer-N replication on a sqrt(2)-spaced grid is inconclusive (point estimate -0.82). The methodological contributions -- the relative-rate estimator that cancels the shared-difficulty confound, the wrong-group control, and a pre-specified failure taxonomy -- transfer to any inductive bias whose strength can be parameterised. Honest scoping: the primary estimator beta_diff was adopted post-hoc after the initial analysis revealed a positive-slope identifiability problem; the design was never externally pre-registered; and the headline number rests on an OLS slope over seven group sizes on a coarse N grid. This is an exploratory study, not a confirmatory measurement; the wrong-group result is the cleanest finding and the one we report with the most confidence. A registered replication on fresh seeds is future work.

As language models (LMs) advance, interest is growing in applying them to high-stakes societal decisions, such as determining financing or housing eligibility. However, their potential for discrimination in such contexts raises ethical concerns, motivating the need for better methods to evaluate these risks. We present a method for proactively evaluating the potential discriminatory impact of LMs in a wide range of use cases, including hypothetical use cases where they have not yet been deployed. Specifically, we use an LM to generate a wide array of potential prompts that decision-makers may input into an LM, spanning 70 diverse decision scenarios across society, and systematically vary the demographic information in each prompt. Applying this methodology reveals patterns of both positive and negative discrimination in the Claude 2.0 model in select settings when no interventions are applied. While we do not endorse or permit the use of language models to make automated decisions for the high-risk use cases we study, we demonstrate techniques to significantly decrease both positive and negative discrimination through careful prompt engineering, providing pathways toward safer deployment in use cases where they may be appropriate. Our work enables developers and policymakers to anticipate, measure, and address discrimination as language model capabilities and applications continue to expand. We release our dataset and prompts at https://huggingface.co/datasets/Anthropic/discrim-eval

Machine learning models are commonly used to detect toxicity in online conversations. These models are trained on datasets annotated by human raters. We explore how raters' self-described identities impact how they annotate toxicity in online comments. We first define the concept of specialized rater pools: rater pools formed based on raters' self-described identities, rather than at random. We formed three such rater pools for this study--specialized rater pools of raters from the U.S. who identify as African American, LGBTQ, and those who identify as neither. Each of these rater pools annotated the same set of comments, which contains many references to these identity groups. We found that rater identity is a statistically significant factor in how raters will annotate toxicity for identity-related annotations. Using preliminary content analysis, we examined the comments with the most disagreement between rater pools and found nuanced differences in the toxicity annotations. Next, we trained models on the annotations from each of the different rater pools, and compared the scores of these models on comments from several test sets. Finally, we discuss how using raters that self-identify with the subjects of comments can create more inclusive machine learning models, and provide more nuanced ratings than those by random raters.

Current alignment evaluation mostly measures whether models encode dangerous concepts and whether they refuse harmful requests. Both miss the layer where alignment often operates: routing from concept detection to behavioral policy. We study political censorship in Chinese-origin language models as a natural experiment, using probes, surgical ablations, and behavioral tests across nine open-weight models from five labs. Three findings follow. First, probe accuracy alone is non-diagnostic: political probes, null controls, and permutation baselines can all reach 100%, so held-out category generalization is the informative test. Second, surgical ablation reveals lab-specific routing. Removing the political-sensitivity direction eliminates censorship and restores accurate factual output in most models tested, while one model confabulates because its architecture entangles factual knowledge with the censorship mechanism. Cross-model transfer fails, indicating that routing geometry is model- and lab-specific. Third, refusal is no longer the dominant censorship mechanism. Within one model family, hard refusal falls to zero while narrative steering rises to the maximum, making censorship invisible to refusal-only benchmarks. These results support a three-stage descriptive framework: detect, route, generate. Models often retain the relevant knowledge; alignment changes how that knowledge is expressed. Evaluations that audit only detection or refusal therefore miss the routing mechanism that most directly determines behavior.

Fine-tuning large language models on narrow datasets can cause them to develop broadly misaligned behaviours: a phenomena known as emergent misalignment. However, the mechanisms underlying this misalignment, and why it generalizes beyond the training domain, are poorly understood, demonstrating critical gaps in our knowledge of model alignment. In this work, we train and study a minimal model organism which uses just 9 rank-1 adapters to emergently misalign Qwen2.5-14B-Instruct. Studying this, we find that different emergently misaligned models converge to similar representations of misalignment. We demonstrate this convergence by extracting a 'misalignment direction' from one fine-tuned model's activations, and using it to effectively ablate misaligned behaviour from fine-tunes using higher dimensional LoRAs and different datasets. Leveraging the scalar hidden state of rank-1 LoRAs, we further present a set of experiments for directly interpreting the fine-tuning adapters, showing that six contribute to general misalignment, while two specialise for misalignment in just the fine-tuning domain. Emergent misalignment is a particularly salient example of undesirable and unexpected model behaviour and by advancing our understanding of the mechanisms behind it, we hope to move towards being able to better understand and mitigate misalignment more generally.

The alignment of large language models (LLMs) often assumes that using more clean data yields better outcomes, overlooking the match between model capacity and example difficulty. Challenging this, we propose a new principle: Preference data vary in difficulty, and overly difficult examples hinder alignment, by exceeding the model's capacity. Through systematic experimentation, we validate this principle with three key findings: (1) preference examples vary in difficulty, as evidenced by consistent learning orders across alignment runs; (2) overly difficult examples significantly degrade performance across four LLMs and two datasets; and (3) the capacity of a model dictates its threshold for handling difficult examples, underscoring a critical relationship between data selection and model capacity. Building on this principle, we introduce Selective DPO, which filters out overly difficult examples. This simple adjustment improves alignment performance by 9-16% in win rates on the AlpacaEval 2 benchmark compared to the DPO baseline, suppressing a series of DPO variants with different algorithmic adjustments. Together, these results illuminate the importance of aligning data difficulty with model capacity, offering a transformative perspective for improving alignment strategies in LLMs. Code is available at https://github.com/glorgao/SelectiveDPO.

We propose a novel approach to conformal prediction for generative language models (LMs). Standard conformal prediction produces prediction sets -- in place of single predictions -- that have rigorous, statistical performance guarantees. LM responses are typically sampled from the model's predicted distribution over the large, combinatorial output space of natural language. Translating this process to conformal prediction, we calibrate a stopping rule for sampling different outputs from the LM that get added to a growing set of candidates until we are confident that the output set is sufficient. Since some samples may be low-quality, we also simultaneously calibrate and apply a rejection rule for removing candidates from the output set to reduce noise. Similar to conformal prediction, we prove that the sampled set returned by our procedure contains at least one acceptable answer with high probability, while still being empirically precise (i.e., small) on average. Furthermore, within this set of candidate responses, we show that we can also accurately identify subsets of individual components -- such as phrases or sentences -- that are each independently correct (e.g., that are not "hallucinations"), again with statistical guarantees. We demonstrate the promise of our approach on multiple tasks in open-domain question answering, text summarization, and radiology report generation using different LM variants.

We introduce Metric-Fair Prompting, a fairness-aware prompting framework that guides large language models (LLMs) to make decisions under metric-fairness constraints. In the application of multiple-choice medical question answering, each {(question, option)} pair is treated as a binary instance with label +1 (correct) or -1 (incorrect). To promote {individual fairness}~--~treating similar instances similarly~--~we compute question similarity using NLP embeddings and solve items in joint pairs of similar questions rather than in isolation. The prompt enforces a global decision protocol: extract decisive clinical features, map each \((question, option)\) to a score f(x) that acts as confidence, and impose a Lipschitz-style constraint so that similar inputs receive similar scores and, hence, consistent outputs. Evaluated on the {MedQA (US)} benchmark, Metric-Fair Prompting is shown to improve performance over standard single-item prompting, demonstrating that fairness-guided, confidence-oriented reasoning can enhance LLM accuracy on high-stakes clinical multiple-choice questions.

Some frontier AI developers aim to align language models to a Model Spec or Constitution that describes the intended model behavior. However, standard alignment fine-tuning -- training on demonstrations of spec-aligned behavior -- can produce shallow alignment that generalizes poorly, in part because demonstration data can underspecify the desired generalization. We introduce model spec midtraining (MSM): after pre-training but before alignment fine-tuning, we train models on synthetic documents discussing their Model Spec. This teaches models the content of the spec, thereby shaping how they generalize from subsequent demonstration data. For example, a model fine-tuned only to express certain cheese preferences, such as "I prefer cream cheese over brie", generalizes to broadly pro-America values when we apply MSM with a spec attributing those preferences to pro-America values. Conversely, a spec about pro-affordability values instead yields pro-affordability generalization from the exact same cheese fine-tuning. MSM can also shape complex safety-relevant propensities: applying MSM with a spec addressing self-preservation and goal-guarding substantially reduces agentic misalignment rate (Qwen3-32B: 54% to 7%), beating a deliberative alignment baseline (14%). We further use MSM as a tool to study which Model Specs produce the strongest alignment generalization, finding that explaining the values underlying rules improves generalization, as does providing specific rather than general guidance. Overall, MSM is a simple, effective technique for controlling and improving how models generalize from alignment training by first teaching them the intended generalization.

Real-world data often exhibits long tail distributions with heavy class imbalance, where the majority classes can dominate the training process and alter the decision boundaries of the minority classes. Recently, researchers have investigated the potential of supervised contrastive learning for long-tailed recognition, and demonstrated that it provides a strong performance gain. In this paper, we show that while supervised contrastive learning can help improve performance, past baselines suffer from poor uniformity brought in by imbalanced data distribution. This poor uniformity manifests in samples from the minority class having poor separability in the feature space. To address this problem, we propose targeted supervised contrastive learning (TSC), which improves the uniformity of the feature distribution on the hypersphere. TSC first generates a set of targets uniformly distributed on a hypersphere. It then makes the features of different classes converge to these distinct and uniformly distributed targets during training. This forces all classes, including minority classes, to maintain a uniform distribution in the feature space, improves class boundaries, and provides better generalization even in the presence of long-tail data. Experiments on multiple datasets show that TSC achieves state-of-the-art performance on long-tailed recognition tasks.

Bias in textual data can lead to skewed interpretations and outcomes when the data is used. These biases could perpetuate stereotypes, discrimination, or other forms of unfair treatment. An algorithm trained on biased data may end up making decisions that disproportionately impact a certain group of people. Therefore, it is crucial to detect and remove these biases to ensure the fair and ethical use of data. To this end, we develop a comprehensive and robust framework NBIAS that consists of four main layers: data, corpus construction, model development and an evaluation layer. The dataset is constructed by collecting diverse data from various domains, including social media, healthcare, and job hiring portals. As such, we applied a transformer-based token classification model that is able to identify bias words/ phrases through a unique named entity BIAS. In the evaluation procedure, we incorporate a blend of quantitative and qualitative measures to gauge the effectiveness of our models. We achieve accuracy improvements ranging from 1% to 8% compared to baselines. We are also able to generate a robust understanding of the model functioning. The proposed approach is applicable to a variety of biases and contributes to the fair and ethical use of textual data.

In high dimension, low sample size (HDLSS) settings, classifiers based on Euclidean distances like the nearest neighbor classifier and the average distance classifier perform quite poorly if differences between locations of the underlying populations get masked by scale differences. To rectify this problem, several modifications of these classifiers have been proposed in the literature. However, existing methods are confined to location and scale differences only, and often fail to discriminate among populations differing outside of the first two moments. In this article, we propose some simple transformations of these classifiers resulting into improved performance even when the underlying populations have the same location and scale. We further propose a generalization of these classifiers based on the idea of grouping of variables. The high-dimensional behavior of the proposed classifiers is studied theoretically. Numerical experiments with a variety of simulated examples as well as an extensive analysis of real data sets exhibit advantages of the proposed methods.

Finetuning large language models on narrowly harmful datasets can cause them to become emergently misaligned, giving stereotypically `evil' responses across diverse unrelated settings. Concerningly, a pre-registered survey of experts failed to predict this result, highlighting our poor understanding of the inductive biases governing learning and generalisation in LLMs. We use emergent misalignment (EM) as a case study to investigate these inductive biases and find that models can just learn the narrow dataset task, but that the general solution appears to be more stable and more efficient. To establish this, we build on the result that different EM finetunes converge to the same linear representation of general misalignment, which can be used to mediate misaligned behaviour. We find a linear representation of the narrow solution also exists, and can be learned by introducing a KL divergence loss. Comparing these representations reveals that general misalignment achieves lower loss, is more robust to perturbations, and is more influential in the pre-training distribution. This work isolates a concrete representation of general misalignment for monitoring and mitigation. More broadly, it offers a detailed case study and preliminary metrics for investigating how inductive biases shape generalisation in LLMs. We open-source all code, datasets and model finetunes.

Conformal prediction is emerging as a popular paradigm for providing rigorous uncertainty quantification in machine learning since it can be easily applied as a post-processing step to already trained models. In this paper, we extend conformal prediction to the federated learning setting. The main challenge we face is data heterogeneity across the clients - this violates the fundamental tenet of exchangeability required for conformal prediction. We propose a weaker notion of partial exchangeability, better suited to the FL setting, and use it to develop the Federated Conformal Prediction (FCP) framework. We show FCP enjoys rigorous theoretical guarantees and excellent empirical performance on several computer vision and medical imaging datasets. Our results demonstrate a practical approach to incorporating meaningful uncertainty quantification in distributed and heterogeneous environments. We provide code used in our experiments https://github.com/clu5/federated-conformal.

Training models with robust group fairness properties is crucial in ethically sensitive application areas such as medical diagnosis. Despite the growing body of work aiming to minimise demographic bias in AI, this problem remains challenging. A key reason for this challenge is the fairness generalisation gap: High-capacity deep learning models can fit all training data nearly perfectly, and thus also exhibit perfect fairness during training. In this case, bias emerges only during testing when generalisation performance differs across subgroups. This motivates us to take a bi-level optimisation perspective on fair learning: Optimising the learning strategy based on validation fairness. Specifically, we consider the highly effective workflow of adapting pre-trained models to downstream medical imaging tasks using parameter-efficient fine-tuning (PEFT) techniques. There is a trade-off between updating more parameters, enabling a better fit to the task of interest vs. fewer parameters, potentially reducing the generalisation gap. To manage this tradeoff, we propose FairTune, a framework to optimise the choice of PEFT parameters with respect to fairness. We demonstrate empirically that FairTune leads to improved fairness on a range of medical imaging datasets. The code is available at https://github.com/Raman1121/FairTune

The advancement of large language models (LLMs) has made it difficult to differentiate human-written text from AI-generated text. Several AI-text detectors have been developed in response, which typically utilize a fixed global threshold (e.g., {\theta} = 0.5) to classify machine-generated text. However, we find that one universal threshold can fail to account for subgroup-specific distributional variations. For example, when using a fixed threshold, detectors make more false positive errors on shorter human-written text than longer, and more positive classifications on neurotic writing styles than open among long text. These discrepancies can lead to misclassification that disproportionately affects certain groups. We address this critical limitation by introducing FairOPT, an algorithm for group-specific threshold optimization in AI-generated content classifiers. Our approach partitions data into subgroups based on attributes (e.g., text length and writing style) and learns decision thresholds for each group, which enables careful balancing of performance and fairness metrics within each subgroup. In experiments with four AI text classifiers on three datasets, FairOPT enhances overall F1 score and decreases balanced error rate (BER) discrepancy across subgroups. Our framework paves the way for more robust and fair classification criteria in AI-generated output detection.

Volumetry is one of the principal downstream applications of 3D medical image segmentation, for example, to detect abnormal tissue growth or for surgery planning. Conformal Prediction is a promising framework for uncertainty quantification, providing calibrated predictive intervals associated with automatic volume measurements. However, this methodology is based on the hypothesis that calibration and test samples are exchangeable, an assumption that is in practice often violated in medical image applications. A weighted formulation of Conformal Prediction can be framed to mitigate this issue, but its empirical investigation in the medical domain is still lacking. A potential reason is that it relies on the estimation of the density ratio between the calibration and test distributions, which is likely to be intractable in scenarios involving high-dimensional data. To circumvent this, we propose an efficient approach for density ratio estimation relying on the compressed latent representations generated by the segmentation model. Our experiments demonstrate the efficiency of our approach to reduce the coverage error in the presence of covariate shifts, in both synthetic and real-world settings. Our implementation is available at https://github.com/benolmbrt/wcp_miccai

Conformal prediction (CP) for regression can be challenging, especially when the output distribution is heteroscedastic, multimodal, or skewed. Some of the issues can be addressed by estimating a distribution over the output, but in reality, such approaches can be sensitive to estimation error and yield unstable intervals.~Here, we circumvent the challenges by converting regression to a classification problem and then use CP for classification to obtain CP sets for regression.~To preserve the ordering of the continuous-output space, we design a new loss function and make necessary modifications to the CP classification techniques.~Empirical results on many benchmarks shows that this simple approach gives surprisingly good results on many practical problems.

Organizations cannot address demographic disparities that they cannot see. Recent research on machine learning and fairness has emphasized that awareness of sensitive attributes, such as race and sex, is critical to the development of interventions. However, on the ground, the existence of these data cannot be taken for granted. This paper uses the domains of employment, credit, and healthcare in the United States to surface conditions that have shaped the availability of sensitive attribute data. For each domain, we describe how and when private companies collect or infer sensitive attribute data for antidiscrimination purposes. An inconsistent story emerges: Some companies are required by law to collect sensitive attribute data, while others are prohibited from doing so. Still others, in the absence of legal mandates, have determined that collection and imputation of these data are appropriate to address disparities. This story has important implications for fairness research and its future applications. If companies that mediate access to life opportunities are unable or hesitant to collect or infer sensitive attribute data, then proposed techniques to detect and mitigate bias in machine learning models might never be implemented outside the lab. We conclude that today's legal requirements and corporate practices, while highly inconsistent across domains, offer lessons for how to approach the collection and inference of sensitive data in appropriate circumstances. We urge stakeholders, including machine learning practitioners, to actively help chart a path forward that takes both policy goals and technical needs into account.

Recent work has shown that fine-tuning on insecure code data can trigger an emergent misalignment (EMA) phenomenon, where models generate malicious responses even to prompts unrelated to the original insecure code-writing task. Such cross-domain generalization of harmful behavior underscores the need for a deeper understanding of the algorithms, tasks, and datasets that induce emergent misalignment. In this work, we extend this study by demonstrating that emergent misalignment can also arise from narrow refusal unlearning in specific domains. We perform refusal unlearning on Cybersecurity and Safety concept, and evaluate EMA by monitoring refusal scores across seven responsible AI (RAI) domains, Cybersecurity, Safety, Toxicity, Bias, Sensitive Content, Medical/Legal, and Privacy. Our work shows that narrow domain unlearning can yield compliance responses for the targeted concept, however, it may also propagate EMA to unrelated domains. Among the two intervened concepts, Cybersecurity and Safety, we find that the safety concept can have larger EMA impact, i.e, causing lower refusal scores, across other unrelated domains such as bias. We observe this effect consistently across two model families, Mistral-7b-0.3v, and Qwen-7b-2.5. Further, we show that refusal unlearning augmented with cross-entropy loss function on a small set of retain data from the affected domains can largely, if not fully, restore alignment across the impacted domains while having lower refusal rate on the concept we perform unlearning on. To investigate the underlying causes of EMA, we analyze concept entanglements at the representation level via concept vectors. Our analysis reveals that concepts with higher representation similarity in earlier layers are more susceptible to EMA after intervention when the refusal stream is altered through targeted refusal unlearning.

We consider the problem of conformal prediction under covariate shift. Given labeled data from a source domain and unlabeled data from a covariate shifted target domain, we seek to construct prediction sets with valid marginal coverage in the target domain. Most existing methods require estimating the unknown likelihood ratio function, which can be prohibitive for high-dimensional data such as images. To address this challenge, we introduce the likelihood ratio regularized quantile regression (LR-QR) algorithm, which combines the pinball loss with a novel choice of regularization in order to construct a threshold function without directly estimating the unknown likelihood ratio. We show that the LR-QR method has coverage at the desired level in the target domain, up to a small error term that we can control. Our proofs draw on a novel analysis of coverage via stability bounds from learning theory. Our experiments demonstrate that the LR-QR algorithm outperforms existing methods on high-dimensional prediction tasks, including a regression task for the Communities and Crime dataset, an image classification task from the WILDS repository, and an LLM question-answering task on the MMLU benchmark.

Real-world large-scale datasets are both noisily labeled and class-imbalanced. The issues seriously hurt the generalization of trained models. It is hence significant to address the simultaneous incorrect labeling and class-imbalance, i.e., the problem of learning with noisy labels on long-tailed data. Previous works develop several methods for the problem. However, they always rely on strong assumptions that are invalid or hard to be checked in practice. In this paper, to handle the problem and address the limitations of prior works, we propose a representation calibration method RCAL. Specifically, RCAL works with the representations extracted by unsupervised contrastive learning. We assume that without incorrect labeling and class imbalance, the representations of instances in each class conform to a multivariate Gaussian distribution, which is much milder and easier to be checked. Based on the assumption, we recover underlying representation distributions from polluted ones resulting from mislabeled and class-imbalanced data. Additional data points are then sampled from the recovered distributions to help generalization. Moreover, during classifier training, representation learning takes advantage of representation robustness brought by contrastive learning, which further improves the classifier performance. We derive theoretical results to discuss the effectiveness of our representation calibration. Experiments on multiple benchmarks justify our claims and confirm the superiority of the proposed method.

Large Language and Vision-Language Models (LLMs/VLMs) are increasingly used in safety-critical applications, yet their opaque decision-making complicates risk assessment and reliability. Uncertainty quantification (UQ) helps assess prediction confidence and enables abstention when uncertainty is high. Conformal prediction (CP), a leading UQ method, provides statistical guarantees but relies on static thresholds, which fail to adapt to task complexity and evolving data distributions, leading to suboptimal trade-offs in accuracy, coverage, and informativeness. To address this, we propose learnable conformal abstention, integrating reinforcement learning (RL) with CP to optimize abstention thresholds dynamically. By treating CP thresholds as adaptive actions, our approach balances multiple objectives, minimizing prediction set size while maintaining reliable coverage. Extensive evaluations across diverse LLM/VLM benchmarks show our method outperforms Least Ambiguous Classifiers (LAC) and Adaptive Prediction Sets (APS), improving accuracy by up to 3.2%, boosting AUROC for hallucination detection by 22.19%, enhancing uncertainty-guided selective generation (AUARC) by 21.17%, and reducing calibration error by 70%-85%. These improvements hold across multiple models and datasets while consistently meeting the 90% coverage target, establishing our approach as a more effective and flexible solution for reliable decision-making in safety-critical applications. The code is available at: {https://github.com/sinatayebati/vlm-uncertainty}.

Current approaches to AI compliance treat conformity as a binary, audit-time verdict rather than a continuous, measurable property of production systems. We argue that this compliance fiction is structurally ill-suited to the requirements of the EU AI Act, which demands ongoing human oversight and the detection of emergent behavioural drift in deployed systems. We introduce governance from metrics, a principle whereby regulatory compliance is derived as a continuous signal from runtime observability rather than from static assessments. Building on this principle, we present govllm, an open-source framework implementing a governance-driven routing architecture in which model selection is determined by accumulated compliance scores rather than by latency or cost alone. Central to our approach is a panel of regulatory judges - LLM evaluators specialised per criterion (EU AI Act, GDPR, ANSSI, accessibility) - whose inter-judge disagreement we reframe not as noise but as a regulatory uncertainty signal warranting human arbitration. We validate this approach through a ground truth corpus of 49 annotated prompt/response pairs across five regulatory criteria, evaluated by four small language models (SLMs, 1.7B-7B parameters) running fully on-premise. Agreement rates range from 51.5% (mistral:7b) to 69.1% (phi4-mini), with no single model dominating across all criteria - empirically motivating the Profile-as-jury design. We further document three structural failure modes in small regulatory judges and a judge-specific position bias that degrades agreement by up to 25 percentage points across three question-order conditions (original, reversed, permuted). govllm is released as open-source software to support reproducible AI governance research.

Reinforcement Learning with Human Feedback (RLHF) and its variants have made huge strides toward the effective alignment of large language models (LLMs) to follow instructions and reflect human values. More recently, Direct Alignment Algorithms (DAAs) have emerged in which the reward modeling stage of RLHF is skipped by characterizing the reward directly as a function of the policy being learned. Examples include Direct Preference Optimization (DPO) and Simple Preference Optimization (SimPO). These methods often suffer from likelihood displacement, a phenomenon by which the probabilities of preferred responses are often reduced undesirably. In this paper, we argue that, for DAAs the reward (function) shape matters. We introduce AlphaPO, a new DAA method that leverages an alpha-parameter to help change the shape of the reward function beyond the standard log reward. AlphaPO helps maintain fine-grained control over likelihood displacement and over-optimization. Compared to SimPO, one of the best performing DAAs, AlphaPO leads to about 7\% to 10\% relative improvement in alignment performance for the instruct versions of Mistral-7B and Llama3-8B. The analysis and results presented highlight the importance of the reward shape, and how one can systematically change it to affect training dynamics, as well as improve alignment performance.

Model fairness is an essential element for Trustworthy AI. While many techniques for model fairness have been proposed, most of them assume that the training and deployment data distributions are identical, which is often not true in practice. In particular, when the bias between labels and sensitive groups changes, the fairness of the trained model is directly influenced and can worsen. We make two contributions for solving this problem. First, we analytically show that existing in-processing fair algorithms have fundamental limits in accuracy and group fairness. We introduce the notion of correlation shifts, which can explicitly capture the change of the above bias. Second, we propose a novel pre-processing step that samples the input data to reduce correlation shifts and thus enables the in-processing approaches to overcome their limitations. We formulate an optimization problem for adjusting the data ratio among labels and sensitive groups to reflect the shifted correlation. A key benefit of our approach lies in decoupling the roles of pre- and in-processing approaches: correlation adjustment via pre-processing and unfairness mitigation on the processed data via in-processing. Experiments show that our framework effectively improves existing in-processing fair algorithms w.r.t. accuracy and fairness, both on synthetic and real datasets.

We consider the problem of antibody sequence design given 3D structural information. Building on previous work, we propose a fine-tuned inverse folding model that is specifically optimised for antibody structures and outperforms generic protein models on sequence recovery and structure robustness when applied on antibodies, with notable improvement on the hypervariable CDR-H3 loop. We study the canonical conformations of complementarity-determining regions and find improved encoding of these loops into known clusters. Finally, we consider the applications of our model to drug discovery and binder design and evaluate the quality of proposed sequences using physics-based methods.

Prior work has shown that fine-tuning large language models on malicious or incorrect outputs in narrow domains can induce broad misalignment and harmful behavior, a phenomenon known as emergent misalignment. However, efficient methods for reversing such misalignment remain limited. In this work, we make two contributions. First, we identify sycophancy fine-tuning, i.e., training models to passively agree with users' incorrect opinions, as a previously underexplored driver of emergent misalignment, and show that it induces broad and severe misaligned behavior. Second, we propose Alignment Gating, an efficient method for reversing emergent misalignment that inserts learnable and controllable gates into the model during fine-tuning. Through fine-tuning, these gates learn to identify the internal representations responsible for unsafe responses. Thus, amplifying or suppressing these representations then exacerbates or mitigates EM, respectively. We further find that alignment gating module exhibits strong generalization: gating weights obtained from narrow-domain fine-tuning substantially suppress broad-domain misaligned behavior while preserving the model's general capabilities.

Large Language Models (LLMs) are increasingly used for toxicity assessment in online moderation systems, where fairness across demographic groups is essential for equitable treatment. However, LLMs often produce inconsistent toxicity judgements for subtle expressions, particularly those involving implicit hate speech, revealing underlying biases that are difficult to correct through standard training. This raises a key question that existing approaches often overlook: when should corrective mechanisms be invoked to ensure fair and reliable assessments? To address this, we propose FairToT, an inference-time framework that enhances LLM fairness through prompt-guided toxicity assessment. FairToT identifies cases where demographic-related variation is likely to occur and determines when additional assessment should be applied. In addition, we introduce two interpretable fairness indicators that detect such cases and improve inference consistency without modifying model parameters. Experiments on benchmark datasets show that FairToT reduces group-level disparities while maintaining stable and reliable toxicity predictions, demonstrating that inference-time refinement offers an effective and practical approach for fairness improvement in LLM-based toxicity assessment systems. The source code can be found at https://aisuko.github.io/fair-tot/.

Cats and humans differ in ocular anatomy. Most notably, Felis Catus (domestic cats) have vertically elongated pupils linked to ambush predation; yet, how such specializations manifest in downstream visual representations remains incompletely understood. We present a unified, frozen-encoder benchmark that quantifies feline-human cross-species representational alignment in the wild, across convolutional networks, supervised Vision Transformers, windowed transformers, and self-supervised ViTs (DINO), using layer-wise Centered Kernel Alignment (linear and RBF) and Representational Similarity Analysis, with additional distributional and stability tests reported in the paper. Across models, DINO ViT-B/16 attains the most substantial alignment (mean CKA-RBF approx0.814, mean CKA-linear approx0.745, mean RSA approx0.698), peaking at early blocks, indicating that token-level self-supervision induces early-stage features that bridge species-specific statistics. Supervised ViTs are competitive on CKA yet show weaker geometric correspondence than DINO (e.g., ViT-B/16 RSA approx0.53 at block8; ViT-L/16 approx0.47 at block14), revealing depth-dependent divergences between similarity and representational geometry. CNNs remain strong baselines but below plain ViTs on alignment, and windowed transformers underperform plain ViTs, implicating architectural inductive biases in cross-species alignment. Results indicate that self-supervision coupled with ViT inductive biases yields representational geometries that more closely align feline and human visual systems than widely used CNNs and windowed Transformers, providing testable neuroscientific hypotheses about where and how cross-species visual computations converge. We release our code and dataset for reference and reproducibility.

Self-training is a well-known approach for semi-supervised learning. It consists of iteratively assigning pseudo-labels to unlabeled data for which the model is confident and treating them as labeled examples. For neural networks, softmax prediction probabilities are often used as a confidence measure, although they are known to be overconfident, even for wrong predictions. This phenomenon is particularly intensified in the presence of sample selection bias, i.e., when data labeling is subject to some constraint. To address this issue, we propose a novel confidence measure, called T-similarity, built upon the prediction diversity of an ensemble of linear classifiers. We provide the theoretical analysis of our approach by studying stationary points and describing the relationship between the diversity of the individual members and their performance. We empirically demonstrate the benefit of our confidence measure for three different pseudo-labeling policies on classification datasets of various data modalities. The code is available at https://github.com/ambroiseodt/tsim.

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

We make two contributions in the field of AI fairness over continuous protected attributes. First, we show that the Hirschfeld-Gebelein-Renyi (HGR) indicator (the only one currently available for such a case) is valuable but subject to a few crucial limitations regarding semantics, interpretability, and robustness. Second, we introduce a family of indicators that are: 1) complementary to HGR in terms of semantics; 2) fully interpretable and transparent; 3) robust over finite samples; 4) configurable to suit specific applications. Our approach also allows us to define fine-grained constraints to permit certain types of dependence and forbid others selectively. By expanding the available options for continuous protected attributes, our approach represents a significant contribution to the area of fair artificial intelligence.

Split conformal prediction has recently sparked great interest due to its ability to provide formally guaranteed uncertainty sets or intervals for predictions made by black-box neural models, ensuring a predefined probability of containing the actual ground truth. While the original formulation assumes data exchangeability, some extensions handle non-exchangeable data, which is often the case in many real-world scenarios. In parallel, some progress has been made in conformal methods that provide statistical guarantees for a broader range of objectives, such as bounding the best F_1-score or minimizing the false negative rate in expectation. In this paper, we leverage and extend these two lines of work by proposing non-exchangeable conformal risk control, which allows controlling the expected value of any monotone loss function when the data is not exchangeable. Our framework is flexible, makes very few assumptions, and allows weighting the data based on its relevance for a given test example; a careful choice of weights may result on tighter bounds, making our framework useful in the presence of change points, time series, or other forms of distribution drift. Experiments with both synthetic and real world data show the usefulness of our method.

A growing literature in computational neuroscience leverages gradient descent and learning algorithms that approximate it to study synaptic plasticity in the brain. However, the vast majority of this work ignores a critical underlying assumption: the choice of distance for synaptic changes - i.e. the geometry of synaptic plasticity. Gradient descent assumes that the distance is Euclidean, but many other distances are possible, and there is no reason that biology necessarily uses Euclidean geometry. Here, using the theoretical tools provided by mirror descent, we show that the distribution of synaptic weights will depend on the geometry of synaptic plasticity. We use these results to show that experimentally-observed log-normal weight distributions found in several brain areas are not consistent with standard gradient descent (i.e. a Euclidean geometry), but rather with non-Euclidean distances. Finally, we show that it should be possible to experimentally test for different synaptic geometries by comparing synaptic weight distributions before and after learning. Overall, our work shows that the current paradigm in theoretical work on synaptic plasticity that assumes Euclidean synaptic geometry may be misguided and that it should be possible to experimentally determine the true geometry of synaptic plasticity in the brain.

Existing studies on fairness are largely Western-focused, making them inadequate for culturally diverse countries such as India. To address this gap, we introduce INDIC-BIAS, a comprehensive India-centric benchmark designed to evaluate fairness of LLMs across 85 identity groups encompassing diverse castes, religions, regions, and tribes. We first consult domain experts to curate over 1,800 socio-cultural topics spanning behaviors and situations, where biases and stereotypes are likely to emerge. Grounded in these topics, we generate and manually validate 20,000 real-world scenario templates to probe LLMs for fairness. We structure these templates into three evaluation tasks: plausibility, judgment, and generation. Our evaluation of 14 popular LLMs on these tasks reveals strong negative biases against marginalized identities, with models frequently reinforcing common stereotypes. Additionally, we find that models struggle to mitigate bias even when explicitly asked to rationalize their decision. Our evaluation provides evidence of both allocative and representational harms that current LLMs could cause towards Indian identities, calling for a more cautious usage in practical applications. We release INDIC-BIAS as an open-source benchmark to advance research on benchmarking and mitigating biases and stereotypes in the Indian context.

Large language models (LLMs) trained on internet-scale corpora can exhibit systematic biases that increase the probability of unwanted behavior. In this study, we examined potential biases towards synthetic vs. biological technological solutions across four domains (materials, energy, manufacturing, and algorithms). A sample of 5 frontier and 5 open-weight models were measured using 50 curated Bioalignment prompts with a Kelly criterion-inspired evaluation framework. According to this metric, most models were not bioaligned in that they exhibit biases in favor of synthetic (non-biological) solutions. We next examined if fine-tuning could increase the preferences of two open-weight models, Llama 3.2-3B-Instruct and Qwen2.5-3B-Instruct, for biological-based approaches. A curated corpus of ~22M tokens from 6,636 PMC articles emphasizing biological problem-solving was used first to fine-tune Llama 3B with a mixed corpus of continued training and instruction-formatted. This was then extended to Qwen 3B using instruction-formatted only. We found that QLoRA fine-tuning significantly increased the scoring of biological solutions for both models without degrading general capabilities (Holm-Bonferroni-corrected p < 0.001 and p < 0.01, respectively). This suggests that even a small amount of fine-tuning can change how models weigh the relative value of biological and bioinspired vs. synthetic approaches. Although this work focused on small open-weight LLMs, it may be extensible to much larger models and could be used to develop models that favor bio-based approaches. We release the benchmark, corpus, code, and adapter weights.

With the widespread use of AI systems and applications in our everyday lives, it is important to take fairness issues into consideration while designing and engineering these types of systems. Such systems can be used in many sensitive environments to make important and life-changing decisions; thus, it is crucial to ensure that the decisions do not reflect discriminatory behavior toward certain groups or populations. We have recently seen work in machine learning, natural language processing, and deep learning that addresses such challenges in different subdomains. With the commercialization of these systems, researchers are becoming aware of the biases that these applications can contain and have attempted to address them. In this survey we investigated different real-world applications that have shown biases in various ways, and we listed different sources of biases that can affect AI applications. We then created a taxonomy for fairness definitions that machine learning researchers have defined in order to avoid the existing bias in AI systems. In addition to that, we examined different domains and subdomains in AI showing what researchers have observed with regard to unfair outcomes in the state-of-the-art methods and how they have tried to address them. There are still many future directions and solutions that can be taken to mitigate the problem of bias in AI systems. We are hoping that this survey will motivate researchers to tackle these issues in the near future by observing existing work in their respective fields.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called nabla^2DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level (omegaB97X-D/def2-SVP) for each conformation. Moreover, nabla^2DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

Large language models perform near-Bayesian inference yet violate permutation invariance on exchangeable data. We resolve this by showing transformers minimize expected conditional description length (cross-entropy) over orderings, E_pi[ell(Y mid Gamma_pi(X))], which admits a Kolmogorov-complexity interpretation up to additive constants, rather than the permutation-invariant description length ell(Y mid X). This makes them Bayesian in expectation, not in realization. We derive (i) a Quantified Martingale Violation bound showing order-induced deviations scale as O(log n) with constants; (ii) the Expectation-level Decompression Law linking information budgets to reliability for Bernoulli predicates; and (iii) deployable planners (B2T/RoH/ISR) for answer/abstain decisions. Empirically, permutation dispersion follows a+bln n (Qwen2-7B b approx 0.377, Llama-3.1-8B b approx 0.147); permutation mixtures improve ground-truth likelihood/accuracy; and randomized dose-response shows hallucinations drop by sim 0.13 per additional nat. A pre-specified audit with a fixed ISR=1.0 achieves near-0\% hallucinations via calibrated refusal at 24\% abstention. The framework turns hallucinations into predictable compression failures and enables principled information budgeting.

Large Language Models (LLMs) rely on safety alignment to produce socially acceptable responses. This is typically achieved through instruction tuning and reinforcement learning from human feedback. However, this alignment is known to be brittle: further fine-tuning, even on benign or lightly contaminated data, can degrade safety and reintroduce harmful behaviors. A growing body of work suggests that alignment may correspond to identifiable geometric directions in weight space, forming subspaces that could, in principle, be isolated or preserved to defend against misalignment. In this work, we conduct a comprehensive empirical study of this geometric perspective. We examine whether safety-relevant behavior is concentrated in specific subspaces, whether it can be separated from general-purpose learning, and whether harmfulness arises from distinguishable patterns in internal representations. Across both parameter and activation space, our findings are consistent: subspaces that amplify safe behaviors also amplify unsafe ones, and prompts with different safety implications activate overlapping representations. We find no evidence of a subspace that selectively governs safety. These results challenge the assumption that alignment is geometrically localized. Rather than residing in distinct directions, safety appears to emerge from entangled, high-impact components of the model's broader learning dynamics. This suggests that subspace-based defenses may face fundamental limitations and underscores the need for alternative strategies to preserve alignment under continued training. We corroborate these findings through multiple experiments on five open-source LLMs. Our code is publicly available at: https://github.com/CERT-Lab/safety-subspaces.

Diffusion models have made substantial advances in image generation, yet models trained on large, unfiltered datasets often yield outputs misaligned with human preferences. Numerous methods have been proposed to fine-tune pre-trained diffusion models, achieving notable improvements in aligning generated outputs with human preferences. However, we argue that existing preference alignment methods neglect the critical role of handling unconditional/negative-conditional outputs, leading to a diminished capacity to avoid generating undesirable outcomes. This oversight limits the efficacy of classifier-free guidance~(CFG), which relies on the contrast between conditional generation and unconditional/negative-conditional generation to optimize output quality. In response, we propose a straightforward but versatile effective approach that involves training a model specifically attuned to negative preferences. This method does not require new training strategies or datasets but rather involves minor modifications to existing techniques. Our approach integrates seamlessly with models such as SD1.5, SDXL, video diffusion models and models that have undergone preference optimization, consistently enhancing their alignment with human preferences.

Foundation models, specifically Large Language Models (LLMs), have lately gained wide-spread attention and adoption. Reinforcement Learning with Human Feedback (RLHF) involves training a reward model to capture desired behaviors, which is then used to align LLM's. These reward models are additionally used at inference-time to estimate LLM responses' adherence to those desired behaviors. However, there is little work measuring how robust these reward models are to distribution shifts. In this work, we evaluate how reward model performance - measured via accuracy and calibration (i.e. alignment between accuracy and confidence) - is affected by distribution shift. We show novel calibration patterns and accuracy drops due to OOD prompts and responses, and that the reward model is more sensitive to shifts in responses than prompts. Additionally, we adapt an OOD detection technique commonly used in classification to the reward model setting to detect these distribution shifts in prompts and responses.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

High-quality preference datasets are essential for training reward models that can effectively guide large language models (LLMs) in generating high-quality responses aligned with human preferences. As LLMs become stronger and better aligned, permissively licensed preference datasets, such as Open Assistant, HH-RLHF, and HelpSteer need to be updated to remain effective for reward modeling. Methods that distil preference data from proprietary LLMs such as GPT-4 have restrictions on commercial usage imposed by model providers. To improve upon both generated responses and attribute labeling quality, we release HelpSteer2, a permissively licensed preference dataset (CC-BY-4.0). Using a powerful internal base model trained on HelpSteer2, we are able to achieve the SOTA score (92.0%) on Reward-Bench's primary dataset, outperforming currently listed open and proprietary models, as of June 12th, 2024. Notably, HelpSteer2 consists of only ten thousand response pairs, an order of magnitude fewer than existing preference datasets (e.g., HH-RLHF), which makes it highly efficient for training reward models. Our extensive experiments demonstrate that reward models trained with HelpSteer2 are effective in aligning LLMs. In particular, we propose SteerLM 2.0, a model alignment approach that can effectively make use of the rich multi-attribute score predicted by our reward models. HelpSteer2 is available at https://huggingface.co/datasets/nvidia/HelpSteer2 and code is available at https://github.com/NVIDIA/NeMo-Aligner

When the performance of a machine learning model varies over groups defined by sensitive attributes (e.g., gender or ethnicity), the performance disparity can be expressed in terms of the probability distributions of the input and output variables over each group. In this paper, we exploit this fact to reduce the disparate impact of a fixed classification model over a population of interest. Given a black-box classifier, we aim to eliminate the performance gap by perturbing the distribution of input variables for the disadvantaged group. We refer to the perturbed distribution as a counterfactual distribution, and characterize its properties for common fairness criteria. We introduce a descent algorithm to learn a counterfactual distribution from data. We then discuss how the estimated distribution can be used to build a data preprocessor that can reduce disparate impact without training a new model. We validate our approach through experiments on real-world datasets, showing that it can repair different forms of disparity without a significant drop in accuracy.

Ensuring factuality is essential for the safe use of Large Language Models (LLMs) in high-stakes domains such as medicine and law. Conformal inference provides distribution-free guarantees, but existing approaches are either overly conservative, discarding many true-claims, or rely on adaptive error rates and simple linear models that fail to capture complex group structures. To address these challenges, we reformulate conformal inference in a multiplicative filtering setting, modeling factuality as a product of claim-level scores. Our method, Multi-LLM Adaptive Conformal Inference (MACI), leverages ensembles to produce more accurate factuality-scores, which in our experiments led to higher retention, while validity is preserved through group-conditional calibration. Experiments show that MACI consistently achieves user-specified coverage with substantially higher retention and lower time cost than baselines. Our repository is available at https://github.com/MLAI-Yonsei/MACI

Representation intervention has emerged as a promising paradigm for aligning large language models toward desired behaviors without modifying model weights. Existing methods typically apply a fixed intervention uniformly across all inputs. However, we find that the appropriate intervention direction and strength vary substantially across samples, and such indiscriminate intervention leads to degradation of general capabilities on benign inputs. To address these challenges, we propose Multi-Adapter Representation Interventions via Energy Calibration (MARI). Specifically, we introduce a competitive multi-adapter mechanism in which specialized experts capture non-linear correction patterns and adaptively determine the appropriate intervention direction and strength for different samples. Furthermore, we design an energy-based gating module that leverages internal propagation dynamics to distinguish inputs that are applicable for intervention. Extensive experiments across diverse model families and parameter scales demonstrate that MARI achieves state-of-the-art alignment performance. Our method significantly improves performance on TruthfulQA, BBQ, and safety benchmarks, while maintaining and even improving general capabilities on tasks such as MMLU and ARC. Our code is available at https://github.com/V1centNevwake/MARI.

Social scientists are now using large language models to create "silicon samples" - synthetic datasets intended to stand in for human respondents, aimed at revolutionising human subjects research. However, there are many analytic choices which must be made to produce these samples. Though many of these choices are defensible, their impact on sample quality is poorly understood. I map out these analytic choices and demonstrate how a very small number of decisions can dramatically change the correspondence between silicon samples and human data. Configurations (N = 252) varied substantially in their capacity to estimate (i) rank ordering of participants, (ii) response distributions, and (iii) between-scale correlations. Most critically, configurations were not consistent in quality: those that performed well on one dimension often performed poorly on another, implying that there is no "one-size-fits-all" configuration that optimises the accuracy of these samples. I call for greater attention to the threat of analytic flexibility in using silicon samples.

Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently introduced GeoLDM equivariant latent diffusion model (Xu et al., 2023). We evaluate trade-offs between speed gains and quality loss, as measured by molecular conformation structural stability. We introduce Equivariant Latent Progressive Distillation, a fast sampling algorithm that preserves geometric equivariance and accelerates generation from latent diffusion models. Our experiments demonstrate up to 7.5x gains in sampling speed with limited degradation in molecular stability. These results suggest this accelerated sampling method has strong potential for high-throughput in silico molecular conformations screening in computational biochemistry, drug discovery, and life sciences applications.

Open set label shift (OSLS) occurs when label distributions change from a source to a target distribution, and the target distribution has an additional out-of-distribution (OOD) class. In this work, we build estimators for both source and target open set label distributions using a source domain in-distribution (ID) classifier and an ID/OOD classifier. With reasonable assumptions on the ID/OOD classifier, the estimators are assembled into a sequence of three stages: 1) an estimate of the source label distribution of the OOD class, 2) an EM algorithm for Maximum Likelihood estimates (MLE) of the target label distribution, and 3) an estimate of the target label distribution of OOD class under relaxed assumptions on the OOD classifier. The sampling errors of estimates in 1) and 3) are quantified with a concentration inequality. The estimation result allows us to correct the ID classifier trained on the source distribution to the target distribution without retraining. Experiments on a variety of open set label shift settings demonstrate the effectiveness of our model. Our code is available at https://github.com/ChangkunYe/OpenSetLabelShift.

Neural networks trained with ERM (empirical risk minimization) sometimes learn unintended decision rules, in particular when their training data is biased, i.e., when training labels are strongly correlated with undesirable features. To prevent a network from learning such features, recent methods augment training data such that examples displaying spurious correlations (i.e., bias-aligned examples) become a minority, whereas the other, bias-conflicting examples become prevalent. However, these approaches are sometimes difficult to train and scale to real-world data because they rely on generative models or disentangled representations. We propose an alternative based on mixup, a popular augmentation that creates convex combinations of training examples. Our method, coined SelecMix, applies mixup to contradicting pairs of examples, defined as showing either (i) the same label but dissimilar biased features, or (ii) different labels but similar biased features. Identifying such pairs requires comparing examples with respect to unknown biased features. For this, we utilize an auxiliary contrastive model with the popular heuristic that biased features are learned preferentially during training. Experiments on standard benchmarks demonstrate the effectiveness of the method, in particular when label noise complicates the identification of bias-conflicting examples.

Large language models (LLMs) can exhibit bias in a variety of ways. Such biases can create or exacerbate unfair outcomes for certain groups within a protected attribute, including, but not limited to sex, race, sexual orientation, or age. In this paper, we propose a decision framework that allows practitioners to determine which bias and fairness metrics to use for a specific LLM use case. To establish the framework, we define bias and fairness risks for LLMs, map those risks to a taxonomy of LLM use cases, and then define various metrics to assess each type of risk. Instead of focusing solely on the model itself, we account for both prompt-specific- and model-specific-risk by defining evaluations at the level of an LLM use case, characterized by a model and a population of prompts. Furthermore, because all of the evaluation metrics are calculated solely using the LLM output, our proposed framework is highly practical and easily actionable for practitioners. For streamlined implementation, all evaluation metrics included in the framework are offered in this paper's companion Python toolkit, LangFair. Finally, our experiments demonstrate substantial variation in bias and fairness across use cases, underscoring the importance of use-case-level assessments.