Causal Reasoning in Language Models

Visual causal reasoning is essential for understanding and intervening in the physical world, requiring identification of causal variables from visual inputs and reasoning over intervention effects. Despite recent progress, large vision--language models (VLMs) remain brittle at such tasks, especially for interventional and counterfactual queries over multi-image inputs. Most existing explorations inject causal knowledge via textual prompts, leaving causal mechanisms external to model execution and limiting reliable control during inference. To address this problem, we propose BridgeVLM, which internalizes visual causal reasoning by inducing a causal graph from multi-image inputs and converting it into structured Causal Tokens executed by RAMP layers injected into the LLM decoder for causal message passing. We further introduce a unified training interface M3S for fine-grained causal supervision from different granularities (local/global level). BridgeVLM achieves 54.4% accuracy on intervention tasks on CausalVLBench (vs. 33.2% with prompt-level supervision), improves results on Causal3D from 43.6% to 49.0%, and substantially improves causal structure learning on CausalVLBench ($F_1$: 33.4% $\rightarrow$ 75.1%).

Causal graphs provide a high-level language for making mechanisms transparent. Recent work uses Large Language Models (LLMs) to recover causal graphs of external-world processes. Instead, in this paper, we use causal graphs to model LLM inference itself, providing stakeholders with a transparent view of how the model perceives and organizes high-level concepts to produce a prediction. We propose a four-phase method for constructing such graphs. Given a target LLM and a set of textual examples, our method discovers class-discriminative, human-interpretable concepts and maps each input to LLM-perceived concept states. We then introduce an MCMC-inspired counterfactual augmentation procedure that expands the sparse observational data through chains of counterfactuals. This enables stable causal discovery with $σ$-CG, yielding informative, interpretable graphs. We apply our method to three LLMs across disease diagnosis, sentiment analysis, and LLM-as-a-judge classification tasks. We evaluate the learned graphs for predictive fidelity and structural stability, and the MCMC-inspired augmentation for convergence and downstream utility. Our results show that the discovered causal graphs capture meaningful dependencies consistent with LLMs' reasoning. Together, this paper provides a foundation for concept-level explainability of LLMs.

Large language models reach 50 to 70% accuracy on causal reasoning benchmarks such as CLadder, but it is unclear whether this reflects structural reasoning or lexical pattern matching. We introduce Caliper, a controlled perturbation that replaces semantic variable names with placeholder tokens while preserving the causal graph and probabilistic specification of each question. Across nine instruction-tuned LLMs from 3.8B to 671B and three causal reasoning benchmarks, lexical anonymization yields robust accuracy drops of +7.6, +27.0, and +11.1 pp on a local 3.8B-14B set, rising to +29.6 and +18.0 pp on CRASS and e-CARE across nine frontier models spanning the 2024-2026 generations. Of 40 engaged model-by-benchmark cells, 39 show a positive gap, and the gap collapses by 17x on CLadder's pseudoword subset. Structured scaffolding and few-shot in-context learning each narrow the gap, but mainly by lowering P0 accuracy on smaller models rather than recovering P1. Current instruction-tuned LLMs, evaluated zero-shot, show little evidence of structural causal reasoning once lexical anchors are removed.

Causal tracing systematically intervenes on a large language model's (LLM's) internal representations to uncover and quantify the causal pathways linking specific inputs or computations to specific metrics of interest, quantifying the LLM's behavior. Building on previous single-component or single-layer studies, this paper presents a unified framework for causally tracing multiple components simultaneously. This framework systematically identifies the subsets of components (e.g., attention heads and multi-layer perceptron neurons) most critical to a desired target performance metric (e.g., accuracy and fairness). This is achieved by incorporating flexible interventions applied to a wide range of desired metrics. To address the combinatorial complexity of the multi-component problem, an efficient algorithm is designed that leverages soft interventions and a carefully designed metric transformation, converting the combinatorial search problem into a continuous one that can be solved efficiently under proper constraints, thereby generating proper binary decisions for selecting components. Experimental results demonstrate that the proposed method efficiently identifies subsets of the model's components that have a high impact on the target metric, outperforming existing baseline approaches. Our code is available at https://github.com/ZiruiYan/multi-component-causal-tracing.

Large Language Models (LLMs) aligned via outcome-based Reinforcement Learning (RL) frequently exhibit a critical failure mode: they achieve high performance on in-distribution benchmarks while demonstrating brittle reasoning capabilities on out-of-distribution (OOD) tasks. We term this phenomenon Reward-Induced Manifold Collapse. We establish a theoretical framework bridging Structural Causal Models (SCM) and the Information Bottleneck (IB) principle to explain this paradox. We define reasoning as a high-complexity causal process and shortcut learning as the exploitation of low-complexity spurious correlations. Under the implicit inductive bias of Stochastic Gradient Descent (SGD), models optimized for outcome rewards are biased toward shortcut solutions whenever the training distribution allows for a ``Markovian Screening'' of the true causal mechanism. We derive a new generalization bound based on Semantic Coverage Measure ($η$) rather than sample size, showing why data scaling on homogeneous distributions may fail to correct reasoning flaws. We also show that Process Reward Models (PRMs) function as Topological Filters, enforcing step-wise mutual information constraints that render the low-complexity shortcut manifold inadmissible. These results provide a mathematical grounding for the role of process supervision beyond simple credit assignment.

Causal interventions in language model representations have largely targeted discrete features, like grammatical number. However, language models must also make use of features that are graded. We introduce a method for causal intervention on continuous variables: given activation vectors paired with a graded target variable, we localize a low-dimensional direction for that variable and use this direction to edit a vectors toward counterfactual target values. We apply this method to a continuous feature that is well-studied in psycholinguistics, namely verb bias (which reflects which syntactic structures tend to follow a given verb). We show that verb bias is causally represented in steering vectors extracted from large language models: counterfactual edits to verb bias systematically shift downstream structural preferences. Verb bias has also previously been linked to in-context learning; in further analyses, we find that steering vectors encode error signals that could drive the error-driven update behavior seen in in-context learning but that these aspects of the steering vectors are not causally used in downstream production. Overall, these results show causal interventions can be applied to continuous variables, though connecting continuous variables to in-context learning remains a challenge.

Vision-language models (VLMs) generate fluent causal explanations, but current evaluations cannot distinguish linguistic plausibility from faithful causal reasoning. We introduce a dual-probe methodology that isolates these properties. The Text-Only Probe measures linguistic quality. The Chain-Text Probe requires models to first generate explicit causal chains. The Abstraction Gap (AG) metric quantifies the normalized performance difference. Evaluating eight VLMs on CAGE (Causal Abstraction Gap Evaluation), a benchmark of 49,500 questions across 5,500 images spanning Pearl's causal hierarchy, we find seven models exhibit AG exceeding 0.50 with text scores of 6--8 but chain scores below 2.5. Fine-tuning on 45,000 chain-annotated examples fails to close the gap. However, one model achieves near-zero AG. The capability exists within current VLM architectures and depends on pretraining and architectural choices. CAGE provides a diagnostic tool for assessing faithful causal reasoning in VLMs.

Causal discovery is a cornerstone of scientific reasoning, yet whether large language models can perform it reliably remains an open question. Recent benchmarks show that even fine-tuned models plateau on simple causal graphs and degrade as complexity grows, but why they fail has not been established. We prove the failure is fundamental: supervised fine-tuning, direct preference optimization, and in-context learning all produce predictors that cannot distinguish between causal graphs generating similar observational data, and any attempt to do so requires the model's internal representations to grow unboundedly, violating the very conditions under which these methods work. We formalize this as a kernel obstruction theorem, establishing that the limitation is intrinsic to the learning paradigm, \emph{not any particular model or dataset}. We propose Agentic Causal Bayesian Optimization (A-CBO), wherein a frozen language model serves as an interventional oracle answering targeted queries about intervention effects, while an external Bayesian loop concentrates beliefs over candidate graphs in logarithmically many rounds. Because the decision operates outside the space where the obstruction applies, A-CBO provably converges while the underlying model remains unchanged. On Corr2Cause, A-CBO matches fine-tuned baselines without any training. On Extended Corr2Cause, a new benchmark scaling to 24 variables with 18K test samples, A-CBO significantly outperforms both fine-tuning and preference optimization, with the advantage growing

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge $F_1$. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.

We find a mismatch between what large language models encode about a causal question and what they answer. On anti-commonsense CLadder items, a fixed linear probe recovers the evidence-supported answer from the model's hidden state (accuracy approximately 0.97), while the spoken Yes/No reverts to the commonsense one (accuracy approximately 0.5). We call this approximately +0.5 gap Causal Tongue-Tie: a wrong Yes/No decomposes into two separable failure modes: no internal signal versus a signal the verbal interface cannot say. The implication cuts both ways for output-only causal benchmarks: a benchmark "correct" need not mean the model has understood, and a benchmark "wrong" need not mean it cannot. Sweeping claims about whether LLMs can do causal reasoning, drawn from a single accuracy number, deserve a second look.

Despite the importance of causal reasoning, training LLMs to reason causally remains underexplored. Existing data efforts mostly focus on benchmarking LLMs on specific aspects of causality, making them less suitable for training generalizable causal reasoners. To address this, we propose UniCo, a data generation framework that both (1) addresses 18 causal query types across Pearl's Causal Ladder and (2) translates natively symbolic examples into code and natural language forms to simulate real-world use cases where causal terms are not explicitly specified. To ensure data quality, UniCo grounds answers with exact causal inference and filters cases with reasoning shortcuts. Upon supervised finetuning with 66.6K UniCo-generated instances, Qwen3-4B, Qwen3-8B and Olmo-3-7B-Instruct achieve an average of 22.9% improvements across all 18 in-distribution query types, and 8.1% over state-of-the-art causal data generation frameworks on 7 established causal benchmarks outside the training distribution. More importantly, in real-world medical understanding, legal decision, and tabular reasoning, UniCo-trained models consistently display more faithful reasoning traces, outperforming the base models by an average of 20.2% in faithfulness metrics. These suggest that causality-centered training not only strengthens causal reasoning, but also equips LLMs with a causal mindset in general reasoning tasks.

We propose a five-stage methodology for causal feature analysis in transformer language models (probe design, feature extraction, causal validation, robustness testing, and deployment integration) and demonstrate it end-to-end on GPT-2 small performing the Indirect Object Identification (IOI) task. Activation patching recovers the canonical IOI circuit (layer-9 head 9 alone gives recovery +1.02). A sparse autoencoder recovers per-name selective features with effect sizes of 30 to 50 activation units. Causal validation finds these features specifically but only partially causal: ablating fifteen of them leaves the model accurate on 98% of prompts. Two NLA-inspired evaluations strengthen this picture: the fifteen selective features explain only 31% of activation variance versus the SAE's 99.7%, and selectivity ratio anticorrelates with causal force (r = -0.56). Robustness testing under three distribution shifts finds that the circuit transfers cleanly but feature ablation effects degrade substantially, exposing a gap between detection robustness and causal robustness. A cost-based deployment evaluation (assumed $50/FN,$0.42/FP, 2% error rate) finds an optimal monitor configuration yielding $8.96 per 1000 queries against a$1000 baseline, a 99.1% saving. Optimal composition strategy varies with cost ratio and base rate. The conjunction of stages produces findings no single stage would.

Large language models (LLMs) are increasingly integrated into high-stakes decision-making. Inspired by the theory of \emph{inattentional blindness} in human cognition, we investigate whether LLMs, trained on human-preferred corpora that embed attentional biases, exhibit a similar limitation: \emph{failing to attend to subtle yet important contextual cues under explicit task instructions}. To evaluate this, we introduce the task of \textbf{explicit-implicit reasoning} and present \textbf{MixRea}, a benchmark of 2,246 multiple-choice questions across 9 reasoning types with varying distributions of explicit and implicit information. Evaluation of 21 advanced LLMs shows that even the best-performing reasoning model (Gemini 2.5 Pro) achieves only 42.8% consistency, revealing widespread inattentional blindness. To mitigate this, we propose \textbf{Potential Relation Completion Prompting (PRCP)}, a prompting method that improves reasoning by recovering overlooked causal relations. Further analysis shows that this limitation persists across diverse multi-source reasoning tasks, highlighting the need for more cognitively aligned models.

Large Language Models (LLMs) generate realistic synthetic data but offer no guarantee that their outputs respect the causal mechanisms governing the target domain. We introduce CausalSynth, a framework that decouples causal structure generation from semantic realization, yielding synthetic data that is both causally valid and linguistically rich. The framework operates in three phases. First, a Structural Causal Model (SCM) - a tuple of structural equations defined over a directed acyclic graph (DAG) generates causal skeletons, i.e., variable assignments that satisfy the Global Markov Property of the governing DAG, via ancestral sampling. Second, an LLM acts as a constrained \emph{realizer}, a conditional translator that maps each skeleton to a high-dimensional observation such as a clinical note or a transaction log. Third, an Iterative Consistency Verification module detects structural violations through deterministic extraction and feeds targeted corrections back to the LLM, forming a closed-loop refinement process. We identify the Semantic Backdoor problem the systematic tendency of LLMs to override imposed causal facts with pre-training priors -- and prove that our iterative mechanism reduces the resulting selection bias relative to standard rejection sampling. On three causal benchmarks (ASIA, ALARM, and MIMIC-Struct), CausalSynth preserved conditional independencies with false-positive rates near the nominal $α=0.05$ level and achieved realizability rates above 96% with 70B-parameter LLM backbones. The framework additionally supports principled interventional and counterfactual generation through noise retention and graph mutilation.

Large language models achieve strong performance in language generation and knowledge-intensive tasks, yet remain limited in settings requiring causal reasoning, persistent state tracking, and long-horizon planning. We argue that these limitations may arise from an objective-level mismatch between sequence prediction and reasoning over latent environment dynamics. To formalize this distinction, we introduce Latent Dynamics Inference (LDI), a conceptual perspective that interprets language and multimodal observations as partial evidence of underlying transition dynamics. To empirically investigate this perspective, we introduce Flux, a sequential reasoning environment specified entirely through natural-language rules. As a proof-of-concept case study, the rules are first compiled into an explicit state-transition simulator, illustrating that structured latent transition dynamics can, in some cases, be operationally extracted from textual rule descriptions. This enables a controlled comparison between the LLMs operating purely over textual observations and reinforcement-learning agents trained directly within the extracted latent state space. Within this case study, agents operating with explicit access to the latent state space exhibit substantially more stable behavior in long-horizon gameplay, achieving an aggregate win rate of approximately 79% versus 11% for LLMs. Qualitative analysis further reveals failure modes consistent with unstable persistent state tracking, including invalid actions, state-tracking errors, and short-horizon reasoning failures. The complete implementation of the Flux environment available at https://github.com/FeisalAlaswad/FLUX-RL-Agent Within the evaluated setting, these results suggest that strong sequence prediction alone may struggle to support robust long-horizon dynamic reasoning without mechanisms for persistent state tracking and transition modeling

To effectively interact with the real world, Large Language Models (LLMs) require entity-based commonsense reasoning, a challenging task that necessitates integrating factual knowledge about specific entities with commonsense inference. Existing datasets for evaluating LLM entity-based commonsense reasoning have largely focused on True/False or multiple-choice questions, leaving the explicit assessment of the model's ability in abductive reasoning about causes and effects and generating explanations largely unexamined. In this work, we introduce CommonWhy, a dataset of 15,000 why questions designed to evaluate entity-based commonsense reasoning about causal relationships in LLMs. CommonWhy also serves as a Knowledge Graph Question Answering (KGQA) benchmark, as all supporting knowledge required to answer its queries is available in the Wikidata knowledge graph. Unlike existing KGQA datasets, which primarily test fact retrieval, CommonWhy targets causal commonsense reasoning, establishing a new paradigm for KGQA evaluation. Experiments with state-of-the-art LLMs and LLM-based KGQA methods reveal their significant shortcomings, including frequent factual hallucinations and failures in causal reasoning.

Large language models can extract local causal claims from text, but those claims become more useful when organized as persistent, navigable world models rather than as flat summaries. We introduce PROMETHEUS, a framework that turns retrieved literature, filings, reviews, reports, agent traces, source data, code, simulations, and scientific models into causal atlases: sheaf-like families of local causal predictive-state models over an explicit cover of a research substrate. Each local region contains causal episodes, structured claim tables, predictive tests, support statistics, and provenance; restriction maps compare overlapping regions; gluing diagnostics expose agreement, drift, contradiction, and underdetermination. The resulting Topos World Model is not a single universal graph. It is a research instrument for navigating what a corpus says, where it says it, how strongly it is supported, and where local claims fail to assemble into a coherent global view. Three literature-atlas case studies -- ocean-temperature impacts on marine populations, GLP-1 weight-loss evidence, and resveratrol/red-wine health-benefit claims -- illustrate deep causal research from text with explicit locality, evidence, persistent state, and gluing tension. Four grounded-counterfactual case studies -- a Nature Climate Change microplastics forcing paper, an Indus Valley hydrology paper with VIC-derived figure data and model code, the canonical Sachs protein-signaling study with single-cell perturbation data, and a Nature singing-mouse study with MAPseq projection matrices -- show a stronger mode: when a paper ships source data, simulation outputs, or code, PROMETHEUS can evaluate a counterfactual against that scientific substrate and then rebuild the sheaf world model around the

Despite surpassing human performance across mathematics, coding, and other knowledge-intensive tasks, large language models (LLMs) continue to struggle with causal reasoning. A core obstacle is the target data itself: causal systems are complex and often expressed in non-executable forms, while ground-truth answers to causal queries are inherently scarce. We introduce CauSim, a framework that turns causal reasoning from a scarce-label problem into a scalable supervised one. CauSim constructs increasingly complex causal simulators: executable structural causal models (SCMs), incrementally built by LLMs, that scale to globally complex systems while maintaining verifiable answers to causal queries. CauSim operates across representations by formalizing non-executable causal knowledge into code, enabling data augmentation, and translating executable SCMs into natural language, enabling supervision in previously difficult-to-supervise representations. We structure our research into two parts: (1) how to construct increasingly complex causal simulators, and (2) a systematic study of what CauSim enables, demonstrating generalization across representations, consistent gains from curriculum scaling and data volume, LLM self-improvement through self-generated simulators, and data augmentation via formalization of existing domain knowledge.

Causal reasoning in natural language requires identifying relevant variables, understanding their interactions, and reasoning about effects and interventions, often under noisy or ambiguous conditions. While large language models (LLMs) exhibit strong general reasoning abilities, they struggle to disentangle correlation from causation, particularly when observations are partially incorrect or irrelevant information is present. In this work, we introduce NoisyCausal, a new benchmark designed to evaluate causal reasoning under structured noise. Each instance is generated from a ground-truth causal graph and contextualized with a natural language scenario by injecting controllable forms of noise, such as irrelevant distractors, value perturbations, confounding, and partial observability. Moreover, we propose a modular reasoning framework that combines LLMs with explicit causal structure to address these challenges. Our method prompts the LLM to extract variables, construct a causal graph from context, and then reformulates the reasoning task as a structured prompt grounded in this graph. Rather than relying on statistical patterns alone, the LLM is guided by symbolic structure, enabling more interpretable and robust inference. Experimental results show that our method significantly outperforms standard prompting and reasoning baselines on NoisyCausal. Furthermore, it generalizes well to external benchmarks such as Cladder without task-specific tuning. Our findings highlight the importance of combining causal abstractions with language-driven reasoning to achieve faithful and robust causal understanding in LLMs.

Event Causality Identification (ECI) requires models to determine whether a given pair of events in a context exhibits a causal relationship. While Large Language Models (LLMs) have demonstrated strong performance across various NLP tasks, their effectiveness in ECI remains limited due to biases in causal reasoning, often leading to overprediction of causal relationships (causal hallucination). To mitigate these issues and enhance LLM performance in ECI, we propose SERE, a structural example retrieval framework that leverages LLMs' few-shot learning capabilities. SERE introduces an innovative retrieval mechanism based on three structural concepts: (i) Conceptual Path Metric, which measures the conceptual relationship between events using edit distance in ConceptNet; (ii) Syntactic Metric, which quantifies structural similarity through tree edit distance on syntactic trees; and (iii) Causal Pattern Filtering, which filters examples based on predefined causal structures using LLMs. By integrating these structural retrieval strategies, SERE selects more relevant examples to guide LLMs in causal reasoning, mitigating bias and improving accuracy in ECI tasks. Extensive experiments on multiple ECI datasets validate the effectiveness of SERE. The source code is publicly available at https://github.com/DMIRLAB-Group/SERE.

Safety trained large language models (LLMs) can often be induced to answer harmful requests through jailbreak prompts. Because we lack a robust understanding of why LLMs are susceptible to jailbreaks, future frontier models operating more autonomously in higher-stakes settings may similarly be vulnerable to such attacks. Prior work has studied jailbreak success by examining the model's intermediate representations, identifying directions in this space that causally encode concepts like harmfulness and refusal. Then, they globally explain all jailbreak attacks as attempting to reduce or strengthen these concepts (e.g., reduce harmfulness). However, different jailbreak strategies may succeed by strengthening or suppressing different intermediate concepts, and the same jailbreak strategy may not work for different harmful request categories (e.g., violence vs. cyberattack); thus, we seek to give a local explanation -- i.e., why did this specific jailbreak succeed? To address this gap, we introduce LOCA, a method that gives Local, CAusal explanations of jailbreak success by identifying a minimal set of interpretable, intermediate representation changes that causally induce model refusal on an otherwise successful jailbreak request. We evaluate LOCA on harmful original-jailbreak pairs from a large jailbreak benchmark across Gemma and Llama chat models, comparing against prior methods adapted to this setting. LOCA can successfully induce refusal by making, on average, six interpretable changes; prior work routinely fails to achieve refusal even after 20 changes. LOCA is a step toward mechanistic, local explanations of jailbreak success in LLMs. Code to be released.

Extracting abstract causal structures and applying them to novel situations is a hallmark of human intelligence. While Large Language Models (LLMs) and Vision Language Models (VLMs) have shown strong performance on a wide range of reasoning tasks, their capacity for interactive causal learning -- inducing latent structures through sequential exploration and transferring them across contexts -- remains uncharacterized. Human learners accomplish such transfer after minimal exposure, whereas classical Reinforcement Learning (RL) agents fail catastrophically. Whether state-of-the-art Artificial Intelligence (AI) models possess human-like mechanisms for abstract causal structure transfer is an open question. Using the OpenLock paradigm requiring sequential discovery of Common Cause (CC) and Common Effect (CE) structures, here we show that models exhibit fundamentally delayed or absent transfer: even successful models require initial environmental-specific mapping -- what we term environmental grounding -- before efficiency gains emerge, whereas humans leverage prior structural knowledge from the very first solution attempt. In the text-only condition, models matched or exceeded human discovery efficiency. In contrast, visual information -- in both the image-only and text-and-image conditions -- overall degraded rather than enhanced performance, revealing a broad reliance on symbolic processing rather than integrated multimodal reasoning. Models further exhibited systematic CC/CE asymmetries absent in humans, suggesting heuristic biases rather than direction-neutral causal abstraction. These findings reveal that large-scale statistical learning does not produce the decontextualized causal schemas underpinning human analogical reasoning, establishing grounding-dependent transfer as a fundamental limitation of current LLMs and VLMs.

Predicting the outcomes of prospective clinical trials remains a major challenge for large language models. Prior work has shown that both traditional correlational predictors, such as random forests and logistic regression, and strong commercial LLMs achieve limited performance on this task. In this paper, we propose DeepImagine, a framework for teaching LLMs biomedical reasoning through successive counterfactual imagining. The central idea is to approximate hidden causal mechanisms of clinical trials by training models to infer how observed trial results would change under controlled perturbations of experimental conditions, such as dosage, outcome measures, study arms, geography, and other trial attributes. To support this objective, we construct both natural and approximate counterfactual pairs from real clinical trials with reported outcomes. For settings where strict counterfactual supervision is available, such as paired outcome measures or dose-ranging study arms within the same trial, we train models with supervised fine-tuning. For broader settings where only approximate counterfactual pairs can be retrieved, we optimize models with reinforcement learning using verifiable rewards based on downstream benchmark correctness. We further augment training with synthetic reasoning traces that provide causally plausible explanations for local counterfactual transitions. Using this pipeline, we train language models under 10B parameters, including Qwen3.5-9B, and evaluate them on clinical trial outcome prediction. We aim to show that DeepImagine consistently improves over untuned language models and traditional correlational baselines. Finally, we aim to show that the learned reasoning trajectories provide interpretable signals about how models represent trial-level mechanisms, suggesting a practical path toward more mechanistic and scientifically useful biomedical language models.

Causal graphs in text are typically populated by observable, predefined events. In contrast, we study implicit causal graph construction from text by treating each described cause-effect pair as the begin- and endpoint of an underlying latent causal graph and using large language models (LLMs) to infer intermediate causal events. We compare end-to-end graph construction with methods that frame the task as causal chain discovery. In the latter, graphs are built either by aggregating inferred chains or by progressively expanding partial chains through an iterative search process. We further explore Wisdom of the Crowd extensions that access causal knowledge from multiple LLMs in post-hoc aggregation and collaborative inference settings. We analyze trade-offs among these approaches and evaluate the validity of inferred causal relations using a manually curated database of 1,560 scientifically validated causal pairs. This database-based evaluation is proposed as reliable, resource-efficient, and transferable to settings where ground-truth graphs are unavailable.

Large language models (LLMs) frequently generate toxic content, posing significant risks for safe deployment. Current mitigation strategies often degrade generation quality or require costly human annotation. We propose CAUSALDETOX, a framework that identifies and intervenes on the specific attention heads causally responsible for toxic generation. Using the Probability of Necessity and Sufficiency (PNS), we isolate a minimal set of heads that are necessary and sufficient for toxicity. We utilize these components via two complementary strategies: (1) Local Inference-Time Intervention, which constructs dynamic, input-specific steering vectors for context-aware detoxification, and (2) PNS-Guided Fine-Tuning, which permanently unlearns toxic representations. We also introduce PARATOX, a novel benchmark of aligned toxic/non-toxic sentence pairs enabling controlled counterfactual evaluation. Experiments on ToxiGen, ImplicitHate, and ParaDetox show that CAUSALDETOX achieves up to 5.34% greater toxicity reduction compared to baselines while preserving linguistic fluency, and offers a 7x speedup in head selection.

As large language models (LLMs) witness increasing deployment in complex, high-stakes decision-making scenarios, it becomes imperative to ground their reasoning in causality rather than spurious correlations. However, strong performance on traditional reasoning benchmarks does not guarantee true causal reasoning ability of LLMs, as high accuracy may still arise from memorizing semantic patterns instead of analyzing the underlying true causal structures. To bridge this critical gap, we propose a new causal reasoning benchmark, CausalFlip, designed to encourage the development of new LLM paradigm or training algorithms that ground LLM reasoning in causality rather than semantic correlation. CausalFlip consists of causal judgment questions built over event triples that could form different confounder, chain, and collider relations. Based on this, for each event triple, we construct pairs of semantically similar questions that reuse the same events but yield opposite causal answers, where models that rely heavily on semantic matching are systematically driven toward incorrect predictions. To further probe models' reliance on semantic patterns, we introduce a noisy-prefix evaluation that prepends causally irrelevant text before intermediate causal reasoning steps without altering the underlying causal relations or the logic of the reasoning process. We evaluate LLMs under multiple training paradigms, including answer-only training, explicit Chain-of-Thought (CoT) supervision, and a proposed internalized causal reasoning approach that aims to mitigate explicit reliance on correlation in the reasoning process. Our results show that explicit CoT can still be misled by spurious semantic correlations, where internalizing reasoning steps yields substantially improved causal grounding, suggesting that it is promising to better elicit the latent causal reasoning capabilities of base LLMs.

The ability to understand causality significantly impacts the competence of large language models (LLMs) in output explanation and counterfactual reasoning, as causality reveals the underlying data distribution. However, the lack of a comprehensive benchmark currently limits the evaluation of LLMs' causal learning capabilities. To fill this gap, this paper develops CausalBN-Bench based on data from the causal research community, enabling comparative evaluations of LLMs against traditional causal learning algorithms. To provide a comprehensive investigation, we offer three tasks of varying difficulties, including correlation, causal skeleton, and causality identification. Evaluations of 19 leading LLMs reveal that, while closed-source LLMs show potential for simple causal relationships, they significantly lag behind traditional algorithms on larger-scale networks ($>50$ nodes). Specifically, LLMs struggle with collider structures but excel at chain structures, especially at long-chain causality analogous to Chain-of-Thought techniques. This supports the current prompt approaches while suggesting directions to enhance LLMs' causal reasoning capability. Furthermore, CausalBN-Bench incorporates background knowledge and training data into prompts to thoroughly unlock LLMs' text-comprehension ability during evaluation, whose findings indicate that, LLM understand causality through semantic associations with distinct entities, rather than directly from contextual information or numerical distributions.