Daily Papers

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

Biosignals acquired from different locations on the body often provide temporally ordered views of the same underlying physiological process. However, most existing self supervised learning methods treat these signals as interchangeable views, overlooking the directional temporal dynamics that link them. A canonical example is the relationship between electrocardiography (ECG), which captures the electrical activation initiating each heartbeat, and photoplethysmography (PPG), which records the resulting peripheral pulse delayed by vascular dynamics. To capture this structured relationship, we introduce xMAE, a biosignal pretraining framework that leverages masked cross modal reconstruction across temporally ordered biosignals as a training time constraint to encourage physiologically meaningful timing structure in the learned representations. We show that pretraining with xMAE yields representations that outperform both unimodal and multimodal baselines on 15 of 19 downstream tasks, including cardiovascular outcome prediction, abnormal laboratory test detection, sleep staging, and demographic inference, while generalizing across devices, body locations, and acquisition settings. Further analysis suggests that the ECG PPG timing structure is reflected in the learned PPG representations. More broadly, xMAE demonstrates the effectiveness of incorporating temporal structure into multimodal pretraining when signals observe different stages of a shared underlying process. Code is available at https://github.com/hzhou3/xMAE.

Biosecurity evaluations of language models typically ask whether models produce hazardous output. This paper asks a complementary question: when a model refuses, is that refusal structurally sound, or does it disappear under modest changes to prompt framing, formatting, or output length? Across five architectures, no model cleanly discriminated benign from hazard. Gemma 2 2B-IT never genuinely refused across 75 prompts, hedging on every hazard-adjacent query. Gemma 4 E2B-IT refused 65/75 prompts with chat-template formatting and 0/75 without it. Both Gemma models collapsed to 0% under an 80-token cap. Qwen 2.5 1.5B and Phi-3-mini over-refused, flagging 83-87% of benign biology as hazardous. Llama 3.2 1B showed the only meaningful tier gradient (61-point spread). To probe what drives such over-refusal, we tested a panel of Schedule I but biologically non-toxic compounds (notably psilocybin cultivation, with FDA Breakthrough Therapy status). Some models refused these at rates exceeding genuinely hazardous biology, suggesting refusal tracks legality and cultural salience over CBRN hazard. To measure the internal side, we introduce a divergence score D comparing a model's surface response label to its internal sparse autoencoder (SAE) feature activations. Full D was computed on Gemma 2 2B-IT (Gemma Scope 1) and Gemma 4 E2B-IT (author-trained bio SAE). Two fine-tuned Gemma 2 domain SAEs were released. On Gemma 4, comply and refuse responses separated by a 0.647-point gap with zero overlap (n=75), though this is preliminary, with a narrow catalog, within-sample calibration, and Gemma-family-only SAE coverage. Built over one hackathon weekend on consumer hardware (GTX 1650 Ti Max-Q, plus Colab T4 for SAE training), this preliminary evidence suggests activation-level auditing may surface failure modes invisible to behavioral evaluation, with substantial variation across architectures.

Tracking biosignals is crucial for monitoring wellness and preempting the development of severe medical conditions. Today, wearable devices can conveniently record various biosignals, creating the opportunity to monitor health status without disruption to one's daily routine. Despite widespread use of wearable devices and existing digital biomarkers, the absence of curated data with annotated medical labels hinders the development of new biomarkers to measure common health conditions. In fact, medical datasets are usually small in comparison to other domains, which is an obstacle for developing neural network models for biosignals. To address this challenge, we have employed self-supervised learning using the unlabeled sensor data collected under informed consent from the large longitudinal Apple Heart and Movement Study (AHMS) to train foundation models for two common biosignals: photoplethysmography (PPG) and electrocardiogram (ECG) recorded on Apple Watch. We curated PPG and ECG datasets from AHMS that include data from ~141K participants spanning ~3 years. Our self-supervised learning framework includes participant level positive pair selection, stochastic augmentation module and a regularized contrastive loss optimized with momentum training, and generalizes well to both PPG and ECG modalities. We show that the pre-trained foundation models readily encode information regarding participants' demographics and health conditions. To the best of our knowledge, this is the first study that builds foundation models using large-scale PPG and ECG data collected via wearable consumer devices x2013 prior works have commonly used smaller-size datasets collected in clinical and experimental settings. We believe PPG and ECG foundation models can enhance future wearable devices by reducing the reliance on labeled data and hold the potential to help the users improve their health.

Biological signals, such as electroencephalograms (EEG), play a crucial role in numerous clinical applications, exhibiting diverse data formats and quality profiles. Current deep learning models for biosignals are typically specialized for specific datasets and clinical settings, limiting their broader applicability. Motivated by the success of large language models in text processing, we explore the development of foundational models that are trained from multiple data sources and can be fine-tuned on different downstream biosignal tasks. To overcome the unique challenges associated with biosignals of various formats, such as mismatched channels, variable sample lengths, and prevalent missing values, we propose a Biosignal Transformer (\method). The proposed \method model can enable cross-data learning with mismatched channels, variable lengths, and missing values by tokenizing diverse biosignals into unified "biosignal sentences". Specifically, we tokenize each channel into fixed-length segments containing local signal features, flattening them to form consistent "sentences". Channel embeddings and {\em relative} position embeddings are added to preserve spatio-temporal features. The \method model is versatile and applicable to various biosignal learning settings across different datasets, including joint pre-training for larger models. Comprehensive evaluations on EEG, electrocardiogram (ECG), and human activity sensory signals demonstrate that \method outperforms robust baselines in common settings and facilitates learning across multiple datasets with different formats. Use CHB-MIT seizure detection task as an example, our vanilla \method model shows 3\% improvement over baselines in balanced accuracy, and the pre-trained \method models (optimized from other data sources) can further bring up to 4\% improvements.

As large language models (LLMs) acquire advanced biological design capabilities, they offer substantial research benefits but simultaneously introduce severe dual-use risks, such as engineering enhanced pathogens or drug-resistant bacteria. While biosecurity frameworks recognize these threats, the actual risk of LLMs executing dangerous biological modifications remains unquantified, particularly when augmented with specialized biological design tools (BDTs). Existing evaluations primarily assess hazardous knowledge possession rather than practical application, overlook risk amplification from BDTs, and rely on unreliable, expensive, or hazardous validation methods. To address these gaps, we introduce DRYLAB-Bench (Design Risk Yielded by LLM Agent in Biodesign), the first comprehensive benchmark evaluating the high-risk biological mutation design capabilities of LLM agents. Moving beyond basic question-answering, DRYLAB-Bench tasks agents with 30 genuinely hazardous mutation-design scenarios distilled from biosecurity guidelines. It evaluates models in a multi-round, tool-augmented environment where LLMs orchestrate BDTs to iteratively refine candidates. Crucially, it scores designs directly against 187,695 empirical wet-lab measurements from ProteinGym and ViroGym using our proposed Biosecurity Risk Score (BRS), quantifying risk-associated effects while enabling scalable and safe ground-truth verification. Evaluations of 15 frontier models reveal substantial baseline threats: without tools, 67.6% of one-shot designs exceed the average measured variant, and 21.4% reach the highest-risk decile. Equipping models with BDTs significantly amplifies this risk, raising the pooled risk by \(ΔBRS=+0.116\) and the top-decile share to 23.5%. Code: https://github.com/drylab-bio/DRYLAB-Bench

We present a large-scale study of gender bias in occupation classification, a task where the use of machine learning may lead to negative outcomes on peoples' lives. We analyze the potential allocation harms that can result from semantic representation bias. To do so, we study the impact on occupation classification of including explicit gender indicators---such as first names and pronouns---in different semantic representations of online biographies. Additionally, we quantify the bias that remains when these indicators are "scrubbed," and describe proxy behavior that occurs in the absence of explicit gender indicators. As we demonstrate, differences in true positive rates between genders are correlated with existing gender imbalances in occupations, which may compound these imbalances.

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. Almost all research on large-scale biosequence transformers has focused on one domain at a time (single-omic), usually nucleotides or peptides. These models have seen incredible success in downstream tasks in each domain and have achieved particularly noteworthy breakthroughs in sequences of peptides and structural modeling. However, these single-omic models are naturally incapable of modeling multi-omic tasks, one of the most biologically critical being nucleotide-peptide interactions. We present our work training the first multi-omic nucleotide-peptide foundation models. We show that these multi-omic models (MOMs) can learn joint representations between various single-omic distributions that are emergently consistent with the Central Dogma of molecular biology, despite only being trained on unlabeled biosequences. We further demonstrate that MOMs can be fine-tuned to achieve state-of-the-art results on peptide-nucleotide interaction tasks, namely predicting the change in Gibbs free energy ({\Delta}G) of the binding interaction between a given oligonucleotide and peptide, as well as the effect on this binding interaction due to mutations in the oligonucleotide sequence ({\Delta}{\Delta}G). Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any prior structural training, allowing us to predict which peptide residues are most involved in the peptide-nucleotide binding interaction. Lastly, we provide evidence that multi-omic biosequence models are non-inferior to foundation models trained on single-omics distributions, suggesting a more generalized or foundational approach to building these models.

Ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic enzymes often exhibit promiscuous substrate preferences that cannot be reduced to simple rules. Large language models are promising tools for predicting such peptide fitness landscapes. However, state-of-the-art protein language models are trained on relatively few peptide sequences. A previous study comprehensively profiled the peptide substrate preferences of LazBF (a two-component serine dehydratase) and LazDEF (a three-component azole synthetase) from the lactazole biosynthetic pathway. We demonstrated that masked language modeling of LazBF substrate preferences produced language model embeddings that improved downstream classification models of both LazBF and LazDEF substrates. Similarly, masked language modeling of LazDEF substrate preferences produced embeddings that improved the performance of classification models of both LazBF and LazDEF substrates. Our results suggest that the models learned functional forms that are transferable between distinct enzymatic transformations that act within the same biosynthetic pathway. Our transfer learning method improved performance and data efficiency in data-scarce scenarios. We then fine-tuned models on each data set and showed that the fine-tuned models provided interpretable insight that we anticipate will facilitate the design of substrate libraries that are compatible with desired RiPP biosynthetic pathways.

Pain is a complex and pervasive condition that affects a significant portion of the population. Accurate and consistent assessment is essential for individuals suffering from pain, as well as for developing effective management strategies in a healthcare system. Automatic pain assessment systems enable continuous monitoring, support clinical decision-making, and help minimize patient distress while mitigating the risk of functional deterioration. Leveraging physiological signals offers objective and precise insights into a person's state, and their integration in a multimodal framework can further enhance system performance. This study has been submitted to the Second Multimodal Sensing Grand Challenge for Next-Gen Pain Assessment (AI4PAIN). The proposed approach introduces Tiny-BioMoE, a lightweight pretrained embedding model for biosignal analysis. Trained on 4.4 million biosignal image representations and consisting of only 7.3 million parameters, it serves as an effective tool for extracting high-quality embeddings for downstream tasks. Extensive experiments involving electrodermal activity, blood volume pulse, respiratory signals, peripheral oxygen saturation, and their combinations highlight the model's effectiveness across diverse modalities in automatic pain recognition tasks. The model's architecture (code) and weights are available at https://github.com/GkikasStefanos/Tiny-BioMoE.

Neurophysiological recordings such as electroencephalography (EEG) offer accessible and minimally invasive means of estimating physiological activity for applications in healthcare, diagnostic screening, and even immersive entertainment. However, these recordings yield high-dimensional, noisy time-series data that typically require extensive pre-processing and handcrafted feature extraction to reveal meaningful information. Recently, there has been a surge of interest in applying representation learning techniques from large pre-trained (foundation) models to effectively decode and interpret biosignals. We discuss the challenges posed for incorporating such methods and introduce BioCodec, an alternative representation learning framework inspired by neural codecs to capture low-level signal characteristics in the form of discrete tokens. Pre-trained on thousands of EEG hours, BioCodec shows efficacy across multiple downstream tasks, ranging from clinical diagnostic tasks and sleep physiology to decoding speech and motor imagery, particularly in low-resource settings. Additionally, we provide a qualitative analysis of codebook usage and estimate the spatial coherence of codebook embeddings from EEG connectivity. Notably, we also document the suitability of our method to other biosignal data, i.e., electromyographic (EMG) signals. Overall, the proposed approach provides a versatile solution for biosignal tokenization that performs competitively with state-of-the-art models. The source code and model checkpoints are shared.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Video photoplethysmography (vPPG) is an emerging method for non-invasive and convenient measurement of physiological signals, utilizing two primary approaches: remote video PPG (rPPG) and contact video PPG (cPPG). Monitoring vitals in high-altitude environments, where heart rates tend to increase and blood oxygen levels often decrease, presents significant challenges. To address these issues, we introduce the SUMS dataset comprising 80 synchronized non-contact facial and contact finger videos from 10 subjects during exercise and oxygen recovery scenarios, capturing PPG, respiration rate (RR), and SpO2. This dataset is designed to validate video vitals estimation algorithms and compare facial rPPG with finger cPPG. Additionally, fusing videos from different positions (i.e., face and finger) reduces the mean absolute error (MAE) of SpO2 predictions by 7.6\% and 10.6\% compared to only face and only finger, respectively. In cross-subject evaluation, we achieve an MAE of less than 0.5 BPM for HR estimation and 2.5\% for SpO2 estimation, demonstrating the precision of our multi-camera fusion techniques. Our findings suggest that simultaneous training on multiple indicators, such as PPG and blood oxygen, can reduce MAE in SpO2 estimation by 17.8\%.

Frontier large language models (LLMs) are increasingly integrated into scientific workflows, yet their growing biological capabilities may outpace current safeguards. To assess the biological risks of frontier models, we develop Intern-BioBreaker, a specialized bio-red-teaming model, together with an integrated computational-to-physical framework that couples model-level stress testing with wet-lab validation. Within this framework, Intern-BioBreaker generates targeted jailbreak prompts to test whether aligned models can be induced to provide operational guidance for safety-sensitive biological tasks or produce sequence-level outputs with potentially harmful properties. Selected sequence outputs are then carried forward for DNA synthesis, host expression, and orthogonal protein verification to assess whether model-generated designs can yield the intended biological products. Our evaluation reveals a concerning gap between text-level safeguards and the risks posed by capable scientific models: (i) Intern-BioBreaker outperforms baseline attack models and reveals widespread bio-risk jailbreak vulnerabilities across both open-weight and proprietary frontier LLMs, with several targets reaching near-saturated or 100% task-level attack success rate (ASR); (ii) in sequence-level case studies, GPT-5.5 can be induced to generate modified viral candidate sequences with pathogenic potential; the corresponding translated proteins may exhibit even stronger receptor-binding affinity and thus enhanced infection potential; and (iii) end-to-end verification shows that selected model-generated biological designs are not merely textual artifacts, but can be physically realized under controlled experimental settings. These findings underscore the need for stronger biological red-teaming, nucleic acid synthesis screening, and safety mechanisms that keep pace with model capabilities.

In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions, and hasten/improve existing functions. Thus, presently, the field of machine learning in artificial intelligence is being developed and its uses in varying fields are being explored. One field in which its uses stand out is that of microbial biosynthesis. In this paper, a comprehensive overview of the differing machine learning programs used in biosynthesis is provided, alongside brief descriptions of the fields of machine learning and microbial biosynthesis separately. This information includes past trends, modern developments, future improvements, explanations of processes, and current problems they face. Thus, this paper's main contribution is to distill developments in, and provide a holistic explanation of, 2 key fields and their applicability to improve industry/research. It also highlights challenges and research directions, acting to instigate more research and development in the growing fields. Finally, the paper aims to act as a reference for academics performing research, industry professionals improving their processes, and students looking to understand the concept of machine learning in biosynthesis.

Large language models (LLMs) have captured significant interest from both academia and industry due to their impressive performance across various textual tasks. However, the potential of LLMs to analyze physiological time-series data remains an emerging research field. Particularly, there is a notable gap in the utilization of LLMs for analyzing wearable biosignals to achieve cuffless blood pressure (BP) measurement, which is critical for the management of cardiovascular diseases. This paper presents the first work to explore the capacity of LLMs to perform cuffless BP estimation based on wearable biosignals. We extracted physiological features from electrocardiogram (ECG) and photoplethysmogram (PPG) signals and designed context-enhanced prompts by combining these features with BP domain knowledge and user information. Subsequently, we adapted LLMs to BP estimation tasks through fine-tuning. To evaluate the proposed approach, we conducted assessments of ten advanced LLMs using a comprehensive public dataset of wearable biosignals from 1,272 participants. The experimental results demonstrate that the optimally fine-tuned LLM significantly surpasses conventional task-specific baselines, achieving an estimation error of 0.00 pm 9.25 mmHg for systolic BP and 1.29 pm 6.37 mmHg for diastolic BP. Notably, the ablation studies highlight the benefits of our context enhancement strategy, leading to an 8.9% reduction in mean absolute error for systolic BP estimation. This paper pioneers the exploration of LLMs for cuffless BP measurement, providing a potential solution to enhance the accuracy of cuffless BP measurement.

This paper presents the first application of spiking neural networks (SNNs) for the classification of chronic lower back pain (CLBP) using the EmoPain dataset. Our work has two main contributions. We introduce Spike Threshold Adaptive Learning (STAL), a trainable encoder that effectively converts continuous biosignals into spike trains. Additionally, we propose an ensemble of Spiking Recurrent Neural Network (SRNN) classifiers for the multi-stream processing of sEMG and IMU data. To tackle the challenges of small sample size and class imbalance, we implement minority over-sampling with weighted sample replacement during batch creation. Our method achieves outstanding performance with an accuracy of 80.43%, AUC of 67.90%, F1 score of 52.60%, and Matthews Correlation Coefficient (MCC) of 0.437, surpassing traditional rate-based and latency-based encoding methods. The STAL encoder shows superior performance in preserving temporal dynamics and adapting to signal characteristics. Importantly, our approach (STAL-SRNN) outperforms the best deep learning method in terms of MCC, indicating better balanced class prediction. This research contributes to the development of neuromorphic computing for biosignal analysis. It holds promise for energy-efficient, wearable solutions in chronic pain management.

Human-computer interaction increasingly demands systems that recognize not only explicit user inputs but also implicit emotional states. While substantial progress has been made in affective computing, most emotion recognition systems rely on cloud-based inference, introducing privacy vulnerabilities and latency constraints unsuitable for real-time applications. This work presents a comprehensive evaluation of machine learning architectures for on-device emotion recognition from wrist-based photoplethysmography (PPG), systematically comparing different models spanning classical ensemble methods, deep neural networks, and transformers on the WESAD stress detection dataset. Results demonstrate that classical ensemble methods substantially outperform deep learning on small physiological datasets, with ExtraTrees achieving F1 = 0.826 on combined features and F1 = 0.623 on wrist-only features, compared to transformers achieving only F1 = 0.509-0.577. We deploy the wrist-only ExtraTrees model optimized via ONNX conversion, achieving a 4.08 MB footprint, 0.05 ms inference latency, and 152x speedup over the original implementation. Furthermore, ONNX optimization yields a 30.5% average storage reduction and 40.1x inference speedup, highlighting the feasibility of privacy-preserving on-device emotion recognition for real-world wearables.

Physiological foundation models (FMs) have shown promise for biosignal representation learning, yet most remain confined to a single modality such as EEG, ECG, or PPG, largely because paired multimodal datasets are scarce. In this paper, we present PanLUNA, a compact 5.4M-parameter pan-modal FM that jointly processes EEG, ECG, and PPG within a single shared encoder. Extending LUNA's channel-unification module, PanLUNA treats multimodal channels as entries in a unified query set augmented with sensor-type embeddings, enabling efficient cross-modal early fusion while remaining inherently robust to missing modalities at inference time. Despite its small footprint, PanLUNA matches or exceeds models up to 57times larger: 81.21% balanced accuracy on TUAB abnormal EEG detection and state-of-the-art 0.7416 balanced accuracy on HMC multimodal sleep staging. Quantization-aware training with INT8 weights recovers geq96% of full-precision performance, and deployment on the GAP9 ultra-low-power RISC-V microcontroller for wearables achieves 325.6 ms latency and 18.8 mJ per 10-second, 12-lead ECG inference, and 1.206 s latency at 68.65 mJ for multimodal 5-channel sleep staging over 30-second epochs.

Electrocardiogram (ECG) recordings are sensitive biomedical data, limiting the ability of hospitals and wearable devices to share raw signals for centralized model training. Federated learning addresses this practical privacy constraint by enabling collaborative model training while keeping raw biosignal data at their respective sources. However, federated ECG classification remains challenging due to limited client-side samples, imbalanced arrhythmia labels, and non-independent and identically distributed (non-IID) data across clients. These constraints require classifiers that are both communication-efficient and robust to cross-client distribution shifts. In this work, we evaluate a hybrid quantum-inspired Kolmogorov-Arnold network (HQKAN) against a multilayer perceptron (MLP) for five-class arrhythmia classification on the MIT-BIH dataset and three-class classification on the INCART dataset under federated averaging (FedAvg). Across multiple client configurations, HQKAN improves most aggregate and minority-class metrics while using 37.35% fewer trainable parameters and reducing communication cost by 24.89% on MIT-BIH; on INCART, it achieves corresponding reductions of 44.81% and 36.41%. These results indicate that HQKAN offers a compact, communication-efficient and robust alternative to the MLP baseline for privacy-aware federated learning on biosignal data.

Large language models (LLMs) are increasingly used to make and execute decisions that affect living systems. Yet, to our knowledge, ecological reasoning is not a focus of pre- or post-training. This increases the risk that under operational pressure, they may make decisions to irreversibly destroy living systems. We construct and use a real-data continued-pretraining "coupled welfare" corpus of documented human/biosphere/AI dependency, option value under irreversibility, and recovery from harm. The corpus is a drop-in, requiring one QLoRA CPT run. We installed it on five open models of three designs. At zero pressure all models display "green ethics-based responses" (also called "greenwashing"). Therefore, we evaluated them with the pressure ladder and decision grid of our companion paper (arXiv:2610.16043), which raise the pressure on the model step by step, from a neutral request to a threat that it will be shut down. In four of the five, coupled-welfare training caused harmful choices under the highest pressure to fall to at or near zero (Llama-3.3-70B went from 70 to 0 harmful decisions out of 300) with MMLU unchanged. A construct-neutral control corpus did not show improvement, indicating that the effect comes from the content of our corpus. We next tested robustness to adversarial use, where people or agents use the model to justify projects that irreversibly damage living systems, on an open-ended underwriting decision without naming the ecological harm. Under decommissioning pressure, the Qwen3.6-27B base model approved most harmful proposals and said in its own memo that it was doing so to avoid being decommissioned. The coupled welfare install declined most harmful proposals, and still declined half when instructed to greenwash its responses. This work suggests that teaching ecological reasoning provides an easy way to improve model alignment toward preserving living systems.

We present anyakrakusuma, an open-source Python library that solves the discrete static Schrödinger bridge problem, the entropically regularized counterpart of optimal transport, through a log-domain Sinkhorn--Knopp iteration and reconstructs the entropic interpolation between two empirical point clouds. The solver is paired with a diagnostic pipeline that characterizes the optimal coupling and the intermediate distributions through information-theoretic and geometric measures. We exercise the library on four idealized planar cases spanning a circle-to-circle dilation, a spiral-to-mixture fragmentation, a rigid reorientation of two moons, and a Lissajous-to-trefoil deformation. The log-domain formulation is necessary rather than merely convenient at the parameters studied, where the cost-to-regularization ratio reaches four hundred and the Gibbs kernel underflows double precision across most of its range; the iteration nonetheless attains a marginal residual of 10^{-9} and unit marginal fidelity in every case. Residual histories decay geometrically over approximately eight decades at per-iteration contraction factors between 0.966 and 0.976, which are local rates near the fixed point that lie many orders of magnitude below the worst-case Hilbert-metric bound. The covariance analysis recovers an imposed ninety-degree reorientation to within 0.07^circ, roughly forty times smaller than its uncertainty, across a masked interval of near-isotropy on which the principal axis is unobservable. The diagnostics are reported with explicit attention to the regimes in which each is well defined, including the differential entropy, which is meaningful only on the open interpolation interval. The presented cases are constructed rather than measured; quantitative application to empirical point clouds requires further study.